A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing

Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection

(2015) Adam D Ewing et al.   NATURE METHODS

An analytical framework for optimizing variant discovery from personal genomes

(2015) Gareth Highnam et al.   Nature Communications

Toward better understanding of artifacts in variant calling from high-coverage samples

(2014) Heng Li   BIOINFORMATICS

Comparison of somatic mutation calling methods in amplicon and whole exome sequence data

(2014) Huilei Xu et al.   BMC GENOMICS

Comparative analysis of methods for identifying somatic copy number alterations from deep sequencing data

(2014) A. Alkodsi et al.   BRIEFINGS IN BIOINFORMATICS

Clinical Interpretation and Implications of Whole-Genome Sequencing

(2014) Frederick E. Dewey et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Comprehensive characterization of complex structural variations in cancer by directly comparing genome sequence reads

(2014) Valentí Moncunill et al.   NATURE BIOTECHNOLOGY

Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls

(2014) Justin M Zook et al.   NATURE BIOTECHNOLOGY

Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications

(2014) Andy Rimmer et al.   NATURE GENETICS

A Note on Exact Differences between Beta Distributions in Genomic (Methylation) Studies

(2014) Emanuele Raineri et al.   PLoS One

Reducing INDEL calling errors in whole genome and exome sequencing data

(2014) Han Fang et al.   Genome Medicine

Comparing somatic mutation-callers: beyond Venn diagrams

(2013) Su Kim et al.   BMC BIOINFORMATICS

A survey of tools for variant analysis of next-generation genome sequencing data

(2013) S. Pabinger et al.   BRIEFINGS IN BIOINFORMATICS

Mutational landscape and significance across 12 major cancer types

(2013) Cyriac Kandoth et al.   NATURE

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

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

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia

(2013)   NEW ENGLAND JOURNAL OF MEDICINE

Coverage Bias and Sensitivity of Variant Calling for Four Whole-genome Sequencing Technologies

(2013) Nora Rieber et al.   PLoS One

Somatic Point Mutation Calling in Low Cellularity Tumors

(2013) Karin S. Kassahn et al.   PLoS One

Deciphering Signatures of Mutational Processes Operative in Human Cancer

(2013) Ludmil B. Alexandrov et al.   Cell Reports

A simple consensus approach improves somatic mutation prediction accuracy

(2013) David L Goode et al.   Genome Medicine

Detecting somatic point mutations in cancer genome sequencing data: a comparison of mutation callers

(2013) Qingguo Wang et al.   Genome Medicine

Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing

(2013) Jason O'Rawe et al.   Genome Medicine

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

(2012) Christopher T. Saunders et al.   BIOINFORMATICS

An integrative variant analysis suite for whole exome next-generation sequencing data

(2012) Danny Challis et al.   BMC BIOINFORMATICS

Dissecting the genomic complexity underlying medulloblastoma

(2012) David T. W. Jones et al.   NATURE

The GEM mapper: fast, accurate and versatile alignment by filtration

(2012) Santiago Marco-Sola et al.   NATURE METHODS

DNA sequencing – spanning the generations

(2012) Steven McGinn et al.   New Biotechnology

Fast Computation and Applications of Genome Mappability

(2012) Thomas Derrien et al.   PLoS One

Molecular subgroups of medulloblastoma: the current consensus

(2011) Michael D. Taylor et al.   ACTA NEUROPATHOLOGICA

Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia

(2011) Xose S. Puente et al.   NATURE

Efficient construction of an assembly string graph using the FM-index

(2010) J. T. Simpson et al.   BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

International network of cancer genome projects

(2010) Thomas J. Hudson (Chairperson) et al.   NATURE

DNMT3AMutations in Acute Myeloid Leukemia

(2010) Timothy J. Ley et al.   NEW ENGLAND JOURNAL OF MEDICINE

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Cancer genome sequencing: a review

(2009) E. R. Mardis et al.   HUMAN MOLECULAR GENETICS