Literature DB >> 23887774

ACMG clinical laboratory standards for next-generation sequencing.

Heidi L Rehm1, Sherri J Bale, Pinar Bayrak-Toydemir, Jonathan S Berg, Kerry K Brown, Joshua L Deignan, Michael J Friez, Birgit H Funke, Madhuri R Hegde, Elaine Lyon.   

Abstract

Next-generation sequencing technologies have been and continue to be deployed in clinical laboratories, enabling rapid transformations in genomic medicine. These technologies have reduced the cost of large-scale sequencing by several orders of magnitude, and continuous advances are being made. It is now feasible to analyze an individual's near-complete exome or genome to assist in the diagnosis of a wide array of clinical scenarios. Next-generation sequencing technologies are also facilitating further advances in therapeutic decision making and disease prediction for at-risk patients. However, with rapid advances come additional challenges involving the clinical validation and use of these constantly evolving technologies and platforms in clinical laboratories. To assist clinical laboratories with the validation of next-generation sequencing methods and platforms, the ongoing monitoring of next-generation sequencing testing to ensure quality results, and the interpretation and reporting of variants found using these technologies, the American College of Medical Genetics and Genomics has developed the following professional standards and guidelines.

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Year:  2013        PMID: 23887774      PMCID: PMC4098820          DOI: 10.1038/gim.2013.92

Source DB:  PubMed          Journal:  Genet Med        ISSN: 1098-3600            Impact factor:   8.822


  18 in total

Review 1.  A survey of sequence alignment algorithms for next-generation sequencing.

Authors:  Heng Li; Nils Homer
Journal:  Brief Bioinform       Date:  2010-05-11       Impact factor: 11.622

Review 2.  Target-enrichment strategies for next-generation sequencing.

Authors:  Lira Mamanova; Alison J Coffey; Carol E Scott; Iwanka Kozarewa; Emily H Turner; Akash Kumar; Eleanor Howard; Jay Shendure; Daniel J Turner
Journal:  Nat Methods       Date:  2010-02       Impact factor: 28.547

3.  Field guide to next-generation DNA sequencers.

Authors:  Travis C Glenn
Journal:  Mol Ecol Resour       Date:  2011-05-19       Impact factor: 7.090

4.  Assuring the quality of next-generation sequencing in clinical laboratory practice.

Authors:  Amy S Gargis; Lisa Kalman; Meredith W Berry; David P Bick; David P Dimmock; Tina Hambuch; Fei Lu; Elaine Lyon; Karl V Voelkerding; Barbara A Zehnbauer; Richa Agarwala; Sarah F Bennett; Bin Chen; Ephrem L H Chin; John G Compton; Soma Das; Daniel H Farkas; Matthew J Ferber; Birgit H Funke; Manohar R Furtado; Lilia M Ganova-Raeva; Ute Geigenmüller; Sandra J Gunselman; Madhuri R Hegde; Philip L F Johnson; Andrew Kasarskis; Shashikant Kulkarni; Thomas Lenk; C S Jonathan Liu; Megan Manion; Teri A Manolio; Elaine R Mardis; Jason D Merker; Mangalathu S Rajeevan; Martin G Reese; Heidi L Rehm; Birgitte B Simen; Joanne M Yeakley; Justin M Zook; Ira M Lubin
Journal:  Nat Biotechnol       Date:  2012-11       Impact factor: 54.908

5.  Good laboratory practices for molecular genetic testing for heritable diseases and conditions.

Authors:  Bin Chen; MariBeth Gagnon; Shahram Shahangian; Nancy L Anderson; Devery A Howerton; Joe D Boone
Journal:  MMWR Recomm Rep       Date:  2009-06-12

6.  ACMG recommendations for standards for interpretation and reporting of sequence variations: Revisions 2007.

Authors:  C Sue Richards; Sherri Bale; Daniel B Bellissimo; Soma Das; Wayne W Grody; Madhuri R Hegde; Elaine Lyon; Brian E Ward
Journal:  Genet Med       Date:  2008-04       Impact factor: 8.822

7.  Duty to re-contact.

Authors:  K Hirschhorn; L D Fleisher; L Godmilow; R R Howell; R R Lebel; E R McCabe; M J McGinniss; A Milunsky; M Z Pelias; R E Pyeritz; E Sujansky; B H Thompson; R E Zinberg
Journal:  Genet Med       Date:  1999 May-Jun       Impact factor: 8.822

8.  A standardized framework for the validation and verification of clinical molecular genetic tests.

Authors:  Christopher J Mattocks; Michael A Morris; Gert Matthijs; Elfriede Swinnen; Anniek Corveleyn; Els Dequeker; Clemens R Müller; Victoria Pratt; Andrew Wallace
Journal:  Eur J Hum Genet       Date:  2010-07-28       Impact factor: 4.246

9.  The diploid genome sequence of an individual human.

Authors:  Samuel Levy; Granger Sutton; Pauline C Ng; Lars Feuk; Aaron L Halpern; Brian P Walenz; Nelson Axelrod; Jiaqi Huang; Ewen F Kirkness; Gennady Denisov; Yuan Lin; Jeffrey R MacDonald; Andy Wing Chun Pang; Mary Shago; Timothy B Stockwell; Alexia Tsiamouri; Vineet Bafna; Vikas Bansal; Saul A Kravitz; Dana A Busam; Karen Y Beeson; Tina C McIntosh; Karin A Remington; Josep F Abril; John Gill; Jon Borman; Yu-Hui Rogers; Marvin E Frazier; Stephen W Scherer; Robert L Strausberg; J Craig Venter
Journal:  PLoS Biol       Date:  2007-09-04       Impact factor: 8.029

10.  ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing.

Authors:  Robert C Green; Jonathan S Berg; Wayne W Grody; Sarah S Kalia; Bruce R Korf; Christa L Martin; Amy L McGuire; Robert L Nussbaum; Julianne M O'Daniel; Kelly E Ormond; Heidi L Rehm; Michael S Watson; Marc S Williams; Leslie G Biesecker
Journal:  Genet Med       Date:  2013-06-20       Impact factor: 8.822

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  310 in total

1.  Evaluation: A Qualitative Pilot Study of Novel Information Technology Infrastructure to Communicate Genetic Variant Updates.

Authors:  Stephanie Klinkenberg-Ramirez; Pamela M Neri; Lynn A Volk; Sara J Samaha; Lisa P Newmark; Stephanie Pollard; Matthew Varugheese; Samantha Baxter; Samuel J Aronson; Heidi L Rehm; David W Bates
Journal:  Appl Clin Inform       Date:  2016-06-01       Impact factor: 2.342

2.  Application of Whole Exome Sequencing in the Clinical Diagnosis and Management of Inherited Cardiovascular Diseases in Adults.

Authors:  Sara B Seidelmann; Emily Smith; Lakshman Subrahmanyan; Daniel Dykas; Maen D Abou Ziki; Bani Azari; Fady Hannah-Shmouni; Yuexin Jiang; Joseph G Akar; Mark Marieb; Daniel Jacoby; Allen E Bale; Richard P Lifton; Arya Mani
Journal:  Circ Cardiovasc Genet       Date:  2017-02

Review 3.  Next-generation sequencing for the diagnosis of hereditary pheochromocytoma and paraganglioma syndromes.

Authors:  Rodrigo A Toledo; Patricia L M Dahia
Journal:  Curr Opin Endocrinol Diabetes Obes       Date:  2015-06       Impact factor: 3.243

4.  De novo nonsense mutations in KAT6A, a lysine acetyl-transferase gene, cause a syndrome including microcephaly and global developmental delay.

Authors:  Valerie A Arboleda; Hane Lee; Naghmeh Dorrani; Neda Zadeh; Mary Willis; Colleen Forsyth Macmurdo; Melanie A Manning; Andrea Kwan; Louanne Hudgins; Florian Barthelemy; M Carrie Miceli; Fabiola Quintero-Rivera; Sibel Kantarci; Samuel P Strom; Joshua L Deignan; Wayne W Grody; Eric Vilain; Stanley F Nelson
Journal:  Am J Hum Genet       Date:  2015-02-26       Impact factor: 11.025

5.  Variability in assigning pathogenicity to incidental findings: insights from LDLR sequence linked to the electronic health record in 1013 individuals.

Authors:  Maya S Safarova; Eric W Klee; Linnea M Baudhuin; Erin M Winkler; Michelle L Kluge; Suzette J Bielinski; Janet E Olson; Iftikhar J Kullo
Journal:  Eur J Hum Genet       Date:  2017-02-01       Impact factor: 4.246

6.  Next-generation sequencing in the clinic.

Authors:  Jason Y Park; Larry J Kricka; Paolo Fortina
Journal:  Nat Biotechnol       Date:  2013-11       Impact factor: 54.908

7.  Determining Performance Metrics for Targeted Next-Generation Sequencing Panels Using Reference Materials.

Authors:  Megan H Cleveland; Justin M Zook; Marc Salit; Peter M Vallone
Journal:  J Mol Diagn       Date:  2018-06-26       Impact factor: 5.568

Review 8.  The hidden genomic landscape of acute myeloid leukemia: subclonal structure revealed by undetected mutations.

Authors:  Margherita Bodini; Chiara Ronchini; Luciano Giacò; Anna Russo; Giorgio E M Melloni; Lucilla Luzi; Domenico Sardella; Sara Volorio; Syed K Hasan; Tiziana Ottone; Serena Lavorgna; Francesco Lo-Coco; Anna Candoni; Renato Fanin; Eleonora Toffoletti; Ilaria Iacobucci; Giovanni Martinelli; Alessandro Cignetti; Corrado Tarella; Loris Bernard; Pier Giuseppe Pelicci; Laura Riva
Journal:  Blood       Date:  2014-12-12       Impact factor: 22.113

Review 9.  A Systematic Literature Review of Whole Exome and Genome Sequencing Population Studies of Genetic Susceptibility to Cancer.

Authors:  Alisa M Goldstein; Elizabeth M Gillanders; Melissa Rotunno; Rolando Barajas; Mindy Clyne; Elise Hoover; Naoko I Simonds; Tram Kim Lam; Leah E Mechanic
Journal:  Cancer Epidemiol Biomarkers Prev       Date:  2020-05-28       Impact factor: 4.254

10.  Developing a genomics rotation: Practical training around variant interpretation for genetic counseling students.

Authors:  Megan E Grove; Shana White; Dianna G Fisk; Shannon Rego; Orit Dagan-Rosenfeld; Jennefer N Kohler; Chloe M Reuter; Devon Bonner; Matthew T Wheeler; Jonathan A Bernstein; Kelly E Ormond; Andrea K Hanson-Kahn
Journal:  J Genet Couns       Date:  2019-02-01       Impact factor: 2.537

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