The Journal of Molecular DiagnosticsOfficial Journal of the Association for Molecular Pathology

January 2014 � Volume 16, Number 1

Continu

On the Cover: SeqReporter, a novel customized software suite, facilitates efficient and accurate variant interpretationby a pathologist, as well as variant management and hands-off reporting with front-end laboratory information systeminterfacing. Schematic of the annotation and classification algorithm is shown. (See page 11.)

Editorial
1 Assessing and Comparing the Performance of Molecular Diagnostic Tests
Timothy J. O’Leary

Special Article
3 Revisiting Oversight and Regulation of Molecular-Based Laboratory-Developed Tests: A Position
Statement of the Association for Molecular Pathology
Andrea Ferreira-Gonzalez, Rajyasree Emmadi, Stephen P. Day, Robert F. Klees, Jennifer Leib, Elaine Lyon, Jan A. Nowak,Victoria M. Pratt, Mary S. Williams, and Roger D. Klein
Commentary
7 Genomic Technologies and the New Era of Genomic Medicine
Arunkanth Ankala and Madhuri Hegde

+ Related article appears on page 89

Technical Advances
11 SeqReporter: Automating Next-Generation Sequencing Result Interpretation and Reporting Workflow in
a Clinical Laboratory
Somak Roy, Mary Beth Durso, Abigail Wald, Yuri E. Nikiforov, and Marina N. Nikiforova
23
A Novel Methylation PCR that Offers Standardized Determination of FMR1 Methylation and CGGRepeat Length without Southern Blot Analysis Marina Grasso, Elles M.J. Boon, Stela Filipovic-Sadic, Patrick A. van Bunderen, Elena Gennaro, Ru Cao, Gary J. Latham,Andrew G. Hadd, and Domenico A. Coviello
Regular Articles
32 DNA Sequence Capture and Next-Generation Sequencing for the Molecular Diagnosis of Genetic
Cardiomyopathies
Valeria D’Argenio, Giulia Frisso, Vincenza Precone, Angelo Boccia, Antonella Fienga, Giuseppe Pacileo,Giuseppe Limongelli, Giovanni Paolella, Raffaele Calabrò, and Francesco Salvatore
45
A Multicenter Blinded Study Evaluating EGFR and KRAS Mutation Testing Methods in the ClinicalNoneSmall Cell Lung Cancer SettingdIFCT/ERMETIC2 Project Part 1: Comparison of Testing Methodsin 20 French Molecular Genetic National Cancer Institute Platforms Michèle Beau-Faller, Hélène Blons, Caroline Domerg, Dorota Gajda, Nicolas Richard, Fabienne Escande,Jérôme Solassol, Marc G. Denis, Anne Cayre, Isabelle Nanni-Metellus, Sylviane Olschwang, Sarab Lizard,Fabienne Piard, Jean-Luc Pretet, Florence de Fraipont, Ivan Bièche, Patricia de Cremoux, Isabelle Rouquette,Pierre-Paul Bringuier, Jean Mosser, Michèle Legrain, Anne-Claire Voegeli, Patrick Saulnier, Franck Morin,Jean-Pierre Pignon, Gérard Zalcman, and Jacques Cadranel
56
Validation and Implementation of Targeted Capture and Sequencing for the Detection of ActionableMutation, Copy Number Variation, and Gene Rearrangement in Clinical Cancer Specimens Colin C. Pritchard, Stephen J. Salipante, Karen Koehler, Christina Smith, Sheena Scroggins, Brent Wood, David Wu,Ming K. Lee, Suzanne Dintzis, Andrew Adey, Yajuan Liu, Keith D. Eaton, Renato Martins, Kari Stricker, Kim A. Margolin,Noah Hoffman, Jane E. Churpek, Jonathan F. Tait, Mary-Claire King, and Tom Walsh
ed

68
Homozygosity for the V122I Mutation in Transthyretin Is Associated with Earlier Onset of CardiacAmyloidosis in the African American Population in the Seventh Decade of Life Honey V. Reddi, Sarah Jenkins, Jason Theis, Brittany C. Thomas, Lawreen H. Connors, Frits Van Rhee, andW. Edward Highsmith Jr.
75
Performance of Common Analysis Methods for Detecting Low-Frequency Single Nucleotide Variants inTargeted Next-Generation Sequence Data David H. Spencer, Manoj Tyagi, Francesco Vallania, Andrew J. Bredemeyer, John D. Pfeifer, Rob D. Mitra, andEric J. Duncavage
89
Validation of a Next-Generation Sequencing Assay for Clinical Molecular Oncology Catherine E. Cottrell, Hussam Al-Kateb, Andrew J. Bredemeyer, Eric J. Duncavage, David H. Spencer, Haley J. Abel,Christina M. Lockwood, Ian S. Hagemann, Stephanie M. O’Guin, Lauren C. Burcea, Christopher S. Sawyer,Dayna M. Oschwald, Jennifer L. Stratman, Dorie A. Sher, Mark R. Johnson, Justin T. Brown, Paul F. Cliften, Bijoy George,Leslie D. McIntosh, Savita Shrivastava, TuDung T. Nguyen, Jacqueline E. Payton, Mark A. Watson, Seth D. Crosby,Richard D. Head, Robi D. Mitra, Rakesh Nagarajan, Shashikant Kulkarni, Karen Seibert, Herbert W. Virgin IV, JeffreyMilbrandt, and John D. Pfeifer
+ Related Commentary appears on page 7

106
Efficient Identification of miRNAs for Classification of Tumor Origin Rolf Søkilde, Martin Vincent, Anne K. Møller, Alastair Hansen, Poul E. Høiby, Thorarinn Blondal, Boye S. Nielsen,Gedske Daugaard, Søren Møller, and Thomas Litman
116
Age at Onset Should Be a Major Criterion for Subclassification of Colorectal Cancer José Perea, Daniel Rueda, Alicia Canal, Yolanda Rodríguez, Edurne Álvaro, Irene Osorio, Cristina Alegre,Bárbara Rivera, Joaquín Martínez, Javier Benítez, and Miguel Urioste
127
Sensitive and Rapid Detection of Chlamydia trachomatis by Recombinase Polymerase AmplificationDirectly from Urine Samples Katrin Krõlov, Jekaterina Frolova, Oana Tudoran, Julia Suhorutsenko, Taavi Lehto, Hiljar Sibul, Imre Mäger,Made Laanpere, Indrek Tulp, and Ülo Langel
136
Multiplex Screening for Blood-Borne Viral, Bacterial, and Protozoan Parasites using an OpenArrayPlatform Elena Grigorenko, Carolyn Fisher, Sunali Patel, Caren Chancey, Maria Rios, Hira L. Nakhasi, and Robert C. Duncan
JMD2014CMEProgram inMolecular Diagnostics appears online. For details aboutobjectives, educational goals, registration, and requiredexamination, seehttp://www.asip.org/CME/index.cfm.The planning committee members and staff have no relevant financial relationships with commercialinterest to disclose. Financial relationships (including the name of the commercial entity and thenature of the relationship) of the authors of selected articles in this journal-based CME activitywill be disclosed in the published article and in each journal CME examination. See below forCME accreditation statement.

Objectives: Upon completion of this journal-based CME activity you will be able to:- discuss the research underway and/or current molecular approaches to the diagnosis and prognosis of

inherited diseases and syndromes, pharmacogenetics, cytogenetics, DNA identity tests, hematopathology,solid and soft tissue tumors, infectious diseases, and acquired diseases spanning systems biology.

- demonstrate a gained level of knowledge of the molecular methods and techniques being used byresearchers and practitioners.

The JMD 2014 CME Program in Molecular Diagnostics qualifies as an American Board of PathologyMaintenance of Certification Part II Self-Assessment Module (SAM). For details, see http://www.asip.org/CME/index.cfm.

ccreditation Statement: This activity (“The JMD 2014 CME Program in Molecular Diagnostics”) has been planned andented in accordance with the Essential Areas and policies of the Accreditation Council for Continuing Medical Education

CME Aimplem(ACCME) through the joint sponsorship of the American Society for Clinical Pathology (ASCP) and the American Society for InvestigativePathology (ASIP). ASCP is accredited by the ACCME to provide continuing medical education for physicians.

The ASCP designates this journal-based CME activity (“The JMD 2014 CME Program in Molecular Diagnostics”) for a maximum of 48AMA PRA Category 1 Credit(s)TM. Physicians should only claim credit commensurate with the extent of their participation in the activity.

http://www.asip.org/CME/index.cfm



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