Validation of a Next-Generation Sequencing Assay for Clinical Molecular Oncology

Walter, 2012, Clonal architecture of secondary acute myeloid leukemia, N Engl J Med, 366, 1090, 10.1056/NEJMoa1106968

Patel, 2012, Prognostic relevance of integrated genetic profiling in acute myeloid leukemia, N Engl J Med, 366, 1079, 10.1056/NEJMoa1112304

Kalari, 2012, Deep sequence analysis of non-small cell lung cancer: integrated analysis of gene expression, alternative splicing, and single nucleotide variations in lung adenocarcinomas with and without oncogenic KRAS mutations, Front Oncol, 2, 12, 10.3389/fonc.2012.00012

Chen, 2010, Activation of signal pathways and the resistance to anti-EGFR treatment in colorectal cancer, J Cell Biochem, 111, 1082, 10.1002/jcb.22905

Duncavage, 2012, Targeted next generation sequencing of clinically significant gene mutations and translocations in leukemia, Mod Pathol, 25, 795, 10.1038/modpathol.2012.29

Vasli, 2012, Next generation sequencing for molecular diagnosis of neuromuscular diseases, Acta Neuropathol, 124, 273, 10.1007/s00401-012-0982-8

Calvo, 2012, Molecular diagnosis of infantile mitochondrial disease with targeted next-generation sequencing, Sci Transl Med, 4, 118ra10, 10.1126/scitranslmed.3003310

Pritchard, 2012, ColoSeq provides comprehensive Lynch and polyposis syndrome mutational analysis using massively parallel sequencing, J Mol Diagn, 14, 357, 10.1016/j.jmoldx.2012.03.002

Voelkerding, 2010, Next generation sequencing for clinical diagnostics–principles and application to targeted resequencing for hypertrophic cardiomyopathy: a paper from the 2009 William Beaumont Hospital Symposium on Molecular Pathology, J Mol Diagn, 12, 539, 10.2353/jmoldx.2010.100043

Sikkema-Raddatz, 2013, Targeted next-generation sequencing can replace Sanger sequencing in clinical diagnostics, Hum Mutat, 34, 1035, 10.1002/humu.22332

Berg, 2011, Next generation massively parallel sequencing of targeted exomes to identify genetic mutations in primary ciliary dyskinesia: implications for application to clinical testing, Genet Med, 13, 218, 10.1097/GIM.0b013e318203cff2

Vandrovcova, 2013, The use of next-generation sequencing in clinical diagnosis of familial hypercholesterolemia, Genet Med, 10.1038/gim.2013.55

Neumann, 2009, Frequency and type of KRAS mutations in routine diagnostic analysis of metastatic colorectal cancer, Pathol Res Pract, 205, 858, 10.1016/j.prp.2009.07.010

Dienstmann, 2011, Molecular predictors of response to chemotherapy in colorectal cancer, Cancer J, 17, 114, 10.1097/PPO.0b013e318212f844

Ladanyi, 2008, Lung adenocarcinoma: guiding EGFR-targeted therapy and beyond, Mod Pathol, 21, S16, 10.1038/modpathol.3801018

Girard, 2010, Thymic tumors: relevant molecular data in the clinic, J Thorac Oncol, 5, S291, 10.1097/JTO.0b013e3181f209b9

Godley, 2012, Profiles in leukemia, N Engl J Med, 366, 1152, 10.1056/NEJMe1200409

College of American Pathologists: Molecular Pathology Checklist. Northfield, IL, College of American Pathologists, 2012

Gargis, 2012, Assuring the quality of next-generation sequencing in clinical laboratory practice, Nat Biotechnol, 30, 1033, 10.1038/nbt.2403

2004

Frazer, 2007, A second generation human haplotype map of over 3.1 million SNPs, Nature, 449, 851, 10.1038/nature06258

Li, 2009, The Sequence Alignment/Map format and SAMtools, Bioinformatics, 25, 2078, 10.1093/bioinformatics/btp352

Quinlan, 2010, BEDTools: a flexible suite of utilities for comparing genomic features, Bioinformatics, 26, 841, 10.1093/bioinformatics/btq033

McKenna, 2010, The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data, Genome Res, 20, 1297, 10.1101/gr.107524.110

DePristo, 2011, A framework for variation discovery and genotyping using next-generation DNA sequencing data, Nat Genet, 43, 491, 10.1038/ng.806

Robinson, 2011, Integrative genomics viewer, Nat Biotechnol, 29, 24, 10.1038/nbt.1754

Thorvaldsdóttir, 2013, Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration, Brief Bioinform, 14, 178, 10.1093/bib/bbs017

Abecasis, 2010, A map of human genome variation from population-scale sequencing, Nature, 467, 1061, 10.1038/nature09534

Wickham, 2011, The split-apply-combine strategy for data analysis, J Stat Software, 40, 1, 10.18637/jss.v040.i01

2012

Wickham, 2009

Abecasis, 2010, A map of human genome variation from population-scale sequencing, Nature, 467, 1061, 10.1038/nature09534

Drmanac, 2010, Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays, Science, 327, 78, 10.1126/science.1181498

Spencer, 2013, Comparison of clinical targeted next-generation sequence data from formalin-fixed and fresh-frozen tissue specimens, J Mol Diagn, 15, 623, 10.1016/j.jmoldx.2013.05.004

Spencer, 2014, Performance of common analysis methods for detecting low-frequency single nucleotide variants in targeted next-generation sequence data, J Mol Diagn, 16, 75, 10.1016/j.jmoldx.2013.09.003

Spencer, 2013, Detection of FLT3 internal tandem duplication in targeted, short-read-length, next-generation sequencing data, J Mol Diagn, 15, 81, 10.1016/j.jmoldx.2012.08.001

Paez, 2004, EGFR mutations in lung cancer: correlation with clinical response to gefitinib therapy, Science, 304, 1497, 10.1126/science.1099314

Stephens, 2004, Lung cancer: intragenic ERBB2 kinase mutations in tumours, Nature, 431, 525, 10.1038/431525b

Kralovics, 2005, A gain-of-function mutation of JAK2 in myeloproliferative disorders, N Engl J Med, 352, 1779, 10.1056/NEJMoa051113

Davies, 2002, Mutations of the BRAF gene in human cancer, Nature, 417, 949, 10.1038/nature00766

Janoueix-Lerosey, 2008, Somatic and germline activating mutations of the ALK kinase receptor in neuroblastoma, Nature, 455, 967, 10.1038/nature07398

Hirota, 1998, Gain-of-function mutations of c-kit in human gastrointestinal stromal tumors, Science, 279, 577, 10.1126/science.279.5350.577

Pao, 2005, KRAS mutations and primary resistance of lung adenocarcinomas to gefitinib or erlotinib, PLoS Med, 2, e17, 10.1371/journal.pmed.0020017

Karapetis, 2008, K-ras mutations and benefit from cetuximab in advanced colorectal cancer, N Engl J Med, 359, 1757, 10.1056/NEJMoa0804385

Falchook, 2012, Dabrafenib in patients with melanoma, untreated brain metastases, and other solid tumours: a phase 1 dose-escalation trial, Lancet, 379, 1893, 10.1016/S0140-6736(12)60398-5

Gilbert, 2007, The isolation of nucleic acids from fixed, paraffin-embedded tissues-which methods are useful when?, PLoS One, 2, e537, 10.1371/journal.pone.0000537

Ley, 2008, DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome, Nature, 456, 66, 10.1038/nature07485

Pleasance, 2010, A small-cell lung cancer genome with complex signatures of tobacco exposure, Nature, 463, 184, 10.1038/nature08629

Govindan, 2012, Genomic landscape of non-small cell lung cancer in smokers and never-smokers, Cell, 150, 1121, 10.1016/j.cell.2012.08.024

Pleasance, 2010, A comprehensive catalogue of somatic mutations from a human cancer genome, Nature, 463, 191, 10.1038/nature08658

Aird, 2011, Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries, Genome Biol, 12, R18, 10.1186/gb-2011-12-2-r18

Hadgu, 2000, Discrepant analysis is an inappropriate and unscientific method, J Clin Microbiol, 38, 4301, 10.1128/JCM.38.11.4301-4302.2000

Lipman, 1998, Quantifying the bias associated with use of discrepant analysis, Clin Chem, 44, 108, 10.1093/clinchem/44.1.108

Shah, 2009, Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution, Nature, 461, 809, 10.1038/nature08489

Mardis, 2009, Recurring mutations found by sequencing an acute myeloid leukemia genome, N Engl J Med, 361, 1058, 10.1056/NEJMoa0903840