Best practices for variant calling in clinical sequencing

A robust benchmark for detection of germline large deletions and insertions

(2020) Justin M. Zook et al.   NATURE BIOTECHNOLOGY

Characterizing the Major Structural Variant Alleles of the Human Genome

(2019) Peter A. Audano et al.   CELL

A Rigorous Interlaboratory Examination of the Need to Confirm Next-Generation Sequencing–Detected Variants with an Orthogonal Method in Clinical Genetic Testing

(2019) Stephen E. Lincoln et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Best practices for benchmarking germline small-variant calls in human genomes

(2019) Peter Krusche et al.   NATURE BIOTECHNOLOGY

An open resource for accurately benchmarking small variant and reference calls

(2019) Justin M. Zook et al.   NATURE BIOTECHNOLOGY

Multi-platform discovery of haplotype-resolved structural variation in human genomes

(2019) Mark J. P. Chaisson et al.   Nature Communications

Structural variation in the sequencing era

(2019) Steve S. Ho et al.   NATURE REVIEWS GENETICS

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

A synthetic-diploid benchmark for accurate variant-calling evaluation

(2018) Heng Li et al.   NATURE METHODS

Implementation of next generation sequencing technology for somatic mutation detection in routine laboratory practice

(2018) Tindaro Giardina et al.   PATHOLOGY

A review of somatic single nucleotide variant calling algorithms for next-generation sequencing data

(2018) Chang Xu   Computational and Structural Biotechnology Journal

Somatic Tumor Variant Filtration Strategies to Optimize Tumor-Only Molecular Profiling Using Targeted Next-Generation Sequencing Panels

(2018) Mahadeo A. Sukhai et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Pathogenic ASXL1 somatic variants in reference databases complicate germline variant interpretation for Bohring-Opitz Syndrome

(2017) Colleen M. Carlston et al.   HUMAN MUTATION

Parental influence on human germline de novo mutations in 1,548 trios from Iceland

(2017) Hákon Jónsson et al.   NATURE

Resolution of Disease Phenotypes Resulting from Multilocus Genomic Variation

(2017) Jennifer E. Posey et al.   NEW ENGLAND JOURNAL OF MEDICINE

Prevalence and detection of low-allele-fraction variants in clinical cancer samples

(2017) Hyun-Tae Shin 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

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

(2017) Sarah Sandmann et al.   Scientific Reports

Systematic Evaluation of Sanger Validation of Next-Generation Sequencing Variants

(2016) T. F. Beck et al.   CLINICAL CHEMISTRY

Clinical exome sequencing: results from 2819 samples reflecting 1000 families

(2016) Daniel Trujillano et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigree

(2016) Michael A. Eberle et al.   GENOME RESEARCH

Comprehensive genetic testing in the clinical evaluation of 1119 patients with hearing loss

(2016) Christina M. Sloan-Heggen et al.   HUMAN GENETICS

Detection and Quantification of Mosaic Mutations in Disease Genes by Next-Generation Sequencing

(2016) Lan Qin et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Sanger Confirmation Is Required to Achieve Optimal Sensitivity and Specificity in Next-Generation Sequencing Panel Testing

(2016) Wenbo Mu et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research

(2016) Zhongwu Lai et al.   NUCLEIC ACIDS RESEARCH

The impact of tumor profiling approaches and genomic data strategies for cancer precision medicine

(2016) Andrea Garofalo et al.   Genome Medicine

Diagnostic Yield of Clinical Tumor and Germline Whole-Exome Sequencing for Children With Solid Tumors

(2016) D. Williams Parsons et al.   JAMA Oncology

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

Clinical Validation of Targeted Next-Generation Sequencing for Inherited Disorders

(2015) Sophia Yohe et al.   ARCHIVES OF PATHOLOGY & LABORATORY MEDICINE

Challenges Posed to Pathologists in the Detection ofKRASMutations in Colorectal Cancers

(2015) Jonathan Dudley et al.   ARCHIVES OF PATHOLOGY & LABORATORY MEDICINE

Sambamba: fast processing of NGS alignment formats

(2015) Artem Tarasov et al.   BIOINFORMATICS

Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications

(2015) Xiaoyu Chen et al.   BIOINFORMATICS

Assessing structural variation in a personal genome—towards a human reference diploid genome

(2015) Adam C English et al.   BMC GENOMICS

Whole-exome sequencing in undiagnosed genetic diseases: interpreting 119 trios

(2015) Xiaolin Zhu et al.   GENETICS IN MEDICINE

Clinical application of whole-exome sequencing across clinical indications

(2015) Kyle Retterer et al.   GENETICS IN MEDICINE

Discriminating somatic and germline mutations in tumor DNA samples without matching normals

(2015) Saskia Hiltemann et al.   GENOME RESEARCH

Confirming Variants in Next-Generation Sequencing Panel Testing by Sanger Sequencing

(2015) Linnea M. Baudhuin et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT)

(2015) Donavan T. Cheng et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

The UK10K project identifies rare variants in health and disease

(2015)   NATURE

Comprehensive evaluation of fusion transcript detection algorithms and a meta-caller to combine top performing methods in paired-end RNA-seq data

(2015) Silvia Liu et al.   NUCLEIC ACIDS RESEARCH

An analytical framework for optimizing variant discovery from personal genomes

(2015) Gareth Highnam et al.   Nature Communications

Novel variation and de novo mutation rates in population-wide de novo assembled Danish trios

(2015) Søren Besenbacher et al.   Nature Communications

Leveraging long read sequencing from a single individual to provide a comprehensive resource for benchmarking variant calling methods

(2015) John C. Mu et al.   Scientific Reports

Performance comparison of four commercial human whole-exome capture platforms

(2015) Daichi Shigemizu et al.   Scientific Reports

Comparison of Accuracy of Whole-Exome Sequencing with Formalin-Fixed Paraffin-Embedded and Fresh Frozen Tissue Samples

(2015) Ensel Oh et al.   PLoS One

Systematic comparison of variant calling pipelines using gold standard personal exome variants

(2015) Sohyun Hwang et al.   Scientific Reports

A Review of Preanalytical Factors Affecting Molecular, Protein, and Morphological Analysis of Formalin-Fixed, Paraffin-Embedded (FFPE) Tissue: How Well Do You Know Your FFPE Specimen?

(2014) B. Paige Bass et al.   ARCHIVES OF PATHOLOGY & LABORATORY MEDICINE

SAMBLASTER: fast duplicate marking and structural variant read extraction

(2014) G. G. Faust et al.   BIOINFORMATICS

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

Unique Molecular Landscapes in Cancer: Implications for Individualized, Curated Drug Combinations

(2014) J. Wheler et al.   CANCER RESEARCH

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

(2014) H. Do et al.   CLINICAL CHEMISTRY

Enhanced utility of family-centered diagnostic exome sequencing with inheritance model–based analysis: results from 500 unselected families with undiagnosed genetic conditions

(2014) Kelly D. Farwell et al.   GENETICS IN MEDICINE

Assessing the necessity of confirmatory testing for exome-sequencing results in a clinical molecular diagnostic laboratory

(2014) Samuel P. Strom et al.   GENETICS IN MEDICINE

An Evaluation of Copy Number Variation Detection Tools from Whole-Exome Sequencing Data

(2014) Renjie Tan et al.   HUMAN MUTATION

Clinical Exome Sequencing for Genetic Identification of Rare Mendelian Disorders

(2014) Hane Lee et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

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

LUMPY: a probabilistic framework for structural variant discovery

(2014) Ryan M Layer et al.   GENOME BIOLOGY

A Prospective, Multi-Institutional Diagnostic Trial to Determine Pathologist Accuracy in Estimation of Percentage of Malignant Cells

(2013) Hollis Viray et al.   ARCHIVES OF PATHOLOGY & LABORATORY MEDICINE

CoNVEX: copy number variation estimation in exome sequencing data using HMM

(2013) Kaushalya C Amarasinghe et al.   BMC BIOINFORMATICS

Detection of Clinically Relevant Copy Number Variants with Whole-Exome Sequencing

(2013) Joep de Ligt et al.   HUMAN MUTATION

Validation and Implementation of Targeted Capture and Sequencing for the Detection of Actionable Mutation, Copy Number Variation, and Gene Rearrangement in Clinical Cancer Specimens

(2013) Colin C. Pritchard et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

The estimation of tumor cell percentage for molecular testing by pathologists is not accurate

(2013) Alexander J J Smits et al.   MODERN PATHOLOGY

Comprehensive molecular characterization of clear cell renal cell carcinoma

(2013)   NATURE

Integrated genomic characterization of endometrial carcinoma

(2013) Gad Getz et al.   NATURE

Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing

(2013) Garrett M Frampton et al.   NATURE BIOTECHNOLOGY

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

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

Clinical Whole-Exome Sequencing for the Diagnosis of Mendelian Disorders

(2013) Yaping Yang et al.   NEW ENGLAND JOURNAL OF MEDICINE

Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia

(2013)   NEW ENGLAND JOURNAL OF MEDICINE

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

(2013) Qingguo Wang et al.   Genome Medicine

SOAPfuse: an algorithm for identifying fusion transcripts from paired-end RNA-Seq data

(2013) Wenlong Jia et al.   GENOME BIOLOGY

Detecting and Estimating Contamination of Human DNA Samples in Sequencing and Array-Based Genotype Data

(2012) Goo Jun et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Contribution of Global Rare Copy-Number Variants to the Risk of Sporadic Congenital Heart Disease

(2012) Rachel Soemedi et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Discovery and Statistical Genotyping of Copy-Number Variation from Whole-Exome Sequencing Depth

(2012) Menachem Fromer et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The Centers for Mendelian Genomics: A new large-scale initiative to identify the genes underlying rare Mendelian conditions

(2012) Michael J. Bamshad et al.   AMERICAN JOURNAL OF MEDICAL GENETICS PART A

CONTRA: copy number analysis for targeted resequencing

(2012) Jason Li et al.   BIOINFORMATICS

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

(2012) Christopher T. Saunders et al.   BIOINFORMATICS

A robust model for read count data in exome sequencing experiments and implications for copy number variant calling

(2012) Vincent Plagnol et al.   BIOINFORMATICS

DELLY: structural variant discovery by integrated paired-end and split-read analysis

(2012) T. Rausch et al.   BIOINFORMATICS

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

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

Comprehensive molecular characterization of human colon and rectal cancer

(2012)   NATURE

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

Comprehensive genomic characterization of squamous cell lung cancers

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate

(2012) Günter Klambauer et al.   NUCLEIC ACIDS RESEARCH

A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes

(2012) D. G. MacArthur et al.   SCIENCE

Reliable detection of subclonal single-nucleotide variants in tumour cell populations

(2012) Moritz Gerstung et al.   Nature Communications

FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution

(2011) Huanying Ge et al.   BIOINFORMATICS

Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data

(2011) T. Carver et al.   BIOINFORMATICS

Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV

(2011) Jarupon Fah Sathirapongsasuti et al.   BIOINFORMATICS

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

(2011) David E. Larson et al.   BIOINFORMATICS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Exome sequencing can detect pathogenic mosaic mutations present at low allele frequencies

(2011) Alistair T Pagnamenta et al.   JOURNAL OF HUMAN GENETICS

Integrated genomic analyses of ovarian carcinoma

(2011) D. Bell et al.   NATURE

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Genome structural variation discovery and genotyping

(2011) Can Alkan et al.   NATURE REVIEWS GENETICS

Rare copy number variations in congenital heart disease patients identify unique genes in left-right patterning

(2011) K. A. Fakhro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-Throughput Detection of Actionable Genomic Alterations in Clinical Tumor Samples by Targeted, Massively Parallel Sequencing

(2011) Nikhil Wagle et al.   Cancer Discovery

Enhanced structural variant and breakpoint detection using SVMerge by integration of multiple detection methods and local assembly

(2011) Kim Wong et al.   GENOME BIOLOGY

TopHat-Fusion: an algorithm for discovery of novel fusion transcripts

(2011) Daehwan Kim et al.   GENOME BIOLOGY

Fine-Scale Survey of X Chromosome Copy Number Variants and Indels Underlying Intellectual Disability

(2010) Annabel C. Whibley et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Robust relationship inference in genome-wide association studies

(2010) Ani Manichaikul et al.   BIOINFORMATICS

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

(2010) Heng Li et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery

(2010) Kai Wang et al.   NUCLEIC ACIDS RESEARCH

Diversity of Human Copy Number Variation and Multicopy Genes

(2010) Peter H. Sudmant et al.   SCIENCE

Population Analysis of Large Copy Number Variants and Hotspots of Human Genetic Disease

(2009) Andy Itsara et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

(2009) K. Ye et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

De novo copy number variants identify new genes and loci in isolated sporadic tetralogy of Fallot

(2009) Steven C Greenway et al.   NATURE GENETICS

Genome-Wide Analyses of Exonic Copy Number Variants in a Family-Based Study Point to Novel Autism Susceptibility Genes

(2009) Maja Bucan et al.   PLoS Genetics

Genetic association analysis of copy-number variation (CNV) in human disease pathogenesis

(2008) Iuliana Ionita-Laza et al.   GENOMICS