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The Journalof the

Association of Genetic Technologists

Volume 33 • Number 2 • Second Quarter 2007



Brain Tickler

Brain Tickler Column Editor: Helen Lawce

The answer to this Brain Tickler appears on page 81.

Clinical Indication:

Peripheral blood was receivedwith a question of Cat-Eye syndrome.

Submitted by:

Luke J. BoydCytogenetics Laboratory

Oregon Health & Sciences UniversityPortland, Oregon



The Journal of the Association of Genetic Technologists 33 (2) 2007

53

The official journal of the Associationof Genetic Technologists (AGT)

Editorial Information

EditorMark Terry, BSc

Associate EditorsTurid Knutsen, MT(ASCP), CLSp(CG)Helen Lawce, BSc, CLSp(CG)

Book Review EditorLaurel Sakaluk-Moody, MS

Editorial BoardHon Fong Louie Mark, PhD, FACMG

Copyright © 2007 by the AGT. All rightsreserved. Contents are not to be reproducedor reprinted without permission of the AGTEditor.

The Journal of the Association of GeneticTechnologists is published four times a yearand is available to individuals and librariesat a subscription rate of $105 per year. Thesubscription rate for members of the AGTis included in the annual membership dues.Back issues can be purchased for members at$5 per issue and for non-members at $25 perissue as long as supplies are available.

Material intended for publication or cor-respondence concerning editorial matters

should be sent to the editor.

JAGT EditorMark Terry1264 Keble LaneOxford, MI 48371(586) 805-9407 (cell)(248) 628-3025 (phone/fax)E-mail: [email protected]

Placement service items of less than 150words and advertisements, requests for backissues, reprint orders, and questions aboutsubscriptions and advertising costs shouldbe sent to the AGT Executive Office [email protected]. Acceptance of adver-

tisements is dependent on approval of theeditor-in-chief.

ISSN 1523-7834

Table of Contents

Brain Tickler . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .Inside front cover

Column Editors and Review Board. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54A Note from the Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55

Letter To The Editor . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 58

Technical ReviewThe Prothrombin 20209C>T Sequence Variant: To Test or Not to Test?

Denise I. Quigley, Jessica K. Booker, Daynna J. Wolff. . . . . . . . . . . . . . . . . . . . . . . . . 59

Technical ArticleTraining Guide for Chromosome Recognition

Daniel G. Kuffel, Austin W. Carlson, Peggy J. Stupca, Syed M. Jalal . . . . . . . . . . . . .62

Profiles and Perspectives

Bruce R. Korf, MD, PhD, FACMGInterviewed by Hon Fong Mark . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69

Abstracts in ReviewThe Triumphant March of the Clinical Use of DNA-Arrays: The Discovery

of Novel Genomic Disorders Through a Targeted Molecular Screeningof the Human Genome . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73

Novel Clinically Distinctive Chromosome Syndromes: Microdeletions of17q21.31 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75Abstracted by Jaime Garcia-Heras

Book ReviewThe World of the Cell

Cells

Reviewed by Helen Lawce . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79

Brain Tickler Summary . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81

Continuing Education OpportunitiesAGT Education Committee Representatives . . . . . . . . . . . . . . . . . . . . . . . . . . . 82Test Yourself #2, 2007 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83AGT Journal Club Order Form . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86

Association Business

News from the President . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 89

Association of Genetic Technologists Contacts . . . . . . . . . . . . . . . . . . . . . . . . 90

Job Placements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91

The AGT Cytogenetics Laboratory Manual 3rd Edition Order Form . . . . . . . . 92

The AGT Cytogenetic Symposia 2nd Edition Order Form . . . . . . . . . . . . . . . . . 93

New Membership Application . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95

Meeting/Workshop Announcements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96

Information for Authors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . inside back cover

The Journal of the Association of Genetic TechnologistsSecond Quarter 2007 Volume 33, Number 2

The Journal of the Association of Genetic Technologists is indexed in the life sciences data-

base BIOSIS and in the National Library of Medicine’s PubMed.



Column Editors


54

Abstract Reviews/Genetics in the News

Jaime Garcia-Heras, MD, PhD

Director of Cytogenetics

The Center for Medical Genetics

7400 Fannin, Suite 700

Houston, TX 77054(713) 432-1991

(713) 432-1661 FAX

E-mail: [email protected]

Book Review Editor

Laurel Sakaluk-Moody, M.S.

7311-93ST

Edmonton, AB, Canada T6E 3C5


Brain Tickler

Helen Lawce, BSc, CLSp(CG)

Clinical Cytogenetics Laboratory

Oregon Health Sciences University

3181 SW Sam Jackson Parkway, MP-350

Portland, OR 97201

(503) 494-2790

(503) 494-6104 FAXE-mail: [email protected]

The Journal of the Association of Genetic Technologists Staff

Linda Ashworth, BSc, CLSp(CG)

(Cytogenetics, Molecular genetics)

Helen Bixenman, BSc, CLSp(CG), CLSup(Prenatal diagnosis)

Judith Brown, MS, CLSp(CG), CLSp(MB)(Cytogenetics)

Kim Bussey, PhD(Cancer genetics, Molecular genetics,Microdissection/PCR/DNA)

Mona Cantú, BSc, CLSp(CG)(Cytogenetics)

Philip D. Cotter, PhD, FACMG(Prenatal diagnosis, Chromosomerearrangements, Molecular genetics)

Jennifer Costanzo, MS, CLSp(CG)(Cytogenetics, Molecular genetics)

Janet Cowan, PhD(Cytogenetics, Cancer genetics,FISH, Solid tumors)

Lezlie Densmore, BSc, CLSp(CG)(Cytogenetics, Molecular genetics)

Janet Finan, BSc, CLSp(CG)(Hemic neoplasms, Somatic cellhybridization)

Sue Fox, BSc, CLSp(CG)(Bone marrow cytogenetics, Prenataldiagnosis, Supervisory/Management)

Jaime Garcia-Heras, MD, PhD

(Clinical cytogenetics)

Robert Gasparini , MS, CLSp(CG)(Prenatal diagnosis, Cytogenetics)

Barbara K. Goodman, PhD, MSc,CLSp(CG)(Molecular cytogenetics)

Michelle M. Hess, MS, CLSp(CG)(Cytogenetics, Cancer cytogenetics)

Lynn Hoyt, BSc, CLSp(CG), CLSup(Classical cytogenetics)

Julia Kawecki, BSc, CLSp(CG)(Cytogenetics, Molecular genetics)

Turid Knutsen, MT(ASCP), CLSp(CG)(Cancer cytogenetics, CGH, SKY)

Anita Kulharya, PhD(Molecular genetics, Clinicalcytogenetics)

Helen Lawce, BSc, CLSp(CG)(Prenatal diagnosis, Solid tumors, FISH,Chromosome structure, Evolution)

Hon Fong Louie Mark, PhD, FACMG(Molecular genetics, Somatic cellgenetics, Cancer cytogenetics, Breastcancer, Trisomies, Laboratory practices,Regulatory practices, FISH)

Jennifer L. McGonigle, BA, CLSp(CG)

(Cytogenetics)

Karen Dyer Montgomery, PhD, FACMG(Cancer cytogenetics, Cytogenetics,Molecular cytogenetics)

Rodman Morgan, MS, CLSp(CG)(Cancer cytogenetics)

Susan B. Olson, PhD(Cancer cytogenetics, Moleculargenetics, Prenatal diagnosis, OB/GYN,Counseling, Cytogenetics)

Jonathan P. Park, PhD(Cytogenetics, Molecular genetics,Cell biology)

David Peakman, AIMLT, CLSp(CG)(Prenatal diagnosis)

Carol Reifsteck, BA(Breakage syndromes, Fanconi’sanemia, Prenatal diagnosis)

Gavin P. Robertson, PhD(Cytogenetics, Molecular genetics,Somatic cell genetics, Tumor suppressorgenes, Cancer genes)

Laurel Sakaluk-Moody, MSc, MLT(CG)(Cytogenetics, Developmental biology,Prenatal cytogenetics)

Debra Saxe, PhD

(Prenatal diagnosis, Cytogenetics)

Jack L. Spurbeck, BSc, CLSp(CG)(Cancer cytogenetics, Moleculargenetics)

Peggy Stupca, MSc, CLSp(CG)(Cytogenetics, Prenatal diagnosis,Breakage syndromes, FISH, Regulations/QA)

Nancy Taylor, BSc, CLSp(CG), MT(ASCP)(Cytogenetics, Cancer cytogenetics)

Thomas Wan, PhD(Cytogenetics, Molecular genetics,Cancer genetics)

James Waurin, MSc,CLSp(CG)(Prenatal diagnosis, Counseling)

Sara Wechter, BSc(Cytogenetics, Cancer)

James Zabawski, MS, CLSp(CG)(Education, Traditional Cytogenetics)

Review Board

Forensic Science & Genetics

Robert W. Allen, PhD

Associate Professor of Forensic

Science

Associate Director, Graduate

Program in Forensic ScienceDirector, Human Identity Testing

Laboratory

Center for Health Sciences

Oklahoma State University

1111 W. 17th Street

Tulsa, OK 74137

(918) 699-8792


Genetics & The Law

James Waurin, MSc,CLSp(CG)

71 Cedar Chip Court

Baltimore, MD 21234

(410) 536 -1616

(410) 737-1266 FAX

E-mail: Jim.L.Waurin@

QuestDiagnostics.com

Just for Fun; Karycature Director

Richard Sherman, PhD, CLSp(CG)

Clinical Cytogenetics Laboratory

Oregon Health Sciences University

3181 SW Sam Jackson Parkway

MP-350Portland, OR 97201

(503) 494-8346

(503) 494-6104 FAX


Letters to the Editor

Mark Terry, JAGT Editor

1264 Keble Lane

Oxford, MI 48371

(586) 805-9407 (cell)

(248) 628-3025 (phone/FAX)


Meeting Notices

Mervat S. Ayad, BS, MBA, CLsp(CG),CLSup, CCSQuest Diagnostics’ Nichols Institute

Cytogenetics and DatabaseDepartments33608 Ortega HighwaySan Juan Capist rano, CA 92690-6130(800) 642-4657 x 4302(949) 728-4302 DIRECT(949) 728-4979 FAXE-mail: [email protected]

Profiles & Perspectives

Hon Fong Louie Mark, PhD, FACMG

President

KRAM Corporation

2 Pine Top Road

Barrington, RI 02806(401) 246- 0487


Special Interests

Turid Knutsen, MT(ASCP), CLSp(CG)

Genetics Branch, NCI

National Institutes of Health

50 South Drive, Room 1408

Bethesda, MD 20892-0913

(301) 496-6501

(301) 402-1204 FAX


Test Yourself

Peter Hu, MS, CLSp(CG), CLSp(MB),CLS(NCA), MP(ASCP), MT(ASCP)Molecular Genetic Technology

ProgramThe University of Texas M.D.Anderson Cancer CenterThe School of Health Sciences(713) 745-1688(713) 745-3337 FAX




55

There are at least two major bills being developed that, ifpassed, are likely to have significant impact on your life in thegenetic laboratory. There are others, as well. When the BushAdministration put into effect Medicare reform, part of the plan,

officially called the Medicare Modernization Act of 2003 (MMA),included a demonstration project for competitive bidding. Thisproject is called the Competitive Lab Bidding Demonstration.To quote Linda Lebovic, MPH, MT(ASCP), the project officerat CMS, the point is “to determine whether competitive biddingcan be used to provide quality laboratory services at pricesbelow current payment rates.” Similar projects were proposed inFlorida and shot down by lawsuits initiated by Quest Diagnostics,LabCorp and the American Clinical Laboratory Association.

As of this writing the demonstration project is in limbo,awaiting the U.S. Office of Management and Budget to approvethe structure and budget of the project. Behind the scenes prettysignificant lobbying—primarily against—the project is ongoing.Many critics and people in the industry feel that competitive

bidding is a doorway to disaster for the laboratory industry, whichwould commoditize a very complex health service, i.e., allow onlylabs that offer the lowest bids in specific regions to offer certaintests requiring Medicare or Medicaid reimbursement. I’m sorry,ma’am, we don’t offer that test here, you’ll have to go elsewhere.

Senator Ted Kennedy’s Bill

Senator Kennedy (D-MA) has sponsored S.736, the LaboratoryTest Improvement Act, with Senator Gordon Smith (R-OR).This bill focuses on laboratory designed tests (LDTs), which is thecurrent name for what we’ve been calling “home brew” tests. Thebill essentially designates LDTs as medical devices which wouldrequire premarket review by the FDA.

If you’re a genetics or cytogenetics lab doing home-brewtests, you’re probably already quivering in your lab coats. This ispotentially expensive, complicated and, based on paperwork I’veseen relevant to FDA certification, overwhelming. Different testswould fall under different classifications, each requiring differentlevels of oversight. Generally speaking, LDTs would be class II

devices. If the LDT is used to screen donated blood or used todiagnose a contagious disease or a condition that is very likely tobe fatal, it would fall under the most stringent control, class III.

Senator Barack Obama’s BillHow Senator Barack Obama (D-IL) found time to introduce

any legislature while promoting his bestselling book andrunning for president is beyond me, but he did. S.976, theGenomics & Personalized Medicine Act, was co-sponsored bySenator Richard Burr (R-NC). S.976 hopes to increase federalgovernment involvement in genetic testing and genomics, thoughit’s friendlier to the healthcare industry, attempting to promotescientific advances and their use in so-called personalizedmedicine. Among its provisions are expanded research, collectionand sharing of data, medical workforce training, and specificguidelines regarding the level of regulatory oversight required andwhich agencies would be responsible.

Commonalities

Both bills call for the establishment of a CLIA specialty forgenetic testing. In 2006 a similar proposal was chopped by CMS.This is probably a positive thing for everyone working in the field,although it’s not clear how it will address such things as geneticcounseling, confidentiality, liability or informed consent.

Also, both bills ask that the Health and Human ServicesSecretary determine if reimbursement is adequate for new genetictests and, when needed, raise them. That strikes me as beingworthy of a “hallelujah” or two, although I never take for grantedthat well-meaning political initiatives won’t have disastroussecondary effects.

Both bills have been referred to the Health, Education, Labor

& Pensions (HELP) Committee. The Journal of the Associationof Genetic Technologists will stay on top of these importantstories as they continue to develop.

Best, Mark Terry, Editor

The Government and Genetic Testing

A Note from the Editor

AGT Website: www.agt-info.orgMember’s Only area:

User Name: agtmember

Password: your AGT member ID#




56

Rainbow Scientific, Inc83 Maple AvenueWindsor, CT 06095Tel: 860-298-8382Fax: [email protected]

For more information please contact:




57

For more information p lease contact:

Rainbow Scientific, Inc83 Maple AvenueWindsor, CT 06095Tel: 860-298-8382Fax: [email protected]




58

Letter To The Editor

Regarding the article “Survey of Candidate Genes for AutismSusceptibility” by Swackhammer and Tatum [Vol 33(1) 2007],I would like to comment on the candidate genes localized to

chromosome 22. The authors cite the article “Terminal 22q13deletion syndrome: a newly recognized cause of speech andlanguage disability in the autism spectrum” by Manning et al.(2004) as presenting ACR (acrosin) and RABL2B as possiblecandidate genes on chromosome 22. While Manning et al.acknowledge that RABL2B and ACR are mapped to 22q13,they state the improbability that ACR contributes to the 22q13phenotype and observe that, because no mutations in the RAB family of GTPases have been previously associated with mentalretardation, it seems unlikely that RABL2B is contributory.

Manning et al. (2004) present evidence that ProSAP2(SHANK3), which also maps to 22q13, is a strong candidategene for the autistic features in individuals with deletion 22q13.ProSAP2 encodes a scaffolding protein in the post-synaptic

density of excitatory synapses and is preferentially expressedin the cerebral cortex and cerebellum. Based on its expressionwithin the brain, its function, and the gene localization to 22q13,ProSAP2 is a much more plausible candidate for the neurologicalfeatures of deletion 22q13 than ACR or RABL2B. Many otherauthors including Luciani et al. (2003), Wilson et al. (2003) andBonaglia et al. (2006) have presented evidence supporting therole of ProSAP2/SHANK3 in the etiology of the neurologicalfeatures (absent speech and developmental delay) associated withdeletion 22q13. Recently, Durand et al. (2007) reported mutationsof ProSAP2 in individuals with autism and Asperger syndrome.

Swackhammer and Tatum have presented a comprehensivereview of candidate genes for autism. This review should include

ProSAP2 (SHANK3) as the most plausible candidate geneassociated with autistic features in individuals with deletion22q13/Phelan-McDermid syndrome.

References

Bonaglia MC, Giorda R, Mani E, Aceti G, Anderlid BM, Baroncini A,Pramparo T, Zuffardi O. Identification of a recurrent breakpoint withinthe SHANK3 gene in the 22q13.3 deletion syndrome. J Med Genet.2006; 43(10):822-8.

Durand CM, Betancur C, Boeckers TM, Bockmann J, Chaste P, FauchereauF, Nygren G, Rastam M, Gillberg IC, Anckarsater H, Sponheim E,Goubran-Botros H, Delorme R, Chabane N, Mouren-Simeoni MC, deMas P, Beith E, Roge B, Heron D, Burglen L, Gillberg C, Leboyer M,Bourgeron T. Mutations in the gene encoding the synaptic scaffoldingprotein SHANK3 are associated with autism spectrum disorders. NatGenet. 2007; 39(1):25-7.

Luciani JJ, de Mas P, Depetris D, Mignon-Ravix C, Bottani A, Prieur M, Jonveaux P, Ph ilippe A, Bourrouillou G, de Martinvil le B, Delobel

B, Vallee L, Croquette M-F, Mattei MG. Telomeric 22q13 deletionsresulting from rings, simple deletions, and translocations: cytogenetic,molecular, and clinical analysis of 32 new observations. J Med Genet.2003; 40(9):690-6.

Manning MA, Cassidy SB, Clericuzio C, Cherry AM, Schwartz S, HudginsL, Enns GM, Hoyme HE. Terminal 22q deletion syndrome: a newlyrecognized cause of speech and language disability in the autismspectrum. Pediatr. 2004; 114(2):451-7.

Kind regards,Katy Phelan, PhDDirector, CytogeneticsMolecular Pathology Laboratory NetworkMaryville, TN

Letter to the Editor




59

Introduction

The G20210A mutation in the 3’ untranslated region of theprothrombin gene is associated with an increased risk for venousthrombosis (Poort et al., 1996). This mutation has been shown toresult in more efficient 3’-processing and increased accumulationof mature mRNA, which ultimately leads to increased plasmaprothrombin levels (Gehring et al., 2001). Individuals hetero-zygous for the G20210A prothrombin mutation have a 3-foldincreased risk for venous thrombosis compared with individuals

without this mutation (Poort et al., 1996). The advent of hybrid-ization probe technology for detection of the G20210A mutationhas allowed for identification of a novel prothrombin variant,which has been determined to be C20209T by sequence analysis(Warshawsky et al., 2002; Schrijver et al., 2003). The clinical sig-nificance of this variant, which has primarily been documentedin individuals of African descent, is unknown (Warshawsky etal., 2002; Schrijver et al., 2003; Soo et al., 2005).

Case Studies

During routine, clinical assessment of thecommon prothrombin mutation, 20210G>A,seven patient samples yielded a result consis-

tent with presence of the C20209T prothrom-bin variant on one allele. These individualswere referred for various indications, includ-ing history of venous thrombosis event andrecurrent pregnancy loss. Patient clinicaldata, including gender and age at the time oftesting, are summarized in Table 1. All of thepatients with the C20209T prothrombin vari-ant were of African-American descent and tothe best of our knowledge, unrelated.

Methodology

Whole blood samples collected in EDTA-collection tubeswere received in the lab and DNA extracted using the MagNAPureTM system (Roche Molecular Biochemicals). Mutation test-ing for prothrombin G20210A was performed on the RocheLightCyclerTM instrument using commercially available primersand hybridization probes according to the manufacturer’s recom-mendations (Roche Molecular Biochemicals). Patient sampleswith a variant prothrombin hybridization probe melting tempera-

ture were subjected to sequence analysis. PCR and sequencingprimers were Forward 5’-GCCACTCATATTCTGGGCTCC-3’and Reverse 5’-GCGTGCACCAGGTGGTGGAT-3’. Sequencingwas performed with PRISM BigDye Terminator Cycle SequencingReady Reaction and run on an ABI Prism 3100 genetic analyzeraccording to the manufacturer’s recommended protocol (AppliedBiosystems).

Technical Review

The Prothrombin 20209C>T Sequence Variant:To Test or Not to Test?Denise I. Quigley, Jessica K. Booker, Daynna J. Wolff

AbstractOnly one mutation in the prothrombin gene (Factor II), 20210G>A, has been definitively associated with an increased risk for venousthrombosis. Using hybridization probe analysis for mutation detection on the LightCycler (Roche Molecular Biochemicals), we identifiedseven patient samples with atypical melt curve patterns. Sequence analyses of each of these samples revealed heterozygosity for a C toT transition at position 20209. As in other reported cases, each of the apparently unrelated patients was of African-American descent,suggesting that the variant is population specific. Two patients were referred for testing due to a history of stroke, one with a rightmajor coronary artery embolic stroke and the other with a right cerebellar stroke. A third patient had chronic renal failure secondary tohypertension with a reported family history of renal failure. Three patients had a history of multiple pregnancy losses. The last patienthad a kidney transplant for end stage renal disease secondary to glomerulonephritis. She was being evaluated for a second transplant,but to our knowledge, had a negative history of venous thrombosis. The prevalence and the clinical significance of the prothrombin20209C>T mutation is unknown. Recently reported functional studies revealed conflicting results. The clinical utility of testing for andreporting this variant remains unresolved.

Keywords

prothrombin, venous thrombosis, sequence variant

Patient Age (y) Gender Clinical History

1 ? M Right cellebellar stroke

2 35 F Glomerulophritis, status post kidney transplant

3 21 F Recurrent pregnancy loss; six first trimester lossesand one second trimester loss.

4 47 M Embolic stroke of the right major coronary arteryregion; likely related to mitral valve vegetations.

5 59 M Chronic renal failure secondary to hypertension;parents reportedly also had renal failure

6 27 F Twin pregnancy loss at 20 weeks gestational age.No history of thrombosis event reported.

7 36 F Recurrent pregnancy loss; two first-trimester losses.

Table 1. Case Studies Data




Technical Review

The Prothrombin 20209C>T Sequence Variant: To Test or Not to Test? — Quigley, Booker, Wolff

Results

The LightCyclerTM-based assayfor the 20210G>A prothrombinmutation yields probe melting curves

of ~60°C and ~50°C for wild typeand mutant alleles, respectively.Each of the individuals presentedshowed two melting curves attemperatures of ~60°C and ~54°C(Figure 1). These findings wereinterpreted as the patient beingheterozygous for one wild typeallele and one variant allele.Sequencing analysis performedon each of these samples revealedthe presence of one normal alleleand one allele with a 20209C>Tsubstitution (Figure 2).

Discussion

Previously, the standard methodfor detection of the 20210G>Amutation was via restriction enzymedigestion, as the G>A substitutioncreates a new cleavage recognition site (Poort etal., 1996). Wild type alleles and other variantsare not digested, thus the 20209C>T wouldyield an apparently normal result. The adventof the hybridization probe-based assay for the20210G>A prothrombin mutation has allowedfor identification of mutations/polymorphisms

not previously recognized (Wylenzek et al., 2001;Warshawsky et al., 2002; Clench et al., 2005;Danckwardt et al., 2006a). These findings haveopened up a new avenue of exploration; however,they have also caused a clinical conundrumas the clinical consequence of such variants isunknown.

Figure 1 shows the predicted hybridizationprobe melt temperatures for the RocheLightCyclerTM hybridization probes for the wildtype, 20210G>A and 20209C>T alleles. Giventhat the 20209C>T has been documented to beassociated with a melting temperature of 54°Cusing these hybridization probes, one might be

inclined to forgo sequence confirmation of sucha finding. However, another novel prothrombinsubstitution, 20221C>T, has been reported in aLebanese/Syrian family that also shows a meltingtemperature of 54°C (Wylenzek et al., 2001). A reflex test, specificfor the 20209C>T would be a nice alternative to sequencing,particularly for laboratories that process a large number ofspecimens from African-American individuals.

The 20209C>T variant has been previously reported in ahandful of individuals (Warshawsky et al., 2002; Schrijver etal., 2003; Soo et al., 2005). Of interest, this finding has pre-

Fig. 1. Representative melt curves from the LightCyclerTM showing samples heterozygousfor the prothrombin 20209C>T variant (long dashes), heterozygous for the prothrombin20210G>A mutation (short dashes) and a negative control (solid line). Note that the meltpeak at about 60°C represents the wild type allele while the melt peaks at about 54°C and50°C represent the 20209C>T and 20210G>T alleles, respectively.

dominantly been observed in individuals of African descent, sug-gesting a founder affect (Schrijver et al., 2003; Soo et al., 2005).However, Danckwardt et al. (2006a) report this variant in threeCaucasian individuals of Jewish-Moroccan descent. The preva-lence of the common prothrombin mutation (20210G>A) in thegeneral African-American population (no known relevant clini-cal history) is reportedly quite low, about 0.2%. This mutation

60

Fig. 2. Representative sequencing electropherogram of a sample

heterozygous for the 20209C>T variant. Note two peaks representing “C”and “T” at position 20209 (arrow) and single peak representing normal “G”at position 20210 (arrowhead).

1512

1404

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61

is about 10-fold more common in Caucasian populations (2.3%)(Poort et al., 1996; Dilley et al., 1998; Rosendaal et al., 1998).Although large population studies to determine the prevalence ofthe 20209C>T substitution in the unselected African-American

population have not been conducted, a small study suggests thatthe prevalence is about 0.4% (Itakura et al., 2005). This andanother small study suggest that the prevalence of the 20209C>Tvariant is higher in individuals with history of a venous throm-boembolism than in control individuals with no relevant clinicalhistory (Itakura et al., 2005; Soo et al., 2005). These data imply aclinical correlation and beg the question as to whether 20209C>Tmutation testing should be standard of care for African-Americanindividuals with a clinical indication for coagulation studies.

Functional studies of the 20209C>T variant have shown mixedresults (Danckwardt et al., 2006a and 2006b; van der Putten etal., 2006). Similar to the 20210G>A mutation, the 20209C>Tvariant may affect the efficiency of 3’ end formation leading toincreased levels of mRNA accumulation and protein synthesis

(Gehring et al., 2001). Schrijver et al. (2003) reported increasedprothrombin levels in three individuals with the 20209C>Tvariant and a history of multiple spontaneous pregnancy lossesand fetal growth retardation. One study showed a 1.4-fold increasein mRNA expression with the 20209C>T variant compared withthe wild type prothrombin sequence. Furthermore, this findingwas correlated with increased protein expression levels and greaterefficiency of 3’ end formation compared to wild type prothrombin(Danckwardt et al., 2006a). Another study reported a 2.2-folddecrease in luciferase reporter expression with the 20209C>Tvariant in the 3’ UTR compared with the wild type prothrombinUTR. These findings are counter intuitive to the proposedfunctional significance of the 20209C>T variant and suggest thatthis variant is most likely not associated with an increased risk for

venous thromboembolism (van der Putten et al., 2006).Larger studies are necessary to determine the clinical

significance of the 20209C>T variant in regard to the risk forthrombosis in the African-American population (Danckwardtet al., 2006b; van der Putten et al., 2006). Family studies inkindreds found to carry this variant, along with detailed clinicalhistories, may help to establish associative data, suggesting clinicalrelevance. Eventually, testing for the prothrombin 20209C>T maybecome standard of care, at least in relevant ethnic populations.Meanwhile, reporting of this variant is a dilemma as the clinicalsignificance is unclear. Is it a greater disservice to report a variantfor which the interpretation and clinical management has not beenestablished? Or shall we convert to a 20210G>A detection methodthat does not serendipitously reveal such sequence variants? This

study is a good example of how advancing technology has allowedfor new discovery and new clinical conundrums.

References

Clench T, Standen GR, Ryan E, Chilcott JL, Mumford AD. Rapid detectionof the prothrombin C20209T transition by light cycler analysis. ThrombHaemost. 2005; 94:1114-1115.

Danckwardt S, Hartmann K, Katz B, Hentze MW, Levy Y, Eichele R,Deutsch V, Kulozik AE, Ben-Tal O. The Prothrombin 20209C>Tmutation in Jewish-Moroccan Caucasians: molecular analysis of gain-of-function of 3’ end processing. J Thromb Haemost. 2006a; 4:1078-1085.

Danckwardt S, Hartmann K, Katz B, Ben-Tal O, Kulozik AE. More on:Functional analysis of two prothrombin 3’UTR variants: the C20209Tvariant, mainly found among African-Americans, and the C20209Avariant. J Thrombo Haemost. 2006b; 4(10):2288-2289.

Dilley A, Austin H, Hooper WC, El-Jamil M, Whitsett C, Wenger NK,

Benson J, Evatt B. Prevalence of the prothrombin 20210G-to-A variantin blacks: infants, patients with venous thrombosis, patients withmyocardial infarction, and control subjects. J Lab Clin Med. 1998;132(6):452-455.

Gehring NH, Franke U, Neu-Yilik G, Hundsdoerfer P, Vetter B, Hentze MW,Kulozik AE. Increased efficiency of mRNA 3’ end formation: a newgenetic mechanism contributing to hereditary thrombophilia. NatureGenet. 2001; 28:389-392.

Itakura H, Telen MJ, Hoppe CC, White DAE, Zehnder JL. Characterizationof a novel prothrombin variant, prothrombin C20209T, as a modifier ofthrombotic risk among African-Americans. J. Thromb Haemost. 2005;3:2357-2359.

Poort SR, Rosendaal FR, Reitsma PH, Bertina RM. A common geneticvariation in the 3’-untranslated region of the prothrombin gene isassociated with elevated plasma prothrombin levels and an increase in

venous thrombosis. Blood. 1996; 88(10):3698-3703. Rosendaal FR, Doggen CJM, Zivelin A, Arruda VR, Aiach M, SiscovickDS, Hillarp A, Watzke HH, Bernardi F, Cumming AM, Preston FE.Geographic distribution of the 10210 G to A prothrombin variant.Thromb Haemost. 1998; 79:706-708.

Schrijver I, Lenzi TJ, Jones CD, Lay MJ, Druzin ML, Zehnder JL.Prothrombin gene variants in non-Caucasians with fetal loss andintrauterine g rowth retardation. J Mol Diag. 2003; 5(4):250-253.

Soo PY, Patel RK, Best S, Arya R, Thein SL. Detection of prothrombin genepolymorphism at position 20209 (PT20209C/T): Pilot study in a blackpopulation in the United Kingdom. Thromb Haemost. 2005; 93:179-180.

Van der Putten HHAGM, Spaargaren-van Riel CC, Bertina RM, Vos HL.Functional analysis of two prothrombin 3’UTR variants: the C20209Tvariant, mainly found among African-Americans, and the C20209Avariant. J Thrombo Haemost. 2006; 4(10):2285-2287.

Warshawsky I, Hren C, Sercia L, Shadrach B, Deitcher SR, Newton E,

Kottke-Marchant K. Detection of a novel point mutation of theprothrombin gene at position 20209. Diag Mol Path. 2002; 11(3):152-156.

Wylenzek M, Geisen C, Stapenhorst L, Wielckens K, Klingler KR. A novelpoint mutation in the 3’ region of the prothrombin gene at position20221 in a Lebanese/Syrian family. Thromb Haemost. 2001; 85:943-944.

Correspondence to:

Denise I. Quigley, PhDDepartment of Pathology and Laboratory MedicineMedical University of South Carolina165 Ashley Ave, Suite 309Charleston, SC 29425Phone: 843-792-1181 Fax: 843-792-1248

e-mail: [email protected]

Jessica K. Booker, PhD, Department of Pathologyand Laboratory MedicineUniversity of North CarolinaChapel Hill, NC

Daynna J. Wolff, PhD, Department of Pathologyand Laboratory MedicineMedical University of South CarolinaCharleston, SC

Technical Review

The Prothrombin 20209C>T Sequence Variant: To Test or Not to Test? — Quigley, Booker, Wolff



Glossary

Technical Article


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Training Guide for Chromosome RecognitionDaniel G. Kuffel, Austin W. Carlson, Peggy J. Stupca, and Syed M. JalalCytogenetics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic and Mayo Foundation, Rochester, MN

The ability to critically identify normal chromosomes and

to recognize chromosome abnormalities is fundamental tohigh quality cytogenetic analysis. Before the development ofbanding techniques, human chromosomes were paired using thedistinguishing characteristics of size and centromere location.At the London conference (London Conference, 1963), theclassification of chromosomes into seven groups (A-G) as proposedby Klaus Patau was officially accepted. Since the development ofG-banding techniques, each homologous chromosome pair canbe identified by specific landmarks, regions, and bands (ParisConference, 1971). The G-banding technique also makes it easyto recognize the X and Y chromosome, which are now most oftenseparated from the C- and G-group autosomes, respectively (ParisConference, 1971).

Chromosome recognition with precision and ease continues tobe a challenge. It often takes new employees several weeks or evenmonths to become competent and confident in recognizing normal

and abnormal patterns of chromosomes. Several publications

deal with details about the chromosome morphology and bandrecognition (ISCN 2005, Richardson 1992, Tharapel 2005) to helpwith chromosome identification. We have developed a trainingguide that combines key components of published informationinto one document. This guideline combines a description, anidiogram and computer images of each chromosome as observedin G-banded preparations at approximately 500 band stage.The guideline is divided into the seven readily distinguishablegroups (A-G) that are used when non-banded chromosomesare analyzed, except that the sex chromosomes are describedseparately. The most recognizable bands for each chromosomeare described and then highlighted on the chromosome imageand the corresponding idiogram. We find this tool very useful

for training individual chromosome recognition to students ofall levels and for reference purposes for trained technologists. Wehope these guidelines will have wide acceptance.

+Acrocentric: Centromere located near the end of the chromosomewith a ratio of long arm to short arm > 1:7.

Band: A part of a chromosome that is distinguishable from thesurrounding parts by virtue of appearing darker or lighterin stain intensity or density. Dark Band (DB); Light Band(LB). According to ISCN nomenclature a band has fourcharacteristics. They are the chromosome number, arm, region,and band, for example, 1p33 indicates band 3 from region 3 ofthe short arm of chromosome 1. Bands can be subdivided intosub-bands using a decimal point at higher resolutions.

“Cap” Band: A telomeric dark or light band in the p-arm or q-arm.Chromosomes 3, 18, and Y have a dark band on the telomericor near telomeric end of the p-arm, like a cap on top of theirp-arm.

Distal: A reference term used to describe a position on a chromosomearm that is closer to the telomere than the centromere.

+Metacentric: Centomere located near the middle of the chromo-some with a ratio of long arm to short arm of 1:1 to 1:1.3.

Pericentric: peri- means surrounding and/or including, i.e.,pericentric is an area surrounding and/or including thecentromere.

Proximal: A reference term used to describe a position on a

chromosome arm that is closer to the centromere than thetelomere.

qh Region: “q” refers to the q-arm and h refers to heterochromatin(chromatin rich in repetitive DNA, non-coding sequences).There are several chromosomes, such as 1, 9, and 16, thathave a distinctive heterochromatic region just below theircentromeres in their q-arms, and the Y chromosome has aregion on the telomeric end of its q-arm referred to as a qhregion. Since the qh regions are rich in highly repetitiveDNA sequences, they are highly polymorphic in size and

sometimes they can undergo pericentric inversion so thatpart of the entire heterochromatic region can be present inthe short arm of the chromosome just above the centromere.This polymorphic region can vary remarkably in size with nopathogenic significance to the individual.

Satellite and secondary constriction regions: Normally onlythe acrocentric chromosomes (13, 14, 15, 21 and 22) havesatellites and secondary constriction regions. The centromeresrepresent the primary constrictions which are the locationof the spindle fiber attachment. Located in the p-arm of anacrocentric chromosome is a secondary constriction which isrich in ribosomal cistrons (DNA that codes for ribosomes).The region telomeric to the secondary constriction of theacrocentric chromosomes represents the satellites that are richin repetitive DNA (non-coding) sequences.

“Shoulder” Band: Visualize the chromosome like a person: thep-arm is the head, the constricted centromere is the neck,and the region below the centromere in the proximal end ofthe q-arm is the shoulder region. Certain chromosomes havea prominent dark band in this region, such as chromosomes4 and 10.

+Submetacentric: Centomere located closer to one end of thechromosome than the other with a ratio of long arm to shortarm of 1:1.3 to 1:7.

“Window”: A chromosome landmark that identifies a cluster oflight bands flanked by two dark bands. This descriptive termis used for certain broad light staining areas on chromosomessuch as 3, 6, and 8.+ = Apply to all mammals, including humans] = key recognizable area* = qh region• = distinctive band described




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Description and Landmarks of G-banded A Group Chromosomes

Chromosome 1:

• Chromosome 1 is the largest human chromosome and is metacentric.• The most distinctive feature of chromosome 1 is the large, light-stain region on the distal

half of the p-arm.• In the proximal half of the p-arm there are two distinct dark bands (DB’s).• Below the centromere on the q-arm is the qh region, which can vary in staining qualities:

high-intensity dark stain, or dark and light. Varies in staining qualities more than the otherqh regions.

• The distal end of the q-arm has three evenly spaced dark bands; the most proximal one hasthe highest stain density of the three.

Chromosome 2:

• Largest submetacentric chromosome.

• The p-arm contains four distinct DB’s that span the whole arm.• The q-arm starts with a light stain region with three low-stain density DB’s.• The distal end of the q-arm has two evenly spaced DB’s with equal stain density.

Chromosome 3:

• Second largest metacentric chromosome• It has a distinct DB cap at the distal end of the p-arm.

• There are two light band (LB) “windows”: one is centrally located in the p-arm, one islocated proximal to center in the q-arm.

• In the distal third of the q-arm there are 3-4 DB’s (depending on band resolution).

Description and Landmarks of G-banded B Group Chromosomes

Chromosome 4:

• Submetacentric chromosome: p:q-arm length ratio of 1:3.• The p-arm has a broad “pure” LB followed by two medium stain density DB’s.

• The proximal end of the q-arm contains a high density dark “shoulder” band.• In the central q-arm there are four closely spaced, medium-stain density DB’s, which mayblend together.

• The distal end of the q-arm contains two DB’s of similar stain density.

Training Guide for Chromosome Recognition — Kuffel, Carlson, Stupca, and Jalal




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Chromosome 5:

• Submetacentric chromosome: p:q-arm length ratio of 1:3.• The p-arm has a distinct central DB.• The proximal end of the q-arm contains a low-stain density “shoulder” DB.

• In the central q-arm there are three closely-spaced, medium stain density DB’s, which mayblend together.• The distal end of the q-arm contains two DB’s of different stain density; the lower band of

the two DB’s is of higher stain density.

Strategy in distinguishing between the B Group chromosomes:

• Chromosome 4 has a characteristic light cap which distinguishes it from chromosome 5.• Chromosome 4 has two DB’s in its p-arm. Chromosome 5 only has one.• Chromosome 4 has a high stain density “shoulder” DB.• Chromosome 4’s distal q-arm has two DB’s of similar stain density; chromosome 5’s distal

q-arm contains two DB’s of different stain density.

Description and Landmarks of G-banded C Group Chromosomes(all C-group chromosomes are submetacentric)

Chromosome 6:

• One of the three largest chromosomes in this group, the others being chromosomes 7 and X.It has a p:q-arm length ratio of 1:2.

• There is a characteristic broad LB “window” in the p-arm.• The q-arm has several DB’s, including two central high stain density DB’s.

Chromosome 7:

• Comparable in size and p:q-arm length ratio to chromosomes 6 and X.• The p-arm has a prominent high stain density DB near the distal end of the arm.• The q-arm has two prominent high stain density DB’s, one located 1/3 and one located

2/3 of the way down the arm.

Chromosome 8:

• Similar in size and p:q-arm length ratio to chromosome 10.• The p-arm has a small LB “window” with two low stain density DB’s on either side of the

“window.”

• The q-arm contains a prominent DB located about 2/3 of the way down the arm.




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Chromosome 9:

• Similar in size and p:q-arm length ratio to chromosome 11.• The p-arm has two DB’s which are located in the upper 1/2-2/3 of the arm.• There is a qh region commonly located right below the centromere in the q-arm. This

region varies more in location on chromosome 9 than it does on chromosomes 1, 16, and Y.Alternative locations are as follows: 1) the qh may be split into two sections, one above andone below the centromere 2) the entire region may be located right above the centromere.

• The qh region stains with a light to medium gray stain coloration.• The q-arm has three distinct DB’s: one DB is below the qh region followed by a broad LB;

the other two DB’s are distal to the broad LB.• The q-arm finishes with a broad “pure” LB.

Chromosome 10:

• This chromosome is similar in size and p:q-arm length ratio to chromosome 8.• The p-arm has a distinct central DB.• The q-arm has three evenly spaced DB’s spread across the length of the arm; the first of the

three has the highest stain density.

Chromosome 11:

• Similar in size and p:q-arm length ratio to chromosome 9.• The p-arm has two distinct DB’s located in the lower ½ of the arm.• The q-arm has a DB right below the centromere followed by a broad LB.• There are two distinct DB’s centrally located in the q-arm followed by a large light stain

region with a low density gray DB.• Distinctive features of chromosomes 11 and 12 are that they have broad light and dark

staining regions in their q-arms.

Chromosome 12:• p:q-arm length ratio of 1:3.• Smallest p-arm of any C-group chromosome.• The p-arm has a broad DB.• The q-arm has a DB right below the centromere followed by a broad LB.• The central portion of the q-arm has 3-4 DB’s, depending on band resolution.• The q-arm finishes with a large light stain region.

Description and Landmarks of G-banded D Group Chromosomes

All chromosomes in this group are acrocentric and the p-arm/satellite region on thesechromosomes is polymorphic. This group is made up of the three largest pairs of acrocentric

chromosomes.

Chromosome 13:

• The q-arm has its highest stain density DB’s in the lower half of the arm.• There are three distinctive DB’s in the lower half of the q-arm and one DB in the upper

half.




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Chromosome 14:

• The highest stain density DB’s are located high and low in the q-arm.• There are two DB’s in the proximal end of the q-arm and one DB in the distal end of the

q-arm.

Chromosome 15:

• The highest stain density DB’s are located in the upper half of the q-arm.• There are two distinctive DB’s in the upper half of the q-arm.• The lower half of the q-arm is light stained.

Description and Landmarks of G-banded E Group ChromosomesThe chromosomes in this group are all submetacentric, but chromosome 16 may appear close tometacentric. The p-arm size decreases as we go from chromosome 16 through chromosome 18.

Chromosome 16:

• The p-arm has two low density DB’s.• There is a qh region located right below the centromere in the q-arm. The qh region is a

very high intensity dark staining area.• The q-arm has three evenly spaced DB’s spread across the length of the arm, the first of the

three (the qh) has the highest stain density.

Chromosome 17:• Chromosome 17 is lighter than chromosomes 16 or 18. Its highest stain density DB’s are in a

distal area of the q-arm.• The p-arm has a medium stain density central DB.• The q-arm has a medium stain density “shoulder” DB.• There are two high stain density DB’s in the distal area of the q-arm followed by a broad

“pure” LB on the telomeric end.

Chromosome 18:

• The p-arm has a DB cap. There is a small LB on the telomeric end of the p-arm, but oftenthis LB does not resolve. Instead the LB gives the DB cap a fuzzy edge.

• The p-arm is light after the DB cap and may give the arm an appearance similar to asatellite structure, but it is not a satellite.

• The q-arm has four DB’s at higher levels of band resolution: there are two DB’s in theproximal end of the arm and two DB’s in the distal end of the arm.





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Description and Landmarks of G-banded F Group Chromosomes

The chromosomes in this group are the smallest metacentric chromosomes found in humans.

Chromosome 19:

• This chromosome, in overall appearance, is very light with a dark pericentric area.• The p-arm has a very low stain density central DB.• The q-arm has a very low stain density central DB and a similar DB on the telomeric end

that is hard to see.• The p and q-arms at first glance look very similar, but the way to tell the difference between

them is that the telomere of the p-arm fades into the background and the telomere of the q-arm has a distinctive edge to it.

Chromosome 20:

• The p-arm has a broad, medium to high stain density DB in the middle to distal end(depending on resolution).

• The q-arm has two DB’s evenly spaced down the arm with a LB at the telomeric end.

Description and Landmarks of G-banded G Group Chromosomes

The chromosomes in this group are the smallest human chromosomes and are acrocentric.The p-arm/satellite region of chromosomes 21 and 22 are polymorphic.

Chromosome 21:

• This is the smallest human chromosome and it is acrocentric.• The q-arm has a broad, high stain density DB in the proximal end of the arm.

Chromosome 22:

• This acrocentric chromosome, in overall appearance, is very light with a dark pericentricarea.

• The q-arm has a low stain density central DB.

Description and Landmarks of G-banded Sex Chromosomes

Chromosome X:

• A submetacentric chromosome.• This chromosome is comparable in size and centromere position to chromosomes 6 and 7.• The p-arm has a broad, high stain density mid-arm DB.

• The q-arm also has a broad, high stain density DB located about equal distance from thecentromere as the prominent DB in the p-arm. The prominent DB’s in the p and q-arms areof similar stain density, but the q-arm DB is broader.

• There are three DB’s in the distal area of the q-arm and the third DB is the most distalhigh stain density DB of its size compared to the distal DB’s of all other C group sizechromosomes.




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Chromosome Y:

• A submetacentric chromosome.• The p-arm has a medium stain density DB at the end of the arm.• The q-arm has a narrow, low stain density “shoulder” DB.

• There is a qh region located at the terminal end of the q-arm. The qh region is a very highstain density area typically either medium dark gray or very dark gray in coloration. Due tothe variation of the qh region size, the overall size of a Y-chromosome can vary from smallerthan a chromosome 21 to about the size of a chromosome 13.

References:

ISCN (2005): An International System for Human Cytogenetic Nomenclature. Shaffer LG and Tommerrup N. (eds); S Karger, Basel.2005., pp 16-33.

London Conference on the Normal Human Karyotype. Cytogenetics. 1963;2:264-268.

Paris Conference (1971): Standardization in Human Cytogenetics. BirthDefects: Original Article Series, Vol 8, No 7 (The National Foundation,

New York 1975); also in Cytogenet Cell Genet. 1972; 11:313-362.Richardson AM. Chromosome analysis. In: Barch MJ, Knutson T, Spurbeck

JL ed s. The AGT Cytog ene tic s Laborator y Manua l 3rd edition.Philadelphia: Lippincott-Raven, 1997; pp 487-489.

Tharapel A. Human chromosome nomenclature: An overview anddefinition of terms. In: Gersen SL, Keagle MB eds. The Principles ofClinical Cytogenetics 2nd edition. Totowa, NJ: Humana Press, 2005;pp 28-41.

Correspondence to:Daniel KuffelCytogenetics Laboratory

Department of Laboratory Medicine and Pathology

Mayo Clinic and Mayo Foundation

200 1st Street SWRochester, MN 55905





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Dr. Korf completed his undergraduate studies in biology with a genetics concentration at Cornell University, Ithaca, NY in 1974and then joined the MD/PhD program at Cornell University MedicalCollege/Rockefeller University. His graduate work involved theanalysis of chromosomes in living cells using micromanipulation. Hereceived his PhD in 1979 and MD in 1980. He then moved to Boston,completing a two-year residency in pediatrics at Children’s Hospital,

followed by a fellowship in genetics and cytogenet ics and residency inneurology (child neurology).

Upon completion of his training in 1985 he joined the staffat Children’s Hospital, becoming clinical director of genetics andassociate chief of the Division of Genetics. In 1999 he moved toPartners HealthCare System to become medical director of thenew Harvard-Partners Center for Genetics and Genomics. In thiscapacity, he was involved in organizing clinical and educational

programs aimed at integrat ion of genet ics into medic ine across thePartners system (Massachusetts General Hospital and Brigham andWomen’s Hospital).

In 2003 Dr. Korf moved to the University of Alabama atBirmingham (UAB) to chair a new department of genetics, which isboth a clinical and basic science department that includes 25 facultymembers and provides a full range of clinical and clinical laboratoryservices. Dr. Korf is author or co-author of several books, includingHuman Genetics and Genomics: A Problem-Based Approach,Medical Genetics at a Glance, and Neurofibromatosis: A Guidefor Patients, Families, and Healthcare Professionals. He is also co-

editor of Current Protocols in Human Genetics and Emery andRimoin’s Principles and Practice of Medical Genetics.Dr. Korf has served on the board of directors of the American

College of Medical Genetics and the American Society of HumanGenetics, is past president of the Association of Professors of Humanand Medical Genetics and president-elect of the American Collegeof Medical Genetics. He also serves on the Board of ScientificCounselors of the National Cancer Institute and chairs the medicalaffairs committee of the Children’s Tumor Foundation. He has alongstanding research interest in the diagnosis and management ofneurofibromatosis, and also in the integration of genetics into medical

practice. Dr. Korf lives in Birmingham, Alabama with his wife Micheleand has two grown daughters, Jessica and Kathyrn.

HFM: How did you choose to enter the field of medicalgenetics after graduating from college?

BRK: I actually became interested in medical genetics duringhigh school(!), after spending a summer in a laboratoryat Roswell Park Memorial Institute. I continued thisinterest working in a clinical cytogenetics lab aftergraduating high school and through college, and didan honors thesis as an undergraduate at Cornell oncytogenetics. Therefore, by the time I entered medicalschool/graduate school, I was already sure that I wanted

to go into medical genetics. I saw the field as an ideal placeto be for someone who was interested both in clinicalcare and research. I can’t claim to have anticipatedthe explosion of knowledge that would result from therevolution in molecular genetics and genomics, but I didsee at that time that genetics would be a major driver inunderstanding health and disease.

HFM: What were the fields of cytogenetics and moleculargenetics like when you first started?

BRK: I began working in cytogenetics in 1968, just prior tothe advent of chromosome banding. I remember cuttingout chromosomes and placing them on a karyotype withno real certainty of where some of the chromosomesbelonged. I also remember when the first quinacrine-staining techniques were introduced. Molecular geneticsat the time was in its infancy, at least as applied tomedical genetics. I didn’t really begin to learn this in

earnest until after I completed graduate school and wasin fellowship. It was a remarkable time, in retrospect,with so many major technical advances happeningquickly. But then, the same can be said for today, exceptthat the power of the approaches and the pace of changeare vastly greater than when I entered the field.

HFM: It is difficult for scientists of either gender when theyare trying to get established in the field, especiallya rapidly changing field. I often asked my femaleinterviewees how they managed to balance theircareers and families in the beginning of their careers.Let me ask you the same question even though youare of the other gender.

BRK: I will admit that my wife, who is a professional involvedin educational television, bore the majority of thechildcare responsibilities as our two children grew up.That she managed to be there when our daughterscame home from school when they were young andsimultaneously built a successful department at a majortelevision station gives you a hint of how good she is atwhat she does, and how fortunate I have been. Neitherof our daughters has chosen to enter science or medicine--perhaps that says something about the example I set,

Profiles and Perspectives Column Editor: Hon Fong L. Mark, PhD, MBA, FACMG

Dr. Bruce Korf

Bruce R. Korf, MD, PhD, FACMGInterviewed by Hon Fong L Mark




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Dr. Bruce Korf — Mark


but I don’t think so. We have a great relationship now(one is just graduating college, one has been workingafter graduation for several years), which I think in partis based on being supportive of their career choices, as Iwas supported in mine.

HFM: I know that you have made many importa ntcontributions to the practice of medical genetics. Inyour view, which of your accomplishments do youconsider the most significant?

BRK: I feel that my career has had two major facets. Onehas been in the diagnosis and management ofneurofibromatosis type 1. Although I do not claim tobe responsible for major scientific breakthroughs in thefield, I think I have been effective working behind thescenes to set the stage for clinical trials of new therapiesand to advocate for funding and public education. Theother area has been in education, and specifically ineducating a generation of physicians, other health

professionals, and medical geneticists in how geneticswill transform medical practice.

HFM: Please elaborate.

BRK: In the area of neurofibromatosis, I have had a longstand-ing relationship with the National NeurofibromatosisFoundation, now called the Children’s TumorFoundation, helping them to identify research priori-ties and educate both the public and professionals. Ialso played a role in developing imaging approaches formeasurement of neurofibromas, and in establishing aconsortium to perform clinical trials in NF1. In educa-tion, I am most proud of having had a role in traininga long list of students, postdoctoral fellows, and resi-

dents. I co-directed the medical school course in genet-ics (an integrated course called “Genetics, Embryology,and Reproduction”) for many years at Harvard MedicalSchool and also established the Harvard Medical SchoolGenetics Training Program as a collaboration of themajor Harvard teaching hospitals. On a national level,I have co-directed the American College of MedicalGenetics, Genetics Review Course for the past severalyears. I have also played a role in educating non-geneticshealth professionals, both when I was at Harvard andnow at UAB. Finally, I have been very concerned aboutthe dwindling number of residents entering medicalgenetics, and organized two conferences at the BanburyConference Center to seek solutions.

HFM: Please tell our readers the solutions you came up withat the Banbury Conference Center.

BRK: Regarding the solutions to the dwindling number ofresidents, there is widespread concern that the numberof individuals seeking training in medical genetics isinsufficient to meet the anticipated need, particularlygiven the major advances that are occurring in thefield. In order to help to address this, we have held twoconferences at the Banbury Conference Center, in 2004

and 2006. The first focused on approaches to increasingthe number of trainees (Korf et al., 2005), and thesecond on the scope of practice of the medical geneticist(manuscript in preparation). Several recommendationswere made in the hope of attracting an increased

number of trainees. These include increased effortsto recruit medical students, strengthening the coretraining of medical geneticists, and partnering withother specialties. The second Banbury Conference willmake recommendations regarding the role of the medicalgeneticist and the relationship with other specialties.

HFM: I want to thank you for writing an excellent chapterwith Dr. Nancy Schneider for my book (Korf andSchneider, 2000). Please summarize for our readersyour distinguished publication list.

BRK: My research bibliography spans a long period of timeand reflects gradual shifts in my interests over the years,especially from laboratory-based studies to more clinical

research studies. My most recent research publicationsfocus on quantification of neurofibromas in NF1, whichis an important prelude to measuring outcomes ofclinical trials. I’ve written a large number of reviews, themajority about neurofibromatosis and many also aboutgenetics education. Finally, I’ve written or edited severalbooks. Human Genetics: A Problem-Based Approach Iwrote solo and is now in its third edition. There is also apatient-oriented handbook about neurofibromatosis, inits second edition. I am a co-editor of Current Protocolsin Human Genetics, my area of responsibility beingmedical and forensic applications, and also co-editedPrinciples and Practice of Medical Genetics, focusing onneurogenetics, psychiatric genetics, and the genetics of

hearing and ophthalmological disorders.

HFM: Of all these publications, which one was yourfavorite?

BRK: This is very difficult. I think that the paper “Diagnosticoutcome of children with multiple café-au-lait spots,”which was one of the first I wrote on NF1, has beenfairly widely quoted and made a contribution to NF1clinical diagnosis. Given how much time I’ve livedwith the task, I’d have to say that I’m proud also of thetextbook (Human Genetics and Genomics: A Problem-Based Approach).

HFM: How did you first get involved in the American College

of Medical Genetics (ACMG)? I have been told that itis a relatively exclusive organization.

BRK: I hope that the College is not perceived as exclusive,though I’ll admit that I was a little intimidated by theluminaries in the field when I first became a member.I began to be involved by serving on the ProgramCommittee, being invited to join by a former mentor.After a time in this role I was elected to serve on theBoard of Directors, which was a six-year term. I wasprivileged during that time to watch the college grow




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enormously in its role and influence nationally. This isevidenced, in part, by the major growth in attendanceat the national meeting, which has tripled from when Ijoined the board.

HFM: It is an honor to be elected as the new President ofthe ACMG. What are your goals and visions for theorganization for the next few years?

BRK: Medical genetics is at a crossroads. We have historicallyfocused on the diagnosis and management of patientswith rare disorders, which are very important to theaffected individuals and their families, though comprisingonly a very small area of medical practice. We areseeing two major developments which are transformingthe field. One is the ability to use molecular testingfor diagnosis and the increasing possibility of treating,as well as diagnosing, genetic disorders. We must, asa profession, embrace these new opportunities and beprepared to follow our patients and supervise their

treatment to a greater extent than was true in the past.Second, the genetic contributions to common disordersare rapidly coming into focus. Although I do not expectthe medical genetics community to take over the careof patients with common conditions such as asthmaor diabetes, we should be prepared to lead the way inthe application of genetic approaches to risk assessmentand choice of treatment. Providing such leadership is amajor opportunity and challenge for our profession. Iam hopeful that the College can serve as a catalyst inbringing about these transformations.

HFM: What steps do you plan to take to make the ACMGmore diverse and inclusive?

BRK: We need to do a better job in communicating howthe College is serving the medical genetics community,and the medical community as a whole. “Organizedmedicine” is a very complicated terrain, and medicalgenetics will only have a voice that is heeded if we speakthrough the vehicle of our professional society. I hopethat we will be able to engage our colleagues acrossthe entire spectrum of genetic practice to advocate forthe roles of diverse genetics professionals in the careof patients with rare and common disorders as well asprevention of disease.

HFM: What advice would you give a young person today, whohas an interest in going into the field of genetics?

BRK: Today’s trainees are faced with unprecedentedopportunities to understand the genetic contributionsto both rare and common disorders and develop newapproaches to diagnosis and treatment. In addition totraining in the “classical” areas of genetics, it will becritical to be conversant in genomics and informatics.Beyond this, I would advise young people interested ingenetics to be alert to new opportunities, to partner withcolleagues in other areas of medicine and to lead the

effort to integrate genetics into all branches of medicalpractice.

HFM: What do you think are the most urgent scientificquestions that need to be answered in our field in the

coming years?BRK: We are only beginning to understand the various

elements of the genome and how they interact with oneanother. The traditional “central dogma” of DNA toRNA to protein is but one of multiple functions of thegenome. I believe that the coming generation of clinicaland laboratory investigators will have the opportunityto put all of this together to achieve an understandingof the function of biological systems, and to apply thissystems approach to medical care.

HFM: What challenges do you see facing genetics laboratoriesin the twenty-first century? Where do you thinklaboratory genetics is heading? Do you see genetic

testing being performed mainly in large commerciallaboratories in the future?

BRK: Laboratory genetics has been evolving, and the paceof change is likely to accelerate as large-scale genomicapproaches become increasingly dominant. This will beespecially true if the “$1,000 genome sequence” nowbeing talked about becomes a reality. It is true thatthe technological demands of such testing may only beavailable in large regional centers, which could well turnout to be commercial laboratories or very large and well-organized academic laboratories. This, however, is likelyto evolve over some period of time, and I believe thatacademic laboratories can (and should) play a major roleas we move forward.

HFM: What do you see as the future for these academicmedical center laboratories?

BRK: I believe that academic laboratories will, for a long time tocome, have important roles at two ends of the spectrumof genetic testing. For the more straightforward tests,including some single-gene disorders and cytogenetictesting, local laboratories can play a role if they providea package of high value, including competitive costsand exemplary service. The academic laboratories dohave the possibility of developing a relationship oftrust with local providers, but they must do so whileremaining cost-competitive, which admittedly is noteasy to do. At the other end of the spectrum, academiclaboratories will have a niche for some time to come inhandling rare disorders and very complicated tests thatrequire intimate knowledge of a specific genetic system.The academic labs would do well to establish consortiawhere specific labs provide a subset of tests for suchdisorders that are not likely to be handled by the largecommercial labs. This also provides an opportunity tostudy genotype-phenotype correlations, which is anideal role for the academic labs to spearhead.




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HFM: If you can start over again, what career would youhave pursued, if not medical genetics?

BRK: I have always been intrigued by physics and astronomy,and think I could have been happy in a career in theseareas; yet at this point it is hard to imagine being

involved in a field that is more dynamic and excitingthan medical genetics.

HFM: This column often ends with a saying or an importantpiece of advice. Before ending this very interestinginterview, is there something you would like to leavewith our readers?

BRK: Our generation is privileged to see the medical mysteriesof all history gradually become understood. Medicinewill be transformed to become almost unrecognizable inthe coming years, and the groundwork is now being laidto bring about that transformation. There has never, inthe history of medicine, been a more exciting time to beinvolved in medical practice or research.

References Cited

Korf BR and Schneider NR. Cytogenetics in Medicine. In: Mark HFL (ed).Medical Cytogenetics. New York: Marcel Dekker, Inc; 2000.

Korf BR, Feldman G and Wiesner G. 2005. Report of the Banbury Summitmeeting on training of physicians in medical genetics, October 20-22,2004. Genetics in Medicine. 2005;7: 433-438.

Hon Fong L. Mark, PhD, MBA, FACMG, a board-certifiedClinical Cytogeneticist, and Editor of the cytogenetics textbook,“Medical Cytogenetics,” is President of KRAM Corporation anda Clinical Professor at the Brown University Medical Schoolin Providence, Rhode Island. She was formerly Director ofCytogenetics at the Lifespan Academic Medical Center/BrownUniversity in Providence, RI and Director of the CytogeneticsDepartment at Presbyterian Laboratory Services/Novant Healthin Charlotte, North Carolina, and is currently Director of theCytogenetics Laboratories at the Center for Human Genetics,and Clinical Professor of Pathology and Laboratory Medicine atthe Boston University School of Medicine, Boston, MA. This

column is dedicated to the cytogenetic technologists of hercurrent and former laboratories.




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Abstracts in Review

The Triumphant March of the Clinical Use of DNA-Arrays:The Discovery of Novel Genomic Disorders Through aTargeted Molecular Screening of the Human Genome

Abstracted by Jaime Garcia-Heras

Sharp AJ, Hansen S, Selzer RR, Cheng Z, Regan R, Hurst JA,Stewart H, Price SM, Blair E, Hennekam RC, Fitzpatrick CA,Segraves R, Richmond TA, Guiver C, Albertson DG, Pinkel D, EisPS, Schwartz S, Knight SJL, Eichler EE. Discovery of previouslyunidentified genomic disorders from the duplication architecture of thehuman genome. Nature Genetics. 2006. 38:1038-1042.

Approximately five percent of the human genome consists ofDNA stretches of at least 1 Kb in length and with >90 percent ofsequence homology called segmental duplications (or low copyrepeats). These duplications are between an intervening DNA

sequence of variable size and are thought to mediate a processcalled non-allelic homologous recombination (NAHR) thatoften leads to deletions, duplications and inversions. Segmentalduplications are frequently associated with genomic disorders andwith the recently discovered DNA polymorphisms called copynumber polymorphisms (CNPs).

The occurrence of genomic disorders and CNPs at sitesflanked by segmental duplications suggests that the architectureof the human genome makes these regions very unstable andprone to rearrangements. Based on this assumption, Sharp andcollaborators speculated that there might be other similar regionsassociated with genetic disease yet to be discovered. To test thishypothesis they first examined the sequence of the human genomeand identified 130 potentially unstable hot spots flanked by

segmental duplications. They then developed a BAC microarray of 2,007 BACs that targeted these regions (segmental duplicationarray) with the purpose of detecting genetic imbalances in them.The rearrangement hot spots were defined as 50Kb to 10 Mb of unique DNA intervening sequenceflanked by segmental duplications >10 Kb inlength with >95 percent of sequence homology(Figure 1).

The first step of this study was to determine thebaseline frequency of polymorphisms at the same130 selected rearrangement hotspots in 316 normalindividuals. A total of 384 putative polymorphicsites were observed. Then 290 children and adultswith idiopathic mental retardation with or without

dysmorphism or congenital anomalies were tested.All these individuals had a normal karyotype at550-bands of resolution and most of them hadtested negative for FRAXA mutations. All thecases except 35 were reported as normal in studiesfor cryptic subtelomeric rearrangements by FISH.

Copy number changes that involved two ormore adjacent BACs were considered potentiallydisease-related only if they were present in the testpopulation and absent in the controls. Deletions

or duplications of hot-spot regions and copy number variationsof the LCRs were reported when the log2 ratio of fluorescencemeasurements in at least two or more adjacent BACs exceededtwo standard deviations from the corresponding values in anormal control male.

A total of sixteen individuals (5.5%) with microdeletions ormicroduplications were identified. This included two probableunbalanced translocations (a dup of 6q27→qter with a delof 11q25→qter and a del of 10q26.3→pter with a dup of13q34→qter) and recurrent abnormalities seen in genomicdisorders (deletions/duplications of 22q11.2 for DiGeorge-

VCF syndrome, a duplication of 17p11.2 in the Smith-Magenissyndrome region, and a deletion of 1p36.3).It was quite remarkable that four individuals showed a deletion

of the same four contiguous BACs spanning a ~500 Kb regionwithin band 17q21.31. These deletions were confirmed by FISHand were characterized with a custom duplex high-densityoligonucleotide array consisting of 166,000 isothermal 45-70 basepairs probes (mean density of one probe every 131 base pairs). Thedeletion boundaries seemed to coincide with a pair of directly-oriented segmental duplications 38 Kb in length with 98 percentof sequence homology and separated by 740 Kb. Most likelythese deletions were due to a NAHR mediated by the flankingsegmental duplications at the breakpoints.

The phenotype of the four individuals was similar so the

conclusion was that this deletion of 17q21.31 represented apreviously unrecognized microdeletion syndrome. A comparativemapping delineated a recurrently deleted critical interval of 478

Fig. 1. The design of the BAC array targeting regions flanked by segmentalduplications (LCRs). The “hot spot” of an intervening DNA stretch of uniquesequence is shown in a red line. It is flanked by two segmental duplicationsor LCRs (light blue rectangles) and covered by several overlapping BACs(black lines). Each LCR is covered by two overlapping BACs (blue lines).




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Abstracts in Review

Kb that harbors six known genes including CRHR1 and MAPT. Both genes are ubiquitously expressed in the brain and havebeen implicated in neurodegenerative diseases and behavioraldisorders, so they were considered excellent candidates for thissyndrome.

The distinctive phenotype of deletions 17q21.31 and a CGH

study with the same array led to the diagnosis of a deletionspanning the same four BAC clones in a fifth case.Five other rearrangements found in the test population were

also delineated in detail with the same high-density oligonucleotidearray. These were a dup 17q12 (1.46 Mb), a del 15q24.1-24.3(3.9 Mb), a del 1q21.1 (1.47 Mb), a del 15q13.1-q13.3 (3.95 Mb)and a del 15q23-24.2 (3.81 Mb). With the exception of thedel 15q23-24.2, the breakpoints in the other cases mapped toclusters of segmental duplications. For this reason NAHR seemedto be the likely mechanism exactly like the deletions of 17q21.31.By contrast the breakpoints of the del 15q23-24.2 existed withinunique sequences, which suggested it was not mediated by NAHRand therefore was an unlikely recurrent event.

This study also documented that normal individuals carry

copy number polymorphisms at the same clusters of segmentalduplications flanking the five pathogenic rearrangements(del 17q21.31, dup 17q12, del 15q24.1-24.3, del 1q21.1, and thedel 15q13.1-13.3). The most conspicuous example was the del17q21.31, which was the most frequently detected abnormality.It is significant that copy number polymorphisms and inversionsalso occur at the sites of segmental duplications in other humangenomic disorders. These data led the authors to propose thatsegmental duplications with polymorphisms are probably apredictive feature of regions prone to recurrent rearrangementsat a higher frequency.

The deletion of 17q21.31 occurs in a region with a ~900Kb inversion polymorphism present in about 20 percent ofEuropeans. It is quite interesting that molecular studies in other

human genomic disorders had also reported associations betweena constitutional inversion and a deletion in a specific region. Theconspicuous examples are Williams-Beuren syndrome (about one-third of the parents carry a 1.5 Mb inversion at band 7q11.23),Angelman syndrome (one third of parents carry an inversionof 4 Mb at band 15q12) and Sotos syndrome (most fathers of

Japanese patients with a deletion of 5q35 carry a 1.9 Mb inversionof this region). Of the cases with a del 17q21.31 from this study,two proved to be inherited from the parental chromosome17 carrying the inversion-haplotype. Given the fact that this

inversion at 17q21.31 is more frequent in Europeans, the authorshinted that microdeletions of 17q21.31 could be more frequentin this population but they recommended a confirmation of thishypothesis. This study of 290 individuals of European originsuggests that the del of 17q21.31 has a 1 percent frequency butthe authors emphasized that other populations should be tested

to determine its worldwide frequency.According to the authors, the sequencing and the architectureof the human genome are useful data for developing arrays thatallow screening and identification of recurrent rearrangementsassociated with previously unreported genetic diseases. Suchan approach with a segmental duplication array permitted thedescription of a novel 17q21.31 deletion syndrome that concurswith two simultaneous publications using genomic arrays (Koolenet al., 2006; Shaw-Smith et al., 2006). In addition Sharp et al.reported four new candidate regions of genomic disorders (1q21,15q13.1-q13.3, 15q24.1-24.3 and 17q12). For these reasons theauthors advocated an expanded high resolution screening ofgenetic imbalances at unstable regions flanked by segmentalduplications as an effective strategy to uncover novel genomic

disorders arisen de novo. The fact that three groups reported atthe same time that the deletion of 17q21.31 is a novel geneticsyndrome supports the clinical implementation of such targetedhigh-resolution molecular analysis.

References

Koolen DA, Vissers LELM, Pfundt R, de Leeuw N, Knight SJL, Regan R,Kooy RF, Reyniers E, Romano C, Fichera M, Schinzel A, Baumer A,Anderlid B-M, Schoumans J, Knoers NV, van Kessel AG, SistermansEA, Veltman JA, Brunner HG, de Vries BBA. A new chromosome17q21.31 microdeletion syndrome associated with a common inversionpolymorphism. Nature Genet. 2006; 38: 999-1001.

Shaw-Smith C, Pittman AM, Willatt L, Martin H, Rickman L, Gribble S,Curley R, Cumming S, Dunn C, Kalaitzopoulos D, Porter K, Prigmore E,Krepischi-Santos ACV, Varela MC, Koiffmann CP, Lees AJ, Rosenberg

C, Firth HV, de Silva R, Carter NP. Microdeletion encompassing MAPT at chromosome 17q21.31 is associated with developmental delay andlearning disability. Nature Genet. 2006; 38: 1032-1037.

Reprint requests to:Dr. Evan E. Eichler. Department of Genome Sciences and TheHoward Hughes Medical Institute. University of WashingtonSchool of Medicine. 1705 NE Pacific St. Seattle. WA 98195. USA.E-mail: [email protected].




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Abstracts in Review

Koolen DA, Vissers LELM, Pfundt R, de Leeuw N, Knight SJL,Regan R, Kooy RF, Reyniers E, Romano C, Fichera M, Schinzel A,Baumer A, Anderlid B-M, Schoumans J, Knoers NV, van Kessel

AG, Sistermans EA, Veltman JA, Brunner HG, de Vries BB. Anew chromosome 17q21.31 microdeletion syndrome associated with acommon inversion polymorphism. Nat Genet. 2006; 38:999-1001.

Shaw-Smith C, Pittman AM, Willatt L, Martin H, Rickman L,Gribble S, Curley R, Cumming S, Dunn C, Kalaitzopoulos D, PorterK, Prigmore E, Krepischi-Santos ACV, Varela MC, Koiffmann CP,Lees AJ, Rosenberg C, Firth HV, de Silva R, Carter NP. Microdeletionencompassing MAPT at chromosome 17q21.3 is associated withdevelopmental delay and learning disability. Nat Genet. 2006;38:1032-1037.

Sharp AJ, Hansen S, Selzer RR, Cheng Z, Regan R, Hurst JA,Stewart H, Price SM, Blair E, Hennekam RC, Fitzpatrick CA,Segraves R, Richmond TA, Guiver C, Albertson DG, Pinkel D, EisPS, Schwartz S, Knight SJL, Eichler EE. Discovery of previouslyunidentified genomic disorders from the duplication architecture of thehuman genome. Nat Genet. 2006; 38:1038-1042.

The use of genomic arrays (array-CGH) has reshaped thelaboratory diagnostics in medical genetics by improving thedetection of submicroscopic abnormalities in individuals withmental retardation, developmental delay and malformations. Thesecond phase of this “array-CGH era” seems to be the ascertainmentof previously unrecognized syndromes with a clinically distinctivephenotype and the discovery that the architecture of the humangenome is a contributing factor for genomic disorders. Aconspicuous example is the simultaneous publication of threerecent papers about the microdeletion 17q21.31 syndrome and itsassociation with a constitutional inversion polymorphism in thesame region involved in the deletion.

The first study was done in 360 individuals with MR who hada normal karyotype (550 bands) and did not carry subtelomericabnormalities. A genome-wide tiling path BAC array (32,477clones with complete coverage of the genome) permitted theidentification of one deletion of ~600 Kb within band 17q21.31. Ascreening of 840 individuals using MLPA with probes from genes

within 17q21.31 ( MAPT and CRHR1) prompted the diagnosis oftwo other cases with identical deletions. The three deletions wereconfirmed by FISH and were of de novo origin. The phenotypeconsistently showed moderate mental retardation, severehypotonia, characteristic facial features, and brain anomalies byMRI (Koolen et al., 2006).

Another study was in 50 individuals referred to geneticevaluation due to familial learning disability, overgrowth orgrowth failure, behavioral problems, seizures, facial dysmorphism,and clinical or radiological evidence of brain, trunk or limbanomalies. These patients had a normal karyotype (400-500

bands) and most of them (41/50) did not have subtelomericabnormalities. Three de novo heterozygous deletions of 500-650Kb at 17q21.3 with phenotypic similarities were identified usinga whole genome array with an average of one clone per ~1 Mb.The clinical findings were low birth weight (below the secondcentile), neonatal hypotonia and/or poor feeding, delayed motorand speech development, and mildly dysmorphic features (Shaw-Smith et al., 2006).

Sharp and collaborators took a different approach that led tothe identification of various abnormalities including deletionswithin 17q21.31. Based on the assumption that 130 hot spotsin the human genome flanked by segmental duplications were candidates for novel genomic disorders, they developeda so-called “segmental duplication BAC array” targeting theseregions. They then studied 290 children and young adults withidiopathic MR with or without malformations/dysmorphism andidentified five deletions of 17q21.31. These patients had normalkaryotypes (550 bands) and most of them had a previous normalsubtelomeric study by FISH (n=255) or had tested negative for

FRAXA mutations. The authors reported that the phenotype ofthe deletions of 17q21.31 had overlapping clinical features with adeletion size of ~500 Kb that encompassed four contiguous BACs. All the deletions were confirmed by FISH. A subsequent detailedcharacterization with a high-density oligonucleotide array (meandensity of one probe per 131 base pairs) demonstrated that thedeletion breakpoints mapped within clusters of flanking segmentalduplication and showed a critical deletion region of ~478 Kb. Thedeletion boundaries consisted of segmental duplications 38 Kblong that had 98 percent of sequence homology and a 740 Kb ofintervening DNA sequence (Sharp et al., 2006).

The conclusions of these studies were the following: a) thedeletions of 17q21.31 were recurrent events in a region that harborsa polymorphic 900 Kb inversion, b) non-allelic homologousrecombination (NAHR) was the likely mechanism, c) themost relevant genes within the deleted interval were MAPT and CRHR1, d) the patients showed a clinically recognizablephenotype.

The region spanning the polymorphic 900 Kb inversion at17q21.31 has a complex genomic architecture and two haplotypes named H1 (the ancestral haplotype) and H2 (the inversion-specific

haplotype seen in ~20 percent of northern Europeans and MiddleEastern ethnicities). There are substantial differences in copynumber, orientation, and position of segmental duplications andSNPs between H1 and H2. The deletion breakpoints were alwaysflanked by segmental duplications with an inverted orientation inthe H1 haplotype.

By contrast, the H2 haplotype had the same segmentalduplications in direct orientation at each side of the deletedinterval. The latter configuration would explain the occurrenceof deletions by NAHR in the chromosome with the H2 haplotypeand their inheritance from parents carrying this haplotype. A

Novel Clinically Distinctive Chromosome Syndromes:Microdeletions of 17q21.31Abstracted by Jaime Garcia-Heras




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preliminary inference from these findings was that H2 could bea risk factor to have offspring with deletions of 17q21.31 and thatthis syndrome could be more prevalent in geographic areas withlarge clusters of H2 carriers. But among the authors there wasconsensus for the need to confirm this hypothesis because theH2 haplotype is more frequent than deletions of 17q21.31, and H2may be a necessary predisposing factor but is still not sufficient tocause these deletions.

NAHR mediated by the misaligned pairing of segmentalduplications appears to be a fairly common mechanism thatgenerates deletions, duplications and almost certainly geneticvariation and evolutionary changes in DNA. The association of

NAHR, a polymorphic inversion and deletions of 17q21.31, wasnot unexpected. Several human genomic disorders previouslydescribed also arise through NAHR at sites of constitutionalpolymorphic inversions (e.g., the syndromes of Smith-Magenis, DiGeorge-VCF, Angelman, Williams-Beuren, Sotos and Charcot-Marie Tooth).

The common deleted interval within 17q21.31 harbors thegenes MAPT (microtubule associated protein Tau), CRHR1

(corticotrophin releasing hormone receptor 1), theintramembraneprotease 5 (IMP5) and saitohin (STH). The predicted genes NP_689679.1 and KIAA1267 that encode hypothetical proteinsof unknown function also lie in this interval.

The haploinsufficiency of MAPT , CRHR1, IMP5 and STH may explain some manifestations of the syndrome. The hypotoniaand mild mental retardation may result from the MAPT haploinsufficiency. MAPT encodes the microtubule associatedprotein Tau, a neuronal protein considered critical for the normalfunction of neurons. Tau is also a key component of neurofibrillardeposits in Alzeimer’s disease and other neurodegenerativediseases called tauopathies.

The phenotypic contribution of CRHR1 seemed less clearalthough there is evidence of its presence and expression during

development of the cerebellum in mice. The functions of IMP5 and STH are not fully understood yet but recent data may explaintheir role in the syndrome. A haploinsufficiency of IMP5 could

cause a reduced synthesis of key regulatory transmembraneproteins with the end result of a faulty control of cell signalingpathways critical for a normal development. The loss of one STH gene copy could impair the delicate balance that the PRDX6 geneseems to maintain between protection of important biomolecules(DNA, lipids, proteins and carbohydrates) against damage causedby reactive oxygen species (ROS) and the need of adequateROS levels for effective mechanisms of gene regulation, signaltransduction, cell proliferation and growth, the function of someenzymes and phagocytosis.

Deletions of 17q21.31 appear to have a phenotype with mentalretardation or developmental delay, hypotonia and distinctivecraniofacial features that should prompt a presumptive diagnosisupon clinical examination. Given the small number of patientsreported to date however, an assessment of the natural history andclinical variability of the syndrome are pending. One prevalenceestimate of 17q21.31 deletions was 1 in 13,000 to 1 in 20,000which is comparable to the range of 1 in 10,000 to 1 in 20,000in Williams-Beuren syndrome (Kool et al., 2006). Sharp et al.calculated a one percent frequency among individuals with mental

retardation, but they recommended studies in other populationsto determine the worldwide frequency (Sharp et al., 2006).These papers highlight important issues about the etiology of

sporadic human genetic diseases far beyond the delineation ofa novel microdeletion syndrome of 17q21.31. The broad and farreaching repercussion of the findings is that many other sporadicdisorders are likely to be recurrent in human populations becausethe architecture of DNA predisposes to unbalanced genomicrearrangements that trigger disease onset. Gene dosage defectsand genomic diseases caused by NAHR are probably morefrequent than initially anticipated, and it will only be a matter oftime before the causes of other diseases are identified with target-specific arrays. Time should tell if array-CGH and genomic arrayswill be seen retrospectively as revolutionary hallmarks of an era,

like the new chromosomal banding techniques were for clinicalcytogenetics in the early ‘70s.

Abstracts in Review




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Glossary

Abstracts in Review

BAC microarray: A collection of BACs corresponding toselected intervals of the genome that is placed on a glassslide with the purpose of detecting genetic imbalances

with a hybridization assay.BACs: Bacterial artificial chromosomes. These are largeplasmids that function as vectors carrying DNA inserts of100 to 300 Kb in size. They can be propagated in bacteriaand are frequently used as probes for sequencing, mappingor hybridization assays to detect genetic imbalances at highresolution.

CRHR1: The gene that encodes the corticotrophin-releasinghormone receptor 1. This is a transmembrane receptorwidely expressed in the brain and the corticotropic cells ofthe anterior pituitary. Corticotrophic cells synthesize andare stimulated to release the ACTH hormone after theCRHR1 is activated by the binding of the corticotrophinreleasing hormone (CRH). ACTH is the hormone that

stimulates the adrenal gland to synthesize and releaseglucocorticoids, corticosteroids and androgens. CRHR1,CRH and ACTH are key regulatory molecules of thehypothalamic, pituitary-adrenal axis that controls thefunction of the adrenal gland.

Copy number polymorphisms (CNPs): Gains (duplications),losses (deletions) or insertions of DNA ranging from severalKb to hundreds of Kb. They are not considered a directcause of human disease but they frequently map close tothe regions of recurrent chromosome rearrangements orregions associated with genetic disorders. CNPs are widelydistributed in the human genome and are often flankedby segmental duplications. High resolution molecularanalysis with genomic arrays led to the recent discovery

that CNPs are a novel common source of genetic variationand diversity within human populations. The estimate isthat on average a normal healthy individual carries 11to 13 CNPs. Considering the high frequency of CNPs,a consensus has emerged about the need to developdatabases representing different populations to establishtheir contribution to genetic variation, inherited traits andpotential diseases.

FRAXA: The gene that causes fragile X syndrome.Genomic disorders: Genetic conditions caused by

rearrangements involving large regions that resultin deletions, duplications, inversions or an impairedstructure of dosage sensitive genes. These disordershave a recognizable abnormal phenotype of congenital

malformations and mental retardation and are responsiblefor a significant portions of birth defects.

Haploinsufficiency: The presence of only one gene or genes ofa normal diploid locus or loci that results in a single dosewith a reduced expression of gene critical for a normaldevelopment or function. Cryptic or submicroscopicdeletions of variable size and mutations that impair thefunction of a gene are the most frequent causes.

Haplotype: Alleles from two or more closely linked loci thatare inherited as a unit.

Intramembrane protease 5 (IMP5): A protease from thefamily of intramembrane proteases (IMPAS), enzymesthat are embedded in a lipid bilayer membrane and are

capable of catalyzing the hydrolysis of transmembraneproteins. As a result they generate active proteins thatafter their release can exert downstream effects such ascell-signaling, gene regulation, immune surveillance andintercellular communication. This biological processmediated by IMPAS is called regulatory intramembraneproteolysis (RIP).

MAPT: The gene that encodes the microtubule-associatedprotein Tau. This is a neuronal phospho-protein thatlocalizes primarily in the axon and is considered essentialfor a normal function of neurons. Tau is one of the majorand most widely distributed microtubule-associatedproteins in the central nervous system. The role of Tauis probably as a catalyzing factor for the normal assembly

and function of microtubules that maintain cell shape,axonal transport and neuronal polarity. The biologicalfunctions of Tau are tightly regulated by a control of thealternative splicing of its gene and the phosphorylation ofit. There is a clinically significant association of Tau withneurodegenerative disorders because it is a key componentof abnormal neurofibrillar deposits in Alzheimer disease(AD) and other tauopathies (fronto temporal dementiawith parkinsonism linked to chromosome 17, progressivesupranuclear palsy, corticobasal degeneration, Pick’sdisease). Mutations in the Tau gene cause the inheritedfrontotemporal dementia with parkinsonism linked tochromosome 17. The abnormal hyperphosphorylation ofTau is related to the aberrant tau aggregates seen in AD.

MLPA (multiplex ligation-dependent probe amplification): A PCR-based technique that allows the simultaneouscopy number determination of many loci in a multiplexamplification reaction. Every locus is tested using aprobe set of two sequence-specific oligonucleotides thatbind to the target at sites adjacent to each other. Oneoligonucleotide is short, hybridizes to the 3’ end of thetarget DNA sequence and binds a PCR primer at its5’ end. The other oligonucleotide is long, hybridizes to the5’ end of the target DNA sequence and binds the otherPCR primer at its 3’ end. After a hybridization of the twooligonucleotides to one copy of a normal locus that isfollowed by a ligation reaction that joins them, a PCRreaction generates a product of the expected size. The

amount of ligated probes produced by PCR is proportionalto the copy number of the locus under study. A deletionwould result in a lack of PCR product and any duplicationwill yield a product of doubled size. The technique allowsthe use of a pair of universal primers to amplify the testedloci because each locus of interest has a product of a distinctsize that is identifiable by capillary gel electrophoresis.MLPA measures copy number of each locus by comparingthe fluorescent peak height of its PCR product with thecorresponding normal counterpart from a control.




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Glossary, continued

Abstracts in Review

Fig. 2. The molecular mechanism of NAHR mediated by LCRs. The toptwo lines show 2 DNA strands, each one with two highly homologousLCRs in a direct orientation (light blue and light brown boxes). The

intervening stretch of unique sequence flanked by these LCRs is shownby the red star. A misaligned pairing between two LCRs followed byan unequal exchange with breakpoints within the LCRs generates astrand with a duplication (two red stars) and a strand with a deletion(no stars).

Non allelic homologous recombination (NAHR): Themost common mechanism of genomic rearrangements.

NAH R star ts with a mi sa ligned pa ir ing of two

LCRs with high sequence homology positioned in adirect orientation followed by a recombination (DNAexchange) that generates a deletion and a reciprocalduplication when it involves two strands from the samechromosome, or strands from the two homologouschromosomes (Figure 2).

Oligonucleotide: A short DNA molecule (usually eight to50 base pairs) synthesized for its use as a probe or in thepolymerase chain reaction (PCR).

Oligonucleotide array: A collection of oligonucleotide probescovering either the whole genome or a specific regionselected for study. Because of the size of the probes andthe high density of coverage (often of one probe every15-20 base pairs) they are very sensitive to identify small

rearrangements. The average resolution of the mostwidely available oligonucleotide arrays is reported in therange of 30 to 50 Kb.

Peroxiredoxin (PRDX) family: A group of multifunctionalantioxidant enzymes that is widely conserved acrossmany phyla. The major functions of peroxiredoxins arethe protection of cells against oxidative damage causedby reactive oxygen species, a regulation of cell signalingcascades that utilize hydrogen peroxide as a secondmessenger and a control of cell proliferation.

PRDX6: Peroxiredoxin 6 gene. It encodes a bifunctionalprotein from the cytosol with GSH peroxidase andphospholipase A2 activities that is expressed in all

major organs. As an antioxidant protein from the PRDXfamily it protects against the cellular oxidative damageby reducing hydroperoxides. The phospholipase activityis mainly associated with the regulation of turnoverand metabolism of alveolar surfactant phospholipids byalveolar epithelial type II cells in the lung.

Reactive oxygen species (ROS): By-productsgenerated by living organisms in responseto external stimuli or by a normal aerobicmetabolism that are removed or kept atacceptable physiologic levels by means ofantioxidants and antioxidative enzymes. Theyare the superoxide, hydroxyl radicals, hydrogenperoxide, peroxyl radicals and alkoxyl radicals.

ROS were first recognized as toxic by-productsof aerobic metabolism because they can oxidizebiologically important molecules (DNA,proteins, carbohydrates, lipids) and cause celldamage. New data demonstrated they canplay relevant roles in the regulation of geneexpression, cell growth and proliferation, generegulation, the functioning of many enzymes,and mechanisms of phagocytosis.

Saithohin (STH): A gene encoding a peptide of128 amino acids that is located at the intronbetween the exons 9 and 10 of the human taugene. STH does not have homology to anyknown protein or obvious motifs. Its detailed

function is unknown but it interacts withperoxiredoxin 6 (PRDX6), an enzyme withan antioxidant function and a phospholipaseactivity that belongs to the peroxiredoxinfamily. These findings raise the possibility thatSTH functions are linked to the peroxiredoxinfamily of proteins.

Segmental duplications (also called low copy repeats orLCRs): Stretches of DNA usually between 10-500 Kbin size and >95 percent of sequence homology that aresituated at more than one site within the genome. Theycomprise about five percent of the human genome, oftenlie at the breakpoints of genomic rearrangements and canbe the substrates of NAHR. LCRs are also a significant

source of variation in the human genome.SNPs: Single nucleotide polymorphisms. These are the

most common variation (polymorphism) in the humangenome. They are usually present once every 1 to 1.3 Kbwhere the DNA sequence has a site with two alternativebases in more than 1 percent of the population. SNPs arevery suitable markers for mapping because they are stable,frequent and can be tested with automated genotypingmethods.




79

Book Review

The World of the Cell

Wayne M. Becker, Lewis J. Kleinsmith, and Jeff Hardin. SanFrancisco, Pearson Benjamin Cummings. 2006 (6th Edition). U.S.$134.00, U.S. ISBN 0-8053-4680-5.

Cells

Benjamin Lewin, Lynne Cassimeris, Vishwanath R. Lingapappa, andGeorge Plopper (eds.) Sudbury, MA, Jones and Bartlett. 2007. U.S.$114.95. ISBN 978-0-7637-3905-8

These two books on the biology of the cell are similar intopics covered, audience served, and length; however, they arequite different from one another. This is partlybecause of the backgrounds of the authors andeditors of the two books. Benjamin Lewin,

editor of the journals Nature, New Biol ogy,and Cell, also created the “Genes” series(with the current one called “Genes IX”),the indispensable reference/text for seriousmolecular biologists.

Wayne Becker is a botanist and teacher ofundergraduates at the University of Wisconsin.Becker’s group felt that they wanted a text thatnot only shared the current knowledge in thefield, but also stressed what is yet to be foundout for each subject, to inspire their studentsto perhaps find some passion there. Dr. Lewinaimed his book at undergraduates, neophytegrad students, and scientists wishing to know

more about the topics that may be outside theirfield.

The World of the Cell has 24 chapters, andCells has 17. The World of the Cell was completelywritten by the three authors, while an expertin the field being covered wrote each chapterin Cells. Cells also has an emphasis on “What’snext,” with a section after each chapter devotedto the future of that chapter’s subject. Becker’sgroup understandably focuses a little more onplants than does Lewin’s.

Major sections in Cells are “Introduction,”“Membranes and Transport,” “The Nucleus,”“The Cytoskeleton,” “Cell Division,” “Apoptosisand Cancer,” “Cell Communication,”“Prokaryotic and Plant Cells,” followed by aglossary, protein database index, and index.The World of the Cell does not get to thenucleus until Chapters 18 and 19. It also hasa glossary and index. The World of the Cell stresses the chemistry, organelles, energy flow,photosynthesis, and the history of biologyin much more detail than Cells, and Cells seems much morefocused on the nucleus and chromatin. Strangely, however, Cells

does not have a version of the structure of the chromatin fromnucleosome to chromosome, (such as graces the cover of this

journal) while The World of the Cell has a niceset of illustrations to explain this concept.

The illustrations are numerous and excellent

in both books. If you don’t like the illustration inone, it is likely better in the other. For example,the illustration of chromosome territories,or domains, in the interphase nucleus is agorgeous multi-color FISH photo in The Worldof the Cell, but more clearly explained in Cells with a photo and corresponding drawing of theindividual territories and inter-chromosomaldomains in the nucleus. For the text, however,The World of the Cell depends entirely on thepicture of territories (domains) with its caption,while Cells has a whole page dedicated to theorganization of the chromatin in the nucleus.On the other hand, The World of the Cell covers

techniques and methods, while Cells does notgo into much detail about these subjects.

The World of the Cell has a quick guide toeach of its techniques and methods insidethe front cover, and has a whole appendixon microscope methods that I found to beoutstanding. It even covers such topics as“Units of Measurement in Cell Biology,”“Centrifugation,” and the “Scientific Method”in its multitude of sidebars. The authors senseof humor can be seen shining through in onesidebar entitled, “Tempus Fugit and the FineArt of Watchmaking,” which is about efficiencyin the production of macromolecules, but usesa story about Mr. Fugit and someone calledCaveat Emptor. In the funny story, Fugitlearns that subunit assembly will enable himto make more accurate watches faster than thecompetition, similar to the subunit assembly ofmacromolecules in the cell.

Each chapter in Cells has references atthe end, while The World of the Cell includes

a suggested reading section at the end of each chapter, alongwith a set of “Problems/Question” for the student. These are




marked with a red dot if they are more challenging. The answersto these questions are in another book, purchased separately,called Solutions Manual.

Cells is integrated with a website which provides access torelated resources that are referenced in the text with a symbol,as well as interactive figures, animations, and videos about cells.These images are indicated in the text with a special symbolas well. On the website there are some PowerPoint slides of thelecture outlines and all figures for teachers, and test questions.They also have a special e-mail address for suggestions for revisionsor corrections for the next edition.

Comparing the glossaries, The World of the Cell won, handsdown. It has pages and pages more words in smaller font, anduses more scientific and thorough definitions, with the pagenumber in the text that explains the concept. For example, in TheWorld of the Cell, the definition of DNA says: “(deoxyribonucleicacid): macromolecule that serves as the repository of geneticinformation in all cells; constructed from nucleotides consistingof deoxyribose phosphate linked to either adenine, thymine,

cytosine, or guanine; forms a double helix held together bycomplementary base-pairing between adenine and thymine, andbetween cytosine and guanine (p. 53).” Cells doesn’t have anyentry for DNA in its glossary.

Each book has a chapter on cancer. The chapter in Cells ismuch better organized and easier to follow, but the chapter in TheWorld of the Cell has excellent coverage of the various genes andvarious types of treatments, and includes a sidebar on xerodermapigmentosum, a disease caused by a mutation of the excisionrepair pathway which leads to skin cancer rates that are 2,000-foldhigher than normal.

Looking at the Amazon.com reviews for these books, Cells hasno reviews yet, and The World of the Cell has been criticized bystudents for grammatical and typographical errors, for scatteredcoverage with a random order of subjects, and for esotericquestions. However, the illustrations were given high ratings, andI agree with them on that. (The pictures of mitosis are the bestI have seen). I did feel much more at home with Cells, because itcovers more of what I am interested in with greater detail, andfocuses on eukaryotes. However, each is excellent in its own way,so I am happy to own them both.

Reviewed by Helen Lawce Oregon Health & Science University Portland, OR

80

Book Review




81

Brain Tickler

Brain Tickler Summary(see inside front cover)

All twenty metaphase cells examined had what appearsto be a terminal deletion of a chromosome 7 short arm. Usingfluorescent in situ hybridization (FISH) with a chromosome 7psubtelomeric region probe, the probe region was shown to be

deleted in one homolog in each of ten metaphase cells examined.

Karyotype: 46,XX,del(7)(p22).ish del(7)(p22)(7PTEL-)

=




82

Great Lakes

(Illinois, Indiana,Michigan, Minnesota,

Ohio, Wisconsin)

Audra BirriCincinnati Children’s HospitalCytogenetics LaboratoryTCHRF Room 10033333 Burnet Ave.Cincinnati, OH 45229(513) 636-4474(513) 636-4373 [email protected]

Great Plains

(Arkansas, Iowa, Kansas,Missouri, Nebraska,

North Dakota, Oklahoma,South Dakota)

Julie Carstens, M.S.,CLSp(CG,MB)Cytogenetics LaboratoryMunroe-Meyer Institute985440 Nebraska MedicalCenterOmaha, NE 68198-5440(402) 559-4965(402) 559-7248 (FAX) [email protected]

Mid-Atlantic

(Delaware, District ofColumbia, Maryland,

New Jersey, Pennsylvania,Virginia, West Virginia)

Sally J. KochmarMagee-Women’s HospitalDepartment of Genetics300 Halket StreetPittsburgh, PA 15213(412) 641-4882(412) 641-1032 (F)[email protected]

Mountain States

(Arizona, Colorado, Idaho,Montana, New Mexico,

Utah, Wyoming)

Simone HamiltonReproductive GeneticsCenter, P.C.Cytogenetics Laboratory455 S. Hudson Street, Level 3Denver, CO 80246(303) 399-5478(303) 399-9160 (F)[email protected]

New England

(Connecticut, Maine,Massachusetts,New Hampshire,

Rhode Island, Vermont)

Gail BromageDIANON Systems, Inc.Cytogenetics Laboratory200 Watson Blvd.Stratford, CT 06497(800) 328-2666(203) 380-4554 (F)[email protected]

New York State

(New York)

Lori PlaistedSUNY Upstate Medical CenterCytogenetics Laboratory750 E. Adams St.Syracuse, NY 13210(315) 464- 4716(315) 464-6827 (F)[email protected]

Northern Pacific

(Alaska, NorthernCalifornia, Oregon,

Washington)

Shawna PyottUniversity of WashingtonMedical CenterCytogenetics Laboratory,Box 3561001959 NE PacificSeattle, WA 98195(206) 598-4489(206) 598-2610 (F)[email protected]

Southeast(Alabama, Florida,Georgia, Kentucky,

Louisiana, Mississippi,North Carolina, SouthCarolina, Tennessee)

Joan BishopGreenwood Genetics Center125 Gregor Mendel CircleGreenwood, SC 29646(864) 941-8135(864) 941-8133 (F)

[email protected]

Southern Pacific

(Hawaii, Nevada,Southern California)

Mervat AyadQuest Diagnostics Inc.–Nichols InstituteCytogentics Department33608 Ortega HighwaySan Juan Capistrano, CA92690(949) 728-4302(949) 728-4979 (F)[email protected]

Texas

(Texas)P. Alan LennonMolecular GeneticTechnology ProgramUT-MD Anderson CancerCenter1515 Holcombe Blvd., Unit 146Houston, TX 77030(713) 563-3783(713) 745-3337 (F)[email protected]

Canada

(All provinces and

territories)Viola FreemanHamilton Health ScienceCorp.McMaster University Campus1200 Main Street, W,Room 3N14Hamilton, OntarioCANADA L8N 3Z5(905) 521-2100, x 73706(905) 521-2651 (F)[email protected]

Non-US/Canada

Peter HuMolecular GeneticTechnology ProgramUT-MD Anderson CancerCenter1515 Holcombe Blvd., Unit 146Houston, TX 77030(713) 563-3095(713) 745-3337 (F)[email protected]

At-Large

Carol GelinasAffiliated Laboratory, Inc.Genetics Department/Cytogenetics925 Union Street #4Bangor, ME 04401(207) 973-7354(207) 973-5676 (F)[email protected]

Continuing Education Opportunities

If you have questions or experience difficulty locating your representative, please contact the AGT Education Director (see page 90 foraddress).

AGT Education Committee Regional Representatives (2007)




83

Continuing Education Opportunities Column Editor: Martha Keagle, MEd, CLSp(CG)

Test Yourself #2, 2007

The following questions are from: Swackhammer R and TatumOL. Survey of Candidate Genes for Autism Susceptibility. JAssoc Genet Technol. 2007; 33(1):8-16.

1. Linkage to susceptibility to autism has been found on all ofthe following chromosomes except:

a. Chromosome 4b. Chromosome 10c. Chromosome 19d. Y chromosome

2. Which of the following is not a form of autism?

a. Asperger’s Syndromeb. CHARGE Syndromec. Prader-Willi Syndromed. Rett Syndrome

Readers of The Journal of the Association of GeneticTechnologists are invited to participate in this “open book test”as an opportunity to earn continuing education credits (CEUs).AGT offers 0.2 CEUs for this Test Yourself based on articles inVolume 33, Number 1, First Quarter 2007 of The Journal.

Test Yourself is free to AGT members and $10 for non-members. To take this exam, send a copy of your completedAnswer Sheet along with the completed CEU Reporting Formto the AGT Continuing Education Subcommittee representativein your region. The list of representatives is on page 82 of thisissue. Non-members should submit a check payable to AGT for$10 with their answer sheet. Entry material must be post-markedon or before July 30, 2007.

To receive CEUs, 85 percent of your answers must be correct.You will be notified of your score, and if you achieved 85% orbetter your CEU Reporting Form will be approved for credit.

First Name MI Last Name

Address

AInstitution, Association, Journal, etc.

PAddress

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Association of Genetic Technologists CEU REPORTING FORM

I hereby certif y that I have completed the requirements for the continuing education activity requested above. Please attach appropriate documentation to support this CEU request.

___________________________________________ ____________________ ___________________________________________ ____________________ Signature (member) Date Education Committee Approval Date

11/02

Name:

Address:

CEU Area (1, 2, 3, 4): →

T

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. 2 AGT Membership Number:

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CEUs Awarded/Requested:

(check appropriate box)

Florida Program Number Florida License Number California Registration Number




84

3. Approximately ____ of individuals with autism display severedevelopmental delay.

a. 3%b. 9%c. 30%d. 39%

4. Which of the following statements is correct?

a. At birth, children at risk for autism can be diagnosed byhead circumference

b. Autism follows a simple Mendelian inheritance patternc. Both genetic and environmental factors are likely to

contribute to the etiology of autismd. More females than males are affected with autism

5. Which of the following statements concerning autism isincorrect?

a. Autism is assumed to involve a form of frontal lobepathology

b. Cerebellar white matter volume is 39% greater than thenormal average

c. Monozygotic twins have a concordance rate of 2-8%d. The autistic brain has a decreased number of Purkinje

fibers

6. Which of the following has not been shown to be linked toautism?

a. Daily paternal smoking during the pregnancyb. Exposure to valproic acid during early fetal developmentc. Exposure to thalidomide during early fetal developmentd. Increased maternal age

7. Studies had defined all of the following as susceptibilityregions for autism except:

a. Chromosome 2q23-2q33

b. Chromosome 7q21-7q22c. Chromosome 15q11-15q13d. Chromosome 19q13

8. According to this journal article the data analyzed imply thatas many as 40 percent of autism spectrum disorder cases inthe population may be influenced by variation in the ____gene.

a. AMPA2b. EN2c. GLO1d. PTEN

9. A LOD score of _________ is evidence against linkage.

a. -2b. 0 (zero)c. +1d. +3

10. SNP (small nucleotide polymorphism) refers to:

a. A measure of the likelihood of genetic linkage betweenloci

b. Any polymorphism involving only a pyrimidinenucleotide

c. Any polymorphic variation at a single nucleotide

d. Conditions which can not be detected by large scaleautomated scoring

The following questions come from: Coovadia A. PatentingPolicies As Applied to Genetics. J Assoc Genet Technol. 2007;33(1):17-19.

11. Which of the following statements is incorrect?

a. A process can be patentedb. Laws of Nature cannot be patentedc. Once a specific gene or protein is patented no one else

can obtain a patent on that specific gene or proteind. When a patent expires, the right to restriction ceases

12. Although a patent is based on the “first to invent” principle,inventors have:

a. A one year-grace period to file a patent after they publishb. Eighteen months to file their initial USA patent

applicationc. No way to apply for patents outside of the USAd. Three and a half years to file a patent application

13. According to this article which of the following organizationsholds “an exceptionally large number” of genetic testing-related patents?

a. Athena Diagnosticsb. Bio-Rad Laboratoriesc. Myriad Geneticsd. Roche

14. What year did the USPTO release stiffer interim guidelinesfor gene fragments?

a. 1978b. 1995c. 1999d. 2003

The following questions come from: Mark HFL. Profiles andPerspectives: Dr. Dorothy Warburton, PhD. J Assoc GenetTechnol. 2007; 33(1):20-22.

15. Dr. Warburton received her undergraduate and graduateeducation at:

a. Columbia Universityb. Columbia University (undergraduate) and McGill

University (graduate)c. McGill University (undergraduate) and Columbia

University (graduate)d. McGill University






85

16. Dr. Warburton started one of the first clinical cytogeneticslaboratories in the United States in:

a. 1961b. 1964c. 1969d. 1971

17. Dr. Warbutron learned cytogenetic techniques in ____________ laboratory.

a. William Allen’sb. David Carr’sc. Clarke Fraser’sd. Orlando J. Miller’s

18. While working on the Human Genome Project, Dr.Warburton became the senior chromosome editor for:

a. Chromosome 2b. Chromosome 13c. Chromosome aberrationsd. Trisomies

The following questions are from: Sakaluk-Moody L. BookReview: The Implicit Genome. J Assoc Genet Technol. 2007;33(1):23-24.

19. According to the editor of The Implicit Genome, all thechapters in the book deal with one to three of the followingthemes. Which of the following is not one of the underlyingthemes?

a. Genomic information can create specific, regulatedchanges in certain nucleotide sequences

b. Information can be implied and not explicit in thegenome

c. Information that creates variation in the probabilityof different genomic mutations has evolutionaryconsequence

d. The genome is composed of a string of nucleic acidswhich can be read in a one-by-one linear fashion

20. Bacterial fitness can be enhanced by:

a. Alternative splicingb. An increased overall mutation ratec. Increased mutation rates in some regions of the

genome (“hotspots”)d. Selectively removing “junk” DNA

Answer Sheet Please Print Clearly

1.______

2.______

3.______

4.______

5.______

6.______

7.______

8.______

9.______

10.______

11.______

12.______

13.______

14.______

15.______

16.______

17.______

18.______

19.______

20.______




86


JOURNAL CLUB 29

1. Meiotic Origin of Trisomy in ConfinedPlacental Mosaicism is Correlated withPresence of Fetal Uniparental Disomy,High Levels of Trisomy in Trophoblast,and Increased Risk of Fetal IntrauterineGrowth Restriction

2. Microdissection and DOP-PCR-based

Reverse Chromosome Painting as a Fastand Reliable Strategy in the Analysisof Various Structural ChromosomeAbnormalities

3. Estimated Rates of and Indication forPostnatal Diagnosis with Implications forPrenatal Counselling.

JOURNAL CLUB 30

1. Male Infertility and the Y Chromosome

2. Gonadoblastoma, Testicular and ProstateCancers, and the TSPY Gene

3. Genetics of Angelman Syndrome4. Noninvasive Test for Fragile X Syndrome,

Using Hair Root Analysis

JOURNAL CLUB 31

1. Parental Origin and Phenotype ofTriploidy in Spontaneous Abortions

2. Jumping Translocations in SpontaneousAbortions

3. Cytogenetics and Mechanisms ofSpontaneous Abortions

JOURNAL CLUB 32

1. World Health Organization Classificationof Neoplastic Diseases of theHematopoietic and Lymphoid Tissues: AProgress Report

2. World Health Organization Classificationof Neoplastic Diseases of TheHematopoietic and Lymphoid Tissues:Report of The Clinical AdvisoryCommittee Meeting

JOURNAL CLUB 33

1. FISH Identifies inv(16)(p14q22) Maskedby Translocations in Three Cases ofAcute Myeloid Leukemia

2. t(11; 14)-Positive Mantle CellLymphomas Exhibit Complex Karyotypesand Share Similarities with B-CellChronic Lymphocytic Leukemia

3. Isodicentric 7p, idic(7)(q11.3), in AcuteMyeloid Leukemia Associated WithOlder Age and Favorable Responseto Induction Chemotherapy: A New

Clinical Entity?JOURNAL CLUB 34

1. Comparative Genomic Hybridizationin Combination with Flow CytometryImproves Results of Cytogenetic Analysisof Spontaneous Abortions

2. Comparative Genomic Hybridization:A New Approach to Screening forIntrauterine Complete or MosaicAneuploidy

3. Limitations of ChromosomeClassification by Multicolor Karyotyping

JOURNAL CLUB 35

1. Prenatal Diagnosis of Mosaic Trisomy8 with Investigations of the Extent andOrigin of Trisomic Cells

2. Genetics of Beckwith-WiedemannSyndrome-Associated Tumors: CommonGenetic Pathways

3. Velo-Cardio-Facial Syndrome: ADistinctive Behavioral Phenotype

JOURNAL CLUB 36

1. Identification of Uniparental DisomyFollowing Prenatal Detection ofRobertsonian Translocations andIsochromosomes

2. Prenatal Diagnosis using Interphase

Fluorescence in situ Hybridization(FISH): 2-year Multi-center RetrospectiveStudy and Review of the Literature

3. Preimplantation Genetic Diagnosis ofPericentric Inversions

JOURNAL CLUB 37

1. Pharmacogenetics2. Consent and Privacy in Pharmacogenetic

Testing

3. Genetic Information, GenomicTechnologies, and the Future of DrugDiscovery

4. Mapping a Role for SNPs in DrugDevelopment

JOURNAL CLUB 38

1. Double Minute Chromosomes in AcuteMyeloid Leukemia and MyelodysplasticSyndrome

2. Common Fragile Sites Associatedwith the Breakpoints of ChromosomalAberrations in Hematologic Neoplasms

3. High Frequency of Leukemic Clonesin Newborn Screening Blood Samplesof Children with B-precursor AcuteLymphoblastic Leukemia

JOURNAL CLUB 39

1. Prediction by FISH Analysis of theOccurrence of Wilms Tumor in AniridiaPatients

2. Comprehensive Karyotyping of the HT-29Colon Adenocarcinoma Cell Line

3. Cytogenetic Clues to BreastCarcinogenesis

JOURNAL CLUB 40

1. From Chromosomal Alterations toTarget Genes for Therapy: IntegratingCytogenetics and Functional GenomicViews of the Breast Cancer Genome

2. High-throughput Genomic and ProteomicAnalysis Using Microarray Technology

3. DNA Analysis in a Paternity CaseInvolving a Triploid Fetus

JOURNAL CLUB 41

1. Identification of Uniparental Disomyin Phenotypically Abnormal Carriersof Isochromosomes or RobertsonianTranslocations

2. Chromosome 13q Neocentromeres:Molecular Cytogenetic Characterizationof Three Additional Cases and ClinicalSpectrum

3. Microsatellite Analysis in TurnerSyndrome: Paternal Origin of XChromosomes and Possible Mechanismsof Formation of Abnormal Chromosomes

The AGT Education Committee Announces A New Journal Club!

Journal Club #57: Premature Chromosome Condensation

Journal Clubs are a great way to earn Continuing Education Units (CEUs) without leaving your home or lab! Journal Clubs can be completed as a group or individually. Each Journal Club includes a reading list, several discussion questions and

a post-test. The discussion questions provide a starting point for group discussion, and give individuals taking a Journal Club questionsto consider while reading the articles. The post-test is taken after reading the articles and are returned to the regional representativesof the Education Committee to be graded.

Each successfully completed Journal Club is worth 0.4 CEUs. The new Journal Clubs, as well as Journal Clubs #29-#56, can be orderedthrough the AGT Executive Offices.




87

JOURNAL CLUB 42

1. Categorizing Genetic Tests to IdentifyTheir Ethical, Legal, and SocialImplications

2. Genetic Counseling for SexChromosome Abnormalities

3. Carrier Testing in Fragile X Syndrome:

When to Tell and Test

JOURNAL CLUB 43

1. Cancer Genetics2. Nature Reviews: Genetics3. Neocentromeres: Role in Human

Disease, Evolution, and CentromereStudy

JOURNAL CLUB 44

1. Chromosome Positioning in theInterphase Nucleus

2. Evolutionary Conservation ofChromosome Territory Arrangements inCell Nuclei from Higher Primates

3. Non-random Radial Arrangements ofInterphase Chromosome Territories:Evolutionary Considerations andFunctional Implications

JOURNAL CLUB 45

1. 11q23 Balanced Chromosome Aberra-tions in Treatment-related Myelodys-plastic Syndromes and Acute Leukemia:Report from an International Workshop

2. 21q22 Balanced ChromosomeAberrations in Therapy-relatedHematologic Disorders: Report from anInternational Workshop

3. Balanced Chromosome Abnormalitiesinv(16) and t(15; 17) in Therapy-related

Myelodysplastic Syndromes and AcuteLeukemia: Report from an InternationalWorkshop

JOURNAL CLUB 46

1. The Genetics and Pathology ofOxidative Phosphorylation

2. Detection of Mitochondrial DNAMutations by Temporal TemperatureGradient Gel Electrophoresis

3. Comprehensive Scanning of the EntireMitochondrial Genome for Mutations

JOURNAL CLUB 47

1. Prenatal Diagnosis of Down Syndrome:Ten Year Experience in the Israeli

Population2. Pregnancy Outcome and Prenatal

Diagnosis of Sex ChromosomeAbnormalities in Hawaii, 1986-1999

3. Social and Familial Context of PrenatalGenetic Testing Decisions: Are ThereRacial/Ethnic Differences?

JOURNAL CLUB 48

1. Molecular Cytogenetic Aspects ofHematologic Malignancies: ClinicalImplications

JOURNAL CLUB 49

1. The Burden of Genetic Disease onInpatient Care in a Children’s Hospital

2. Contribution of Malformations andGenetic Disorders to Mortality in aChildren’s Hospital

3. A Study of Reciprocal Translocations

and Inversions Detected by LightMicroscopy With Special Referenceto Origin, Segregation, and RecurrentAbnormalities

JOURNAL CLUB 50

1. Cytogenetics and Molecular Genetics ofLung Cancer

2. Chromosome Abnormalities MayCorrelate With Prognosis in Burkitt/Burkitt-Like Lymphomas of Children andAdolescents: A Report from Children’sCancer Group Study CCG-E08

3. Clinical Applications of BCR-ABL

Molecular Testing in Acute LeukemiaJOURNAL CLUB 51

1. Cytogenetic Profile of MyelodysplasticSyndromes with Complex Karyotypes:An Analysis Using Spectral Karyotyping

2. Classical Hodgkin Lymphoma isAssociated with Frequent Gains of 17q

3. Specific Chromosome Aberrationsin Peripheral Blood Lymphocytes areAssociated with Risk of Bladder Cancer

JOURNAL CLUB 52

1. Colour-Changing Karyotyping: AnAlternative to

M-FISH/SKY2. A New Chromosome Banding

Technique, Spectral Color Banding(SCAN), for Full Characterization ofChromosomal Abnormalities

3. Molecular Cytogenetic Analysis of Com-plex Chromosomal Rearrangements inPatients with Mental Retardation andCongenital Malformations: Delineationof 7q21.11 Breakpoints

4. Use of Targeted Array-Based CGH forthe Clinical Diagnosisof Chromosomal Imbalances: Is LessMore?

JOURNAL CLUB 53

1. Five Years of Molecular Diagnosis ofFragile X Syndrome (1997-2001): ACollaborative Study Reporting 95% ofthe Activity in France

2. Changing Demographics of AdvancedMaternal Age (AMA) and the Impacton the Predicted Incidence of DownSyndrome in the United States:

Implications for Prenatal Screening andGenetic Counseling

3. “Everybody in the world is my friend.”Hypersociabilty in Young Children withWilliams Syndrome

JOURNAL CLUB 54

1. Chromosome Breakage Syndromes andCancer

2. DEB Test for Fanconi Anemia Detectionin Patients with Atypical Phenotype

3. Nijmegen Breakage Syndrome: ClinicalManifestation of Defective Response toDNA Double-strand Breaks

JOURNAL CLUB 55

1. Detection of Cryptic ChromosomeAberrations in a Patient with a Balancedt(1; 9)(p34.2; p24) by Array-BasedComparative Genomic Hybridization

2. Array-Based Comparative GenomicHybridization Facilitates Identification of

Breakpoints of a Novel der(1)t(1; 18)(p36.3; q23)dn in a Child Presentingwith Mental Retardation

3. Jumping Translocations in MultipleMyeloma

JOURNAL CLUB 56

1. Fluorescence in situ HybridizationAnalysis of Minimal Residual Diseaseand the Relevance of the der(9)Deletion in Imatinib-treated Patientswith Chronic Myeloid Leukemia

2. Characterization of the t(17; 19)Translocation by Gene-specificFluorescent in situ Hybridization-basedCytogenetics and Detection of the E2A-

HLF Fusion Transcript and Protein inPatient’s Cells

3. Combination of Broad MolecularScreening and Cytogenetic Analysis forGenetic Risk Assignment and Diagnosisin Patients with Acute Leukemia

JOURNAL CLUB 57

1. Premature Chromosome Condensationin Humans Associated withMicrocephaly and Mental Retardation:A Novel Autosomal Recessive Condition

2. Chromosome Condensation: DNACompaction in Real Time

3. Phosphatase Inhibitors and Premature

Chromosome Condensation in HumanPeripheral Lymphocytes at DifferentCell-Cycle Phases

Copyright law prohibits AGT from supplyingreaders with the actual journal articles(electronically or otherwise). Availability ofarticles on-line does not imply the service isfree. Some journals require a subscription orimpose a fee. The web addresses are includedfor the convenience of those wishing to obtainthe articles in this way.





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AGT Members: $10 each ____________ Non-Members: $20 each ____________ Total ____________

Name of Institution ____________________________________________________________________________________________

Person or Department _________________________________________________________________________________________

Address _______________________________________________________________________________________________________

City________________________________________________ State__________________ Zip Code _________________________

Phone No.________________________________________________ FAX ________________________________________________

Method of Payment: Check

VISA MastercardAccount #:_________________________________________________________ Exp. Date: ________________________________

Signature on Account: ________________________________________________________________________________________

Mail or fax order form and payment to: AGT Executive Office Please make check payableP.O. Box 15945-288 to the Association of GeneticLenexa, KS 66285-5945 Technologists, Inc.

Phone: (913) 895-4605 FAX: (913) 895-4652

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AGT Journal ClubQuestion Order Form

To order the AGT Journal Club Questions, please fill in the requested information below. Make check or moneyorder payable to the Association of Genetic Technologists, Inc. Copyright law prohibits AGT from supplying readerswith the actual journal articles (electronically or otherwise). Participants must obtain articles themselves.

Discussion and Question Set for Reading List No. (Please enter the number of copies requested next to eachJournal Club Number)

Answers to Test Yourself #1, 2007Post-marked deadline: May 25, 2007

Passing Score: 85%

Participants must correctly answer 13 questions to receive a passing score.

1. a

2. d

3. b

4. d

5. b

6. d

7. c

8. b

9. d

10. d

11. b

12. b

13. a

14. b

15. c

16. d

17. d

18. a

19. d

20. a





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Hello, I hope you are looking forward to a great getaway this summer! It has been a busy and exciting year for AGT as wecontinue to represent you in many facets of our profession.

• The stage is set for our 32nd Annual AGT Meeting in Denver, CO, May 31 – June 3, 2007. The program offers a variety

of topics with a great opportunity for learning and growing. The exchange of information at the Annual Meeting is oneof our most important benefits. The most important person there will be the one occupying your seat. Please take fulladvantage of this learning and growing opportunity as your participation is the most valuable asset to our organizationand meeting experience.

• The Board of Directors will be presenting some by-law changes at the Annual Meeting that relate to our electionprocedures, allowing for electronic voting, so make sure to be there so that your voice is heard.

This year’s accomplishments and ongoing projects include:

• The website for the meeting has a new and user-friendly format, with the new feature this year of online registration.If you like the format, please provide us with feedback as we are in the initial stages of updating and restructuring theAssociation website.

• Positive progress has been made toward the formation of the Board of Certification while NCA remains committed toaddressing your immediate needs.

• The education committee has been active and productive in providing you with new Journal Clubs and Test YourselfCEU opportunities.

• The PR Committee is pursuing information regarding legislative activities and licensure issues that will affect you andour professions.

• We have been asked to contribute to adding “Cytogenetic Technologist” to the US Department of Labor’s list ofrecognized job titles and descriptions. This is an exciting opportunity for our profession to be nationally recognized andstandardized.

• The Salary Survey was completed and continues to be a valuable tool.

• The Fourth edition of The AGT Cytogenetics Laboratory Manual remains on track and we hope to begin the publishingprocess this year.

• A task force is examining the possibility of making a Molecular Symposia available and another task force is addressing

the options for offering updates to the Cytogenetic Symposia.• The professional promotion CD is and will probably continue to be a work-in-progress. We will have the first edition

available this summer and will establish an ongoing task force to address update issues.

• Our membership continues to grow. Remember to participate in the great membership recruitment drive. You could wina great prize!

Your feedback and support remains our most valuable asset, so please remember to visit the AGT website often, www.agt-info.org, so that you are apprised of the latest news. We would again like to ask that you remember to keep your email address currentwith the AGT Executive office. A substantial amount of information is available through e-mail and you wouldn’t want to beleft out. If your address is current, and you are not receiving our e-mail, please contact your IT Department or check your e-mailset-up to insure that AGT is an approved sender.

It has been a very productive year for AGT and I have been honored to serve as your president. As I pass the gavel to HelenBixenman, your president for the upcoming year, I will assume the past-president role and look forward to continued opportunities

for service. With Helen’s leadership and expertise, AGT is in the best of hands.Please feel free to contact me at [email protected] and thank you again for your support and participation with our

organization.

Robin VandergonAGT President, 2006-07

News from the President




90


Board of Directors

Officers

Robin Vandergon, President U.S. Labs410 W. Fallbrook, #104Fresno, CA 93711Office: (559) 432-5492Fax: (559) 432-5487E-mail: [email protected]

Helen Bixenman, President-Elect

Sun Health13180 North 103rd DriveSun City, AZ 85351Office: (623) 876-5512Fax: (623) 815-6572E-mail: helen.bixenman@

sunhealth.org

Amy R. Groszbach, Past Presidentand Nominating CommitteeChair

Mayo ClinicMolecular Genetics Lab – Hilton 920200 1st St., SWRochester, MN 55905Office: (507) 284-4169Fax: (507) 284-0670


Francie Rebolloso, Secretary- Treasurer

Term: 7/05 – 6/07 UNMC – Human Genetics LabMunroe Meyer Institute985440 Nebraska Med. Ctr.Omaha, NE 68198-5440Office: (402) 559-5699Fax: (402) 559-7248E-mail: [email protected]

Directors

Mervat Ayad, Public RelationsDirector

Term: 7/06 – 6/08

Quest Diagnostics-Nichols Institute33608 Ortega HighwaySan Juan Capistrano, CA 92690Office: (949) 728-4302Fax: (949) 728-4979E-mail: mervat.s.ayad@

questdiagnostics.com

Hilary Blair, Membership Director Term: 7/05 – 6/07 Mayo Clinic1002 GuggenheimRochester, MN 55905Office: (507) 284-0128Fax: (507) 284-0043E-mail: [email protected]

Peter C. Hu, Education Director Term: 7/06 – 6/08 University of Texas M.D. AndersonCancer CenterSchool of Health Sciences1515 Holcomb Blvd, Box 146Houston, TX 77030Office: (713) 745-1688Fax: (713) 745-3337E-mail: [email protected]

Marianne Hausman, 2007 AnnualMeeting Director

Cincinnati Children’s Hospital Med.Ctr.

Cytogenetics Lab3333 Burnet Ave.Cincinnati, OH 45229Office: (513) 636-9816Fax: (513) 636 -4373E-mail: Marianne.Hausman@

cchmc.org

Melanie Hyde, Annual MeetingCo-Director

Vancouver General HospitalHealth Sciences Ctr899 W. 12th Ave. JPS Rm.1800Vancouver, BC V5Z 1M9 CANADAOffice: (604) 875-4129Fax: (604) 875-4333E-mail: [email protected]

Council ofRepresentatives

Peggy Stupca, Representativeto NCA

Term: 7/05 – 6/08 Mayo Clinic514 Hilton Bldg200 First Street, SWRochester, MN 55905Office: (507) 284-3040Fax: (507) 284 -1927E-mail: [email protected]

Denise E. Anamani, Representativeto NCA

Term: 7/04 – 6/07 University of ConnecticutSchool of Allied HealthDiagnostic Genetic Sciences

Program358 Mansfield Rd., Unit 2101Storrs, CT 06269-2101Work: (860) 486-1998Fax: (860) 486-5375E-mail: [email protected]

Betty Dunn, Representative toNAACLS

Term: 7/04 – 6/08 Univ. of Texas HSCSADepartment CLS7703 Floyd Curl DriveSan Antonio, TX 78229-3900Office: (210) 567-8865Fax: (210) 567-8875E-mail: [email protected]

Tara Ellingham, Representativeto Foundation for GeneticTechnology

Term,: 7/06 – 6/08 Office: (843) 792-2363Fax: (843) 792-1248E-mail: [email protected]

Pat Dowling, Representative toCAP/ACMG

Term: 1/04 – 12/07 Quest Diagnostics, Inc.Cytogenetics1 Malcolm AvenueTeterboro, NJ 07608Office: (201) 393-5578Fax: (201) 462-4762E-mail: dowlingp@

questdiagnostics.com

PublicationsKimberly Wiechman, Directory

Editor

Term: 7/06 – 6/08 UNMC – Human Genetics LabMunroe Meyer Institute985440 Nebraska Med. Ctr.Omaha, NE 68198-5440Office: (402) 559-5710Fax: (402) 559-7248E-mail: [email protected]

Mark D. Terry, AGT Journal Editor Term: 10/03 – 10/07 1264 Keble Ln.Oxford, MI 48371(248) 628-3025E-mail: [email protected]

Other Contacts

Jonathan P. Park, NCA AppointedAGT Member

Term: 7/03 – 7/06 Dartmouth-Hitchcock Med. Ctr.Dept. of Pathology, Cyto. LabOne Medical Center Dr.Lebanon, NH 03756Office: (603) 650-7761Fax: (603) 650-4845 Email: [email protected]

Peter Mousseau, FGT Board ofTrustees President

Rainbow Scientific, Inc.83 Maple Ave.Windsor, CT 06095Office: (860) 298-8382Fax: (860) 298-8586E-mail: [email protected]

Executive Office

New Contact Information

P.O. Box 15945-288Lenexa, KS 66285

Fed-Ex Address:18000 W. 105th StreetOlathe, KS 66061

Phone: (913) 895-4605Fax: (913) 895-4652E-mail: agt-info.orgWeb Site: www.agt-info.org

The Association of Genetic Technologists (AGT), originally founded in 1975 as the Association of Cytogenetic Technologists, serves to:

• promote the scientific and professional development of all areas of genetics;• foster the exchange of information between those interested in genetics;• encourage cooperation between those persons actively or formerly engaged in genetics; and• stimulate interest in genetics as a career.

AGT has over 1,300 members. Membership is open to all who are employed or interested in genetics. All regular members are entitledto hold office, vote in elections, attend all AGT meetings, and receive the Journal of the Association of Genetic Technologists and theAGT International Membership Directory.

Association of Genetic Technologists 2007

Visit AGT’s Website at http://www.AGT-INFO.org




91

Job Placements

CYTOGENETICSPROFESSIONALS

LABORATORY SUPERVISOR& TECHNOLOGISTS

AmeriPath Northeast, has opportunities for individuals with aBachelor’s degree or higher and NCA certification/eligibility[(CLSp(CG)]. Experience in cancer cytogenetics and FISHis preferred. Supervisor candidates should have 5+ years ofexperience.

AmeriPath Northeast is a rapidly expanding facility, createdfor the utilization of cutting edge technologies in clinicaldiagnostics. It includes state-of-the-art cytogenetics/FISH,hematopathology (flow cytometry, immunohistochemistry,histology), and G.I. pathology laboratories. Our facility isconveniently located in Shelton, CT with access to majorhighways.

AmeriPath, Inc. offers an above market benefit package,including 401K, health and dental insurance, and tuitionreimbursement. Relocation assistance and sign-on bonusesavailable. Salary commensurate with experience. Sendcover letter and resume to [email protected]. An Equal Opportunity Employer.

Cytogenetics Technologist

Greater Baltimore Medical Center (GBMC) seeks anexperienced Cytogenetics Technologist for a full-time position

(40 hours/week) in its full service Cytogenetics Laboratory. Ourlaboratory is equipped with state of the art equipment such asrobotic harvester, Computer imaging system and LIS system.

Responsibilities will include processing and analyzing amnioticfluid, chorionic villus samples, bone marrow, peripheral bloodand products of conception specimens. Knowledge of FISHanalysis for common and rare microdeletion syndromes andhematological disorders as well as Urovysion is required.

Additional qualifications include 2-3 years experience in a fullservice cytogenetics laboratory and a Bachelor’s degree in abiological science. NCA certification is preferred.

GBMC offers an outstanding compensation package and

generous benefits. To learn more or to apply, please visit our website or contact Connie Vagrin at [email protected],Phone: (443)849-2216, Fax: (443)849-3078. EOE, M/F/D/V

www.gbmc.org/career 6701 N. Charles Street, Baltimore, MD 21204

Prestigious awards. Countless rewards.

passionp a s s i o nfor impact

GENETICS

www.genzyme.com/careers

Great opportunities with aglobal and growing company!

Genzyme Genetics is an award-winning provider of highly sophisticateddiagnostic testing, including Reproductive and Oncology Testing, andReproductive Genetic Counseling services. As a leading source of cancerinformation and analysis nationwide, our goal is to deliver superiorquality service, expertise and innovation. We are a divisionof Genzyme Corporation, ranked one of the foremostbiotechnology companies in the world and namedby FORTUNE magazine in January 2007 as one of the“100 Best Companies to Work For in the United States.”

CYTOGENETIC TECHNOLOGISTS(NCA CERTIFIED OR ELIGIBLE)

We are seeking experienced Cytogenetic Technologists to perform testing

services for diagnosis and monitoring in the fields of Reproductive andOncology Cytogenetics. Exciting opportunities exist for NCA certified oreligible technologists interested in microscopic analysis, tissue culture,cell harvesting and karyotyping on tissue specimens.

A Bachelor’s degree in a Life Science or equivalent, current NCA certification,and 2+ years of lab experience in Cytogenetics are required. To be eligiblefor positions in California, candidates must possess a California license inCytogenetics, and for positions in Florida, candidates must be eligible toobtain Florida licensure in Cytogenetics. In New York State, candidates mustbe eligible to obtain New York licensure. Must be willing to work a flexibleschedule that may include some early mornings, holidays and weekends.

All candidates please contact Gary Roffman at: 212-698-9541or e-mail [email protected]

EOE




92


The Cytogenetics Symposia, 2nd Edition

The second edition of The Cytogenetic Symposia , published in 2005, consists of an introduction, briefly outliningthe development of the practice of cytogenetics, from the seminal work of Tijo and Levan in 1956 to the currentpartnership of cytogenetics and molecular genetics. The succeeding chapters, written by cytogenetic technologists,PhDs, and medical doctors from the United States and Canada, provide up-to-date information on a broad rangeof topics in both cytogenetics and molecular cytogenetics. Many chapters now include molecular informationreflecting the increased recognition of diagnostic complementation of these arenas. Each chapter includes a setof multiple choice questions and most chapters contain a glossary. The answers for chapter questions have beenplaced in an appendix. The intent of The Cytogenetic Symposia is to offer a thorough, but condensed overview ofthe field. This publication is an excellent resource for individuals preparing for the NCA cytogenetics certificationexamination. Use of references cited in each chapter will lead interested parties to more detailed information.

NumberPrice of Copies Total

AGT Members $65

Non-members $80

Shipping (per copy) within North America $2.50

Please supply a credit card or Federal Express account number for orders of 5 or more

within North America and for all International orders: ___________________________________

Name ______________________________________________________________________________________________________________

Address _____________________________________________________________________________________________________________

_____________________________________________________________________________________________________________________

City_________________________________________________________ State_____________________ Zip Code ___________________

Phone No.__________________________________________________ FAX ____________________________________________________

Method of Payment: ■ Check ■ Credit Card: ■ VISA ■ Mastercard

Account #:_________________________________________________________________________ Exp. Date: ___________

Signature on Account: ____________________________________________________________________________________

Please return to: AGT Executive Office, P.O. Box 15945-288, Lenexa, KS 66285 or Fax (913) 895-4652



The AGT Cytogenetics Laboratory ManualIs now available through the AGT Executive Office

ORDER YOUR COPY TODAY!

Margaret J. Barch (Editor), Turid Knutsen (Editor), Jack Spurbeck (Editor)This third edition includes: an expanded FISH chapter; information and protocols for breakage studies;coverage of computer imaging, regulation, and the molecular aspects of leukemia; and chromosomespreading. Over 200 step-by-step protocols are also presented throughout the text.

Softcover, Spiral Bound 688 pages (June 1997)

NumberPrice of Copies Total

AGT Members $90

Non-members $110

Shipping (per copy) within North America $5

Please supply a credit card or Federal Express account number for orders of 3 or more

within North America and for all International orders: ___________________________________

Name ______________________________________________________________________________________________________________

Address _____________________________________________________________________________________________________________

_____________________________________________________________________________________________________________________City_________________________________________________________ State_____________________ Zip Code ___________________

Phone No.__________________________________________________ FAX ____________________________________________________

Method of Payment: ■ Check ■ Credit Card: ■ VISA ■ Mastercard

Account #:_________________________________________________________________________ Exp. Date: ___________

Signature on Account: ____________________________________________________________________________________

Please return to: AGT Executive Office, P.O. Box 15945-288, Lenexa, KS 66285 or Fax (913) 895-4652


93





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Mail application form and appropriate fee for membership in correct U.S currency. Money order or

check in U.S. funds drawn on a U.S. bank only. CHECKS DRAWN ON INTERNATIONAL BANKS

WILL NOT BE ACCEPTED. Make checks payable to Association of Genetic Technologists.

For your convenience, you may pay by VISA or MasterCard. Applications received after

September 15 are applied toward the next membership year. NOTE: Membership expires on

December 31 of each year.

■ VISA ■ MasterCard _______________________________________________________________ Account No. Exp. Date

_______________________________________________________________ Signature

Membership Status: ■ New Member ■ Renewal

Referred By_____________________________________________________________________ Membership # __________________________

Did you use a different name last year:■

Yes■

NoFormer Last Name________________________________________ First Name________________________________ MI _________________

I would like to serve on the following committee(s): Check area(s) of interest

■ Public Relations ■ Education ■ Membership ■ Annual Meeting ■ Publications

Name: _______________________________________________________________________________________________________________ Last First MI Certification

■ Home Address: ______________________________________________________________________________________________________

City, State, Zip: ___________________________________________________________________ Phone:_____________________________

■ Business Name: ______________________________________________________________________________________________________

Business Address: ____________________________________________________________________________________________________

City, State, Zip: ___________________________________________________________________ Phone:_____________________________

Fax:______________________________ E-mail: ___________________________________________________________________________

Position: (check one) ■ Director ■ Supervisor ■ Technologist ■ Lab Manager

■ Head (Lead, Core) Technologist ■ Tissue Culture Tech. ■ Other

Principal area of Genetics: (check one) ■ Biochemical ■ Cytogenetics ■ Molecular ■ Other

Appropriate years experience in Genetics: ■ under 2 ■ 2 to 4 ■ 5 to 7 ■ 8 to 10 ■ over 10

NOTICE: OUR MAILING LIST IS MADE AVAILABLE TO OTHER ORGANIZATIONS AND/OR COMPANIES. IF YOU WISH YOUR NAM

NOT TO APPEAR ON THESE LISTINGS, PLEASE CHECK HERE: ■

MAIL APPLICATION AND FEE TO:

Association ofGenetic Technologists

P.O. Box 15945-288Lenexa, KS 66285-5945Phone: (913) 895-4605

FAX: (913) 895-4652

Please check the membership category you are applying for:

■ Regular Membership $85 (U.S and Canada)

■ International Regular Membership $110 (Outside U.S and Canada)

■ Student Membership $35

■ International Student Membership $60 (Outside U.S and Canada)

■ Emeritus $40

■ Collaborative $40

The supplied address will be published in the directory unless otherwise specified.

■ Do not publish my address in the AGT Membership Directory

New Membership Application

Association

of GeneticTechnologists

2

Please complete all information below. Please indicate in the check box which address you prefer for mail distribution and

directory publication.

1 2 3 4 5




96

2007-2008 Scientific Meeting Schedule &

Abstract Submission Deadlines

If you know of a relevant meeting, please send information to Mervat Ayad at [email protected]

Scientific Meeting Location Meeting Date Internet Address

European Cytogenetics Association’s 6th EuropeanCytogenetics Conference Istanbul, Turkey July 7-10, 2007 http://www.biologia.uniba.it/eca/

American Society of Clinical Laboratory Science(ASCLS) San Francisco, CA July 17-21, 2007 www.ascls.org

California Association for Medical LaboratoryTechnology (CAMLT) Sacramento, CA Sept. 27-Oct. 1, 2007 www.camlt.org

Annual Conference of the German Genetics Society Jena, Germany Oct. 11-13, 2007

National Society of Genetic Counselors (NSGC) Kansas City, MO Oct. 13-16, 2007 www.nsgc.org

American Society for Clinical Pathologists (ASCP)/CAP New Orleans, LA Oct. 18-21, 2007 www.ascp.orgAmerican Society of Human Genetics (ASHG) San Diego, CA Oct. 23-27, 2007 www.faseb.org

American Society of Cytopathology (ASC) Houston, TX Nov. 2-8, 2007 www.cytopathology.org

Association for Molecular Pathology (AMP) Los Angeles, CA Nov. 7-11, 2007 www.ampweb.org

American Society for Cell Biology (ASCB) Washington, DC Dec. 1-5, 2007 www.ascb.org

American College of Medical Genetics (ACMG) Phoenix, AZ March 12-16, 2008 www.acmg.net

Clinical Laboratory Management Association (CLMA) Atlanta, GA March 29–April 1, 2008 www.clma.org

Association of Genetic Technologists 33rd Annual

Meeting Houston, TX June 12-15, 2008 www.agt-info.org

Meeting/Workshop Announcements

More job placement ads are online at

//www.AGT-INFO.org



The Journal of the Association of Genetic Technologists is a peer review journal, and scientific materials for publication containing original researchwill be reviewed by independent referees. Manuscripts that require revision or that contain major editorial changes will be returned to the seniorauthor of the article. Materials submitted will not be retained following publication nor will photographs, disks, or hard copies of manuscripts bereturned to authors. Rejected manuscripts will not normally be returned, although an effort will be made to return original photographs and prints.

Manuscript content is the responsibility of the author(s). All articles published, including editorials, letters, book reviews, invited articles, Brain Ticklers,columns, and reviews, represent the opinions of the authors and do not reflect the official policy of the Association of Genetic Technologists or theinstitution with which the author is affiliated unless specified by the author. The Association of Genetic Technologists, its members, and the editor ofThe Journal of the Association of Genetic Technologists make no warranty and assume no liability with respect to the information contained herein.

Information For AuthorsThe Journal of the Association of Genetic Technologists is pleased to consider manuscripts that describe experience with cytogenetics, moleculargenetics, or biochemical genetics and the application of these disciplines.

Submitted manuscripts must be typed, preferably double-spaced, using a 12 point font and 1” margins. In addition to the original, three copies ofthe manuscript and camera-ready illustrations must be submitted to the editor-in-chief. Items to be italicized or enhanced (bold, underlined) shouldbe clearly indicated. The conversion factor for print equivalency is as follows: two double-spaced typed pages equal approximately a one-halftypeset page.

Authors may supply the material on a 3½” disk, preferably in Microsoft Word, WordPerfect, or ASCII format, along with the hard copy. Macintosh disksare also acceptable, but conversion costs will be assessed accordingly to AGT and a delay in processing may occur. Materials may alternativelybe supplied to the editor via e-mail at the address shown on page 54. E-mail submission is preferred.

Illustrations must be original photographs, computer-generated digitized files (preferably saved as a .tif, .eps, or .bmp file), or black and white line

drawings, professionally prepared. The cost of separating and printing color photographs or illustrations will be charged to the author. Photographsmust be properly identified on the back, including the author’s name, title of article, and top direction. A ball point pen should not be used forlabeling. The affixing of a typewritten label to the illustration or table will prevent damage.

Notation & ReferencesAuthors’ titles must be accompanied by a position description of less than 15 words, which will be printed with the article.

Textual citations to the referenced literature should be parenthetically noted by author’s surname followed by year of publication, and arrangedchronologically and then alphabetically, as demonstrated in the following example: (Lese and Ledbetter, 1998; Reilly, 1998a; Morgan et al., 1999).In situations with more than t wo authors, the first author’s surname should be followed with et al. When references are made to more than onepaper published in the same year by the same author, a lower case a, b, etc. should be appended to the date of publication and should beincluded in both textual citations and the reference list.

References should be listed completely at the end of the paper in alphabetical order by surname of first author, and then by year of publica-tion. When more than one publication appears with the same first author, listings will be alphabetized by the first varying co -author. Irrespectiveof the number of authors, et al. should not be used in the reference list. Journal titles should be abbreviated according to Index Medicus and

book titles should be italicized. Use the following format for references:

Journal Article

Brothman AR, Zhu XL, Maxell T, Cui J, Derbler DA. Advances in the cytogenetics of prostate cancer. J Assoc Genet Technol. 1999; 25(1):1-6.

Book Chapter

Barch MJ and Lawce HJ. The cell and cell division. In: Barch MJ, Knutsen T, Spurbeck JL (eds). The AGT Cytogenetics Laboratory Manual, 3rd ed.

Philadelphia: Lippincott-Raven; 1997:1-18.

Book

Mark HFL. Medical Cytogenetics. New York: Marcel Dekker; 2000.

All references should be complete. Accuracy is the responsibility of the authors. Only published articles and those in press may be included inthe reference list. If necessary, unpublished data and submitted manuscripts should be cited parenthetically within the text.

Reprint OrdersReprints of articles can be purchased by authors at cost within two years after publication. On the order request, specify the journal’svolume and issue numbers, year of publication, page numbers, article title, author(s), and quantity requested. Include the contact name(s),address(es) and phone number(s) to be used for either shipping purposes or related questions. Payment should accompany the order. Checksmust be made payable to the Association of Genetic Technologists. Minimum order is 50 copies.

Reprints are produced on 60# white offset paper, saddle-stitched (unless under four pages), and will appear exactly as they do in the journal.Price is based on article length, quantity ordered, and color requirements. Orders are not processed until payment is received. Once paymentis received, allow four weeks for printing and shipping. Prices quoted include shipping by UPS ground; expedited shipping is available at anadditional charge. Journal copies can be purchased by AGT members for $5/each and by non-members for $25/each, if copies are available.

Please forward reprint orders or questions regarding price quotations to the AGT Association Manager (see inside page 90 for address).

The Journal of the Association of Genetic Technologists



The Journalof the

Association of Genetic Technologists

Second Quarter 2007 Volume 33, Number 2

ISSN 1523-7834

Association of Genetic TechnologistsP.O. Box 15945-288

Lenexa, KS 66285

PRSRT STDU.S. Postage

PAIDShawnee Mission,

KSPermit #727

Featured in this issue

The Prothrombin 20209C>T SequenceVariant: To Test or Not to Test?

Training Guide for Chromosome Recognition

An interview with Dr. Bruce Korf, PhD

Abstracts in Review

Book Review

Test Yourself #2, 2007

And more…

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agt journal 2nd qtr 2007

Documents