Genetic Testing for Genetic Testing for Cystic FibrosisCystic Fibrosis

Dee Quinn, MS, CGCDee Quinn, MS, CGC

August, 2006August, 2006

““Gene Testing Going Gene Testing Going Mainstream”Mainstream”

Cystic Fibrosis Gene Test Offered Cystic Fibrosis Gene Test Offered

By Lauran NeergaardBy Lauran Neergaard AP Medical WriterAP Medical Writer Monday, Oct. 1, 2001; 9:53 p.m. EDTMonday, Oct. 1, 2001; 9:53 p.m. EDT

WASHINGTON –– Gene testing is going WASHINGTON –– Gene testing is going mainstream: Starting this month, tens of mainstream: Starting this month, tens of thousands of white Americans will be offered thousands of white Americans will be offered testing to see if they carry a gene mutation that testing to see if they carry a gene mutation that causes cystic fibrosis even if no one in their causes cystic fibrosis even if no one in their family has the disease. family has the disease.

CFTR GeneCFTR Gene

Identified in 1989Identified in 1989 Cystic Fibrosis Transmembrane Cystic Fibrosis Transmembrane

Conductance Regulator (CFTR)Conductance Regulator (CFTR) 27 exons, 250kB of genomic DNA27 exons, 250kB of genomic DNA Chromosome 7qChromosome 7q

CFTR GeneCFTR Gene cAMP-dependent chloride channelcAMP-dependent chloride channel Expressed in epithelial cells of:Expressed in epithelial cells of:

respiratory tract respiratory tract sweat and salivary glandssweat and salivary glandspancreas pancreas intestine intestine reproductive tractreproductive tract

Clinical PhenotypeClinical Phenotype

RespiratoryRespiratory GI, pancreasGI, pancreas ReproductiveReproductive

CFTR MutationsCFTR Mutations Over 1,000 mutations identifiedOver 1,000 mutations identified Most labs test for 25-87 mutationsMost labs test for 25-87 mutations 13 of the identified CF mutations occur in 13 of the identified CF mutations occur in

more than 1% of CF chromosomesmore than 1% of CF chromosomes 72% of whites with CF are homozygous or 72% of whites with CF are homozygous or

heterozygous for 8 mutationsheterozygous for 8 mutations 5 classes of CFTR mutations5 classes of CFTR mutations Genotype/phenotype correlations may not Genotype/phenotype correlations may not

be helpfulbe helpful

CFTR Mutations- CFTR Mutations- ΔΔF508F508 Most common mutation in North America, Most common mutation in North America,

70-75% of the mutations70-75% of the mutations Deletion of codon 508 Deletion of codon 508 Results in Results in

shortening of the protein productshortening of the protein product Protein product still functioning as Cl Protein product still functioning as Cl

channel, but is retained in the channel, but is retained in the endoplasmic reticulumendoplasmic reticulum

ΔΔF508 (homozygosity): classical F508 (homozygosity): classical phenotypephenotype

EpidemiologyEpidemiology

One of the most common autosomal One of the most common autosomal recessive diseases in Caucasiansrecessive diseases in Caucasians

Occurs in 1 in 3300 birthsOccurs in 1 in 3300 births 30,000 affected persons in the United 30,000 affected persons in the United

StatesStates

Recessive Pedigree

EpidemiologyEpidemiology

971/291/3,300Ashkenazi Jews

301/901/32,100AsianAmericans

691/60-651/15,300African Americans

80-901/521/3,970-1/1,500Native Americans

571/461/8-9,000Hispanics

80-901/291/3,300Caucasians(United States)

SensitivityCarrierFrequency

IncidenceGroup

Congenital Bilateral Absence of the Congenital Bilateral Absence of the Vas Deferens (CBAVD)Vas Deferens (CBAVD)

Vas deferens – carries sperm from the Vas deferens – carries sperm from the epididymis to the ejaculatory ductsepididymis to the ejaculatory ducts

Absence of vas occurs in 95% of males with CFAbsence of vas occurs in 95% of males with CF CBAVD: distinct genetic disorder which overlaps CBAVD: distinct genetic disorder which overlaps

with CF and causes infertilitywith CF and causes infertility Noncoding region of CFTR gene involved: intron Noncoding region of CFTR gene involved: intron

8 with thymidine tracts (5T/7T/9T)8 with thymidine tracts (5T/7T/9T) 60-70% of men with CBAVD carry one mutation 60-70% of men with CBAVD carry one mutation

in the CFTR gene.in the CFTR gene. 5T reduces the number of functional Cl 5T reduces the number of functional Cl

channelschannels

Congenital Bilateral Absence of the Congenital Bilateral Absence of the Vas Deferens (CBAVD)Vas Deferens (CBAVD)

Genotype - Phenotype Genotype - Phenotype CorrelationCorrelation

CFTR GenotypeCFTR Genotype

First AlleleFirst Allele Second AlleleSecond Allele Range of PhenotypesRange of Phenotypes

Classic (e.g., F508)Classic (e.g., F508) ClassicClassic Classic >> nonclassicClassic >> nonclassic

Mild (e.g., A455E)Mild (e.g., A455E) Classic or mildClassic or mild Nonclassic > classicNonclassic > classic

R117H/5TR117H/5T Classic or mildClassic or mild Nonclassic > classicNonclassic > classic

R117H/7TR117H/7T Classic or mildClassic or mild Asymptomatic female or Asymptomatic female or CBAVD > nonclassicCBAVD > nonclassic

5T/TG13 or TG125T/TG13 or TG12 Classic or mildClassic or mild CBAVD or nonclassic CF >> CBAVD or nonclassic CF >> asymptomatic carrierasymptomatic carrier

5T/TG115T/TG11 Classic or mildClassic or mild Asymptomatic > CBAVDAsymptomatic > CBAVD

7T or 9T7T or 9T Classic or mildClassic or mild AsymptomaticAsymptomatic

7T or 9T7T or 9T 7T or 9T7T or 9T AsymptomaticAsymptomatic

(From www.genetests.org)(From www.genetests.org)

Newborn ScreeningNewborn Screening

Blood spots from infants taken within Blood spots from infants taken within days of birth to identify infants at days of birth to identify infants at increased risk for a specific genetic increased risk for a specific genetic disordersdisorders

Justifications:Justifications:– Early treatment of respiratory illnessesEarly treatment of respiratory illnesses– Evidence for nutritional benefitEvidence for nutritional benefit

Currently offered or in planning in Currently offered or in planning in many states – AZ to begin newborn many states – AZ to begin newborn screening by 9/07screening by 9/07

Newborn ScreeningNewborn Screening Initial screen tests levels of IRT Initial screen tests levels of IRT

(immunoreactive trypsinogen)(immunoreactive trypsinogen) Screening program should include:Screening program should include:

– Specific provider and patient educational Specific provider and patient educational materialsmaterials

– Protocol for addressing positive screening Protocol for addressing positive screening resultsresults

Sweat chlorideSweat chloride DNA testingDNA testing

– Development of systems in collaboration with Development of systems in collaboration with specialty care providers to track short-term specialty care providers to track short-term and long-term child outcomes and identify and long-term child outcomes and identify resources to support this activity resources to support this activity

Carrier Screening for CFCarrier Screening for CF

1997- NIH convened a Consensus 1997- NIH convened a Consensus ConferenceConference

1998- ACOG/ACMG formed Steering 1998- ACOG/ACMG formed Steering Committee Committee

10/2001- “Preconception and Prenatal 10/2001- “Preconception and Prenatal Carrier Screening for Cystic Fibrosis”Carrier Screening for Cystic Fibrosis”

ACOG/ACMG ACOG/ACMG RecommendationsRecommendations

Offer screening to:Offer screening to:– Individuals with a family history of CFIndividuals with a family history of CF– Reproductive partners of individuals Reproductive partners of individuals

with CFwith CF– Couples in whom one or both are Couples in whom one or both are

Caucasian and are planning a Caucasian and are planning a pregnancy or seeking prenatal carepregnancy or seeking prenatal care

– Other individuals must be given written Other individuals must be given written informationinformation

ACOG/ACMG ACOG/ACMG RecommendationsRecommendations

Provider’s RoleProvider’s Role::– Purpose of screeningPurpose of screening– Voluntary nature of screeningVoluntary nature of screening– Symptoms of CF, treatment andSymptoms of CF, treatment and

prognosisprognosis– Genetics of CF and population Genetics of CF and population

frequenciesfrequencies– Meaning of positive and negative testMeaning of positive and negative test

resultsresults– Factors to consider in deciding to haveFactors to consider in deciding to have

or not to have screeningor not to have screening

Additional Indications for ScreeningAdditional Indications for Screening

Echogenic bowel detected on Echogenic bowel detected on prenatal ultrasoundprenatal ultrasound

Infertility in malesInfertility in males

Diagnostic Prenatal TestsDiagnostic Prenatal Tests

Testing offered when:Testing offered when:– When both members of a couple are carriers, When both members of a couple are carriers,

ie: 25% risk of having a baby with CFie: 25% risk of having a baby with CF– When one member of a couple is carrier and When one member of a couple is carrier and

other member not available for testingother member not available for testing

– Testing options:Testing options: Chorionic villus sampling (CVS)Chorionic villus sampling (CVS)

– 9-11 weeks9-11 weeks AmniocentesisAmniocentesis

– After 14 weeksAfter 14 weeks

Other ApproachesOther Approaches ProcedureProcedure

– In vitro fertilizationIn vitro fertilization– One cell removed from early embryo to test for One cell removed from early embryo to test for

mutations which were found in parentsmutations which were found in parents– Cell without a CF genotype transferred to Cell without a CF genotype transferred to

mother’s uterusmother’s uterus CaveatsCaveats

– Technically demanding and complex procedureTechnically demanding and complex procedure– Available on a limited basisAvailable on a limited basis– Expensive: $4,000 - $12,000Expensive: $4,000 - $12,000– Ethical implicationsEthical implications

ACOG/ACMG ACOG/ACMG RecommendationsRecommendations

Laboratory’s Role:Laboratory’s Role:

Reports should include results of Reports should include results of screening and an interpretation:screening and an interpretation:

Negative Negative Residual risk given Residual risk given Positive Positive Test other partner Test other partner

Limitations of CF ScreeningLimitations of CF Screening

Does not detect all carriersDoes not detect all carriers Estimate of residual risk applies only when Estimate of residual risk applies only when

family history is negative and to the family history is negative and to the current pregnancycurrent pregnancy

Cannot make reliable predictions for Cannot make reliable predictions for outcome based on mutationsoutcome based on mutations

Non-paternityNon-paternity

Genetic CounselingGenetic Counseling

Various outcomes of prenatal and Various outcomes of prenatal and newborn will generate need for genetic newborn will generate need for genetic counseling:counseling:

– Newly diagnosed child with CFNewly diagnosed child with CF– Healthy males who carry mutations Healthy males who carry mutations

associated with infertilityassociated with infertility– Identification of positive/negative couples Identification of positive/negative couples

who request additional mutational analyses who request additional mutational analyses or counseling to clarify residual riskor counseling to clarify residual risk

– Positive/positive couplesPositive/positive couples

Ethical, Legal, and Social Ethical, Legal, and Social Implications of CF ScreeningImplications of CF Screening

EthicalEthicalUnnecessary anxiety createdUnnecessary anxiety createdInadequate pretest informationInadequate pretest information

LegalLegalInformed ConsentInformed ConsentInsurance discriminationInsurance discrimination

SocialSocialExpense swell health costsExpense swell health costsSocietal pressure not to bear affected offspringSocietal pressure not to bear affected offspring

ResourcesResources

Cystic Fibrosis Foundation Cystic Fibrosis Foundation http://http://www.cff.orgwww.cff.org

http://http://cysticfibrosis.comcysticfibrosis.com GeneTests and GeneReviews GeneTests and GeneReviews http://http://

www.genetests.orgwww.genetests.org National Society of Genetic Counselors National Society of Genetic Counselors http://http://

www.nsgc.orgwww.nsgc.org Mountain States Genetics Network Mountain States Genetics Network http://http://

www.mostgene.orgwww.mostgene.org

ConclusionsConclusions

““It will be very important to see how It will be very important to see how this goes. Certainly it requires the this goes. Certainly it requires the obstetricians to become more obstetricians to become more familiar with genetics than many of familiar with genetics than many of them have previously had occasion them have previously had occasion to do.” to do.”

-Francis Collins-Francis Collins