Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing

A multi-center cross-platform single-cell RNA sequencing reference dataset

(2021) Xin Chen et al.   Scientific Data

A multicenter study benchmarking single-cell RNA sequencing technologies using reference samples

(2020) Wanqiu Chen et al.   NATURE BIOTECHNOLOGY

Genomic profiling reveals spatial intra-tumor heterogeneity in follicular lymphoma

(2018) Shamzah Araf et al.   LEUKEMIA

Towards standardization of next-generation sequencing of FFPE samples for clinical oncology: intrinsic obstacles and possible solutions

(2017) Maxim Ivanov et al.   Journal of Translational Medicine

Spatial heterogeneity in medulloblastoma

(2017) A Sorana Morrissy et al.   NATURE GENETICS

DNA damage is a pervasive cause of sequencing errors, directly confounding variant identification

(2017) Lixin Chen et al.   SCIENCE

Analysis of 100,000 human cancer genomes reveals the landscape of tumor mutational burden

(2017) Zachary R. Chalmers et al.   Genome Medicine

Optimizing Workflows and Processing of Cytologic Samples for Comprehensive Analysis by Next-Generation Sequencing: Memorial Sloan Kettering Cancer Center Experience

(2016) Shaozhou Ken Tian et al.   ARCHIVES OF PATHOLOGY & LABORATORY MEDICINE

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

Extensive sequencing of seven human genomes to characterize benchmark reference materials

(2016) Justin M. Zook et al.   Scientific Data

Validation of a Next-Generation–Sequencing Cancer Panel for Use in the Clinical Laboratory

(2015) Birgitte B. Simen et al.   ARCHIVES OF PATHOLOGY & LABORATORY MEDICINE

BFC: correcting Illumina sequencing errors

(2015) Heng Li   BIOINFORMATICS

INTEGRATE: gene fusion discovery using whole genome and transcriptome data

(2015) Jin Zhang et al.   GENOME RESEARCH

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

(2015) Tyler S. Alioto et al.   Nature Communications

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

Gene Fusions Associated with Recurrent Amplicons Represent a Class of Passenger Aberrations in Breast Cancer

(2015) Shanker Kalyana-Sundaram et al.   NEOPLASIA

Clinical Validation of KRAS, BRAF, and EGFR Mutation Detection Using Next-Generation Sequencing

(2014) Ming-Tseh Lin et al.   AMERICAN JOURNAL OF CLINICAL PATHOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) Huilei Xu et al.   BMC GENOMICS

Analytical validation of whole exome and whole genome sequencing for clinical applications

(2014) Michael D Linderman et al.   BMC Medical Genomics

Sequence Artifacts in DNA from Formalin-Fixed Tissues: Causes and Strategies for Minimization

(2014) H. Do et al.   CLINICAL CHEMISTRY

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

(2014) Justin M Zook et al.   NATURE BIOTECHNOLOGY

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

Clinical Validation of a Next-Generation Sequencing Screen for Mutational Hotspots in 46 Cancer-Related Genes

(2013) Rajesh R. Singh et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

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

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

Discovery and characterization of artifactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation

(2013) Maura Costello et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Qingguo Wang et al.   Genome Medicine

On the reproducibility of science: unique identification of research resources in the biomedical literature

(2013) Nicole A. Vasilevsky et al.   PeerJ

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

(2012) Christopher T. Saunders et al.   BIOINFORMATICS

Raise standards for preclinical cancer research

(2012) C. Glenn Begley et al.   NATURE

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

(2012) Amy S Gargis et al.   NATURE BIOTECHNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

(2011) David E. Larson et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Complex landscapes of somatic rearrangement in human breast cancer genomes

(2009) Philip J. Stephens et al.   NATURE

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY