Standard operating procedure for somatic variant refinement of sequencing data with paired tumor and normal samples

Standards and Guidelines for Validating Next-Generation Sequencing Bioinformatics Pipelines

(2018) Somak Roy et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer

(2017) Marilyn M. Li et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Recurrent and functional regulatory mutations in breast cancer

(2017) Esther Rheinbay et al.   NATURE

An immunogenic personal neoantigen vaccine for patients with melanoma

(2017) Patrick A. Ott et al.   NATURE

CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer

(2017) Malachi Griffith et al.   NATURE GENETICS

Spatial genomic heterogeneity in multiple myeloma revealed by multi-region sequencing

(2017) L. Rasche et al.   Nature Communications

Intersect-then-combine approach: improving the performance of somatic variant calling in whole exome sequencing data using multiple aligners and callers

(2017) Maurizio Callari et al.   Genome Medicine

Examining Sources of Error in PCR by Single-Molecule Sequencing

(2017) Vladimir Potapov et al.   PLoS One

Evaluating Variant Calling Tools for Non-Matched Next-Generation Sequencing Data

(2017) Sarah Sandmann et al.   Scientific Reports

Current practices and guidelines for clinical next-generation sequencing oncology testing

(2016) Samuel P. Strom et al.   Cancer Biology & Medicine

Evaluation of Nine Somatic Variant Callers for Detection of Somatic Mutations in Exome and Targeted Deep Sequencing Data

(2016) Anne Bruun Krøigård et al.   PLoS One

A classification system for clinical relevance of somatic variants identified in molecular profiling of cancer

(2015) Mahadeo A. Sukhai et al.   GENETICS IN MEDICINE

Genome Modeling System: A Knowledge Management Platform for Genomics

(2015) Malachi Griffith et al.   PLoS Computational Biology

Optimizing Cancer Genome Sequencing and Analysis

(2015) Malachi Griffith et al.   Cell Systems

RNF43 is frequently mutated in colorectal and endometrial cancers

(2014) Marios Giannakis et al.   NATURE GENETICS

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

Strelka: accurate somatic small-variant calling from sequenced tumor–normal sample pairs

(2012) Christopher T. Saunders et al.   BIOINFORMATICS

BamView: visualizing and interpretation of next-generation sequencing read alignments

(2012) T. Carver et al.   BRIEFINGS IN BIOINFORMATICS

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

NGS analyses by visualization with Trackster

(2012) Jeremy Goecks et al.   NATURE BIOTECHNOLOGY

Identification of high-confidence somatic mutations in whole genome sequence of formalin-fixed breast cancer specimens

(2012) Shawn E. Yost et al.   NUCLEIC ACIDS RESEARCH

SomaticSniper: identification of somatic point mutations in whole genome sequencing data

(2011) David E. Larson et al.   BIOINFORMATICS

Sequence-specific error profile of Illumina sequencers

(2011) Kensuke Nakamura et al.   NUCLEIC ACIDS RESEARCH

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

(2011) Daniel Aird et al.   GENOME BIOLOGY

Savant: genome browser for high-throughput sequencing data

(2010) M. Fiume et al.   BIOINFORMATICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

The $1,000 genome, the $100,000 analysis?

(2010) Elaine R Mardis   Genome Medicine

Sequencing technologies — the next generation

(2009) Michael L. Metzker   NATURE REVIEWS GENETICS