Guidelines for Validation of Next-Generation Sequencing-Based Oncology Panels: A Joint Consensus Recommendation of the Association for Molecular Pathology and College of American Pathologists.
Lawrence J. Jennings,Maria E. Arcila,Christopher L. Corless,Suzanne Kamel-Reid,Suzanne Kamel-Reid,Ira M. Lubin,John D. Pfeifer,Robyn L. Temple-Smolkin,Karl V. Voelkerding,Karl V. Voelkerding,Marina N. Nikiforova +10 more
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TLDR
The recommendations contained herein are intended to assist clinical laboratories with the validation and ongoing monitoring of NGS testing for detection of somatic variants and to ensure high quality of sequencing results.About:
This article is published in The Journal of Molecular Diagnostics.The article was published on 2017-05-01 and is currently open access. It has received 448 citations till now.read more
Citations
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SF-010-4 Distant metastasis occurs late during the genetic evolution of pancreatic cancer
TL;DR: A quantitative analysis of the timing of the genetic evolution of pancreatic cancer was performed, indicating at least a decade between the occurrence of the initiating mutation and the birth of the parental, non-metastatic founder cell.
Journal ArticleDOI
Updated Molecular Testing Guideline for the Selection of Lung Cancer Patients for Treatment With Targeted Tyrosine Kinase Inhibitors: Guideline From the College of American Pathologists, the International Association for the Study of Lung Cancer, and the Association for Molecular Pathology
Neal I. Lindeman,Philip T. Cagle,Dara L. Aisner,Maria E. Arcila,Mary Beth Beasley,Eric H. Bernicker,Carol Colasacco,Sanja Dacic,Fred R. Hirsch,Keith M. Kerr,David J. Kwiatkowski,Marc Ladanyi,Jan A. Nowak,Lynette M. Sholl,Robyn Temple-Smolkin,Benjamin Solomon,Lesley Souter,Erik Thunnissen,Ming-Sound Tsao,Christina B. Ventura,Murry W. Wynes,Yasushi Yatabe +21 more
TL;DR: The 2013 guideline for molecular analysis of lung cancers was largely reaffirmed with updated recommendations to allow testing of cytology samples, require improved assay sensitivity, and recommend against the use of immunohistochemistry for EGFR testing.
Journal ArticleDOI
Recommendations for the use of next-generation sequencing (NGS) for patients with metastatic cancers: a report from the ESMO Precision Medicine Working Group.
F. Mosele,Jordi Remon,Joaquin Mateo,C. B. Westphalen,Fabrice Barlesi,Martijn P. Lolkema,Nicola Normanno,Aldo Scarpa,Mark E. Robson,Funda Meric-Bernstam,Nikhil Wagle,Albrecht Stenzinger,Julia Bonastre,A. Bayle,Stefan Michiels,Ivan Bièche,Etienne Rouleau,S. Jezdic,J.-Y. Douillard,Jorge S. Reis-Filho,R. Dienstmann,Fabrice Andre +21 more
TL;DR: ESMO recommends routine use of NGS on tumour samples in advanced non-squamous NSCLC, prostate cancers, ovarian cancers and cholangiocarcinoma, and develops multigene sequencing as a tool to screen patients eligible for clinical trials and to accelerate drug development.
Journal ArticleDOI
Updated Molecular Testing Guideline for the Selection of Lung Cancer Patients for Treatment With Targeted Tyrosine Kinase Inhibitors: Guideline From the College of American Pathologists, the International Association for the Study of Lung Cancer, and the Association for Molecular Pathology
Neal I. Lindeman,Philip T. Cagle,Dara L. Aisner,Maria E. Arcila,Mary Beth Beasley,Eric H. Bernicker,Carol Colasacco,Sanja Dacic,Fred R. Hirsch,Keith M. Kerr,David J. Kwiatkowski,Marc Ladanyi,Jan A. Nowak,Lynette M. Sholl,Robyn Temple-Smolkin,Benjamin Solomon,Lesley Souter,Erik Thunnissen,Ming-Sound Tsao,Christina B. Ventura,Murry W. Wynes,Yasushi Yatabe +21 more
TL;DR: The 2013 guideline was largely reaffirmed with updated recommendations to allow testing of cytology samples, require improved assay sensitivity, and recommend against the use of immunohistochemistry for EGFR testing.
Journal ArticleDOI
NCCN Guidelines Insights: Non–Small Cell Lung Cancer, Version 5.2018
David S. Ettinger,Dara L. Aisner,Douglas E. Wood,Wallace Akerley,Jessica Bauman,Joe Y. Chang,Lucian R. Chirieac,Thomas A. D'Amico,Thomas J. Dilling,Michael C. Dobelbower,Ramaswamy Govindan,Matthew A. Gubens,Mark Hennon,Leora Horn,Rudy P. Lackner,Michael Lanuti,Ticiana A. Leal,Rogerio Lilenbaum,Jules Lin,Billy W. Loo,Renato G. Martins,Gregory A. Otterson,Sandip Pravin Patel,Karen L. Reckamp,Gregory J. Riely,Steven E. Schild,Theresa A. Shapiro,James P. Stevenson,Scott J. Swanson,Kurt Tauer,Stephen C. Yang,Kristina M. Gregory,Miranda Hughes +32 more
TL;DR: The NCCN Guidelines for Non-Small Cell Lung Cancer (NSCLC) address all aspects of management for NSCLC and for the 2018 update, a new section on biomarkers was added.
References
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Fast and accurate short read alignment with Burrows–Wheeler transform
Heng Li,Richard Durbin +1 more
TL;DR: Burrows-Wheeler Alignment tool (BWA) is implemented, a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps.
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TL;DR: The GATK programming framework enables developers and analysts to quickly and easily write efficient and robust NGS tools, many of which have already been incorporated into large-scale sequencing projects like the 1000 Genomes Project and The Cancer Genome Atlas.
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Sue Richards,Nazneen Aziz,Nazneen Aziz,Sherri J. Bale,David P. Bick,Soma Das,Julie M. Gastier-Foster,Wayne W. Grody,Madhuri Hegde,Elaine Lyon,Elaine B. Spector,Karl V. Voelkerding,Heidi L. Rehm +12 more
TL;DR: Because of the increased complexity of analysis and interpretation of clinical genetic testing described in this report, the ACMG strongly recommends thatclinical molecular genetic testing should be performed in a Clinical Laboratory Improvement Amendments–approved laboratory, with results interpreted by a board-certified clinical molecular geneticist or molecular genetic pathologist or the equivalent.
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The variant call format and VCFtools
Petr Danecek,Adam Auton,Gonçalo R. Abecasis,Cornelis A. Albers,Eric Banks,Mark A. DePristo,Robert E. Handsaker,Gerton Lunter,Gabor T. Marth,Stephen T. Sherry,Gilean McVean,Richard Durbin +11 more
TL;DR: VCFtools is a software suite that implements various utilities for processing VCF files, including validation, merging, comparing and also provides a general Perl API.
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A framework for variation discovery and genotyping using next-generation DNA sequencing data
Mark A. DePristo,Eric Banks,Ryan Poplin,Kiran V. Garimella,Jared Maguire,Christopher Hartl,Anthony A. Philippakis,Anthony A. Philippakis,Anthony A. Philippakis,Guillermo del Angel,Manuel A. Rivas,Manuel A. Rivas,Matt Hanna,Aaron McKenna,Timothy Fennell,Andrew Kernytsky,Andrey Sivachenko,Kristian Cibulskis,Stacey Gabriel,David Altshuler,David Altshuler,Mark J. Daly,Mark J. Daly +22 more
TL;DR: A unified analytic framework to discover and genotype variation among multiple samples simultaneously that achieves sensitive and specific results across five sequencing technologies and three distinct, canonical experimental designs is presented.
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