Determination of disease phenotypes and pathogenic variants from exome sequence data in the CAGI 4 gene panel challenge

A novel human autoimmune syndrome caused by combined hypomorphic and activating mutations in ZAP-70

(2016) Alice Y. Chan et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Analysis of protein-coding genetic variation in 60,706 humans

(2016) Monkol Lek et al.   NATURE

Multisystem Anomalies in Severe Combined Immunodeficiency with Mutant BCL11B

(2016) Divya Punwani et al.   NEW ENGLAND JOURNAL OF MEDICINE

Whole-genome sequencing expands diagnostic utility and improves clinical management in paediatric medicine

(2016) Dimitri J Stavropoulos et al.   npj Genomic Medicine

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology

(2015) Sue Richards et al.   GENETICS IN MEDICINE

Nijmegen Breakage Syndrome Detected by Newborn Screening for T Cell Receptor Excision Circles (TRECs)

(2015) Jay P. Patel et al.   JOURNAL OF CLINICAL IMMUNOLOGY

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

ClinVar: public archive of interpretations of clinically relevant variants

(2015) Melissa J. Landrum et al.   NUCLEIC ACIDS RESEARCH

A Comparison of Variant Calling Pipelines Using Genome in a Bottle as a Reference

(2015) Adam Cornish et al.   Biomed Research International

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

(2015) Sohyun Hwang et al.   Scientific Reports

FORGE Canada Consortium: Outcomes of a 2-Year National Rare-Disease Gene-Discovery Project

(2014) Chandree L. Beaulieu et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

(2014) Heng Li   BIOINFORMATICS

Analysis of rare variant population structure in Europeans explains differential stratification of gene-based tests

(2014) Matthew Zawistowski et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

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

Targeted gene panel sequencing in children with very early onset inflammatory bowel disease—evaluation and prospective analysis

(2014) Jochen Kammermeier et al.   JOURNAL OF MEDICAL GENETICS

A general framework for estimating the relative pathogenicity of human genetic variants

(2014) Martin Kircher et al.   NATURE GENETICS

In silico prediction of splice-altering single nucleotide variants in the human genome

(2014) Xueqiu Jian et al.   NUCLEIC ACIDS RESEARCH

Mutations in zinc finger 407 [ZNF407] cause a unique autosomal recessive cognitive impairment syndrome

(2014) Marios Kambouris et al.   Orphanet Journal of Rare Diseases

Choice of transcripts and software has a large effect on variant annotation

(2014) Davis J McCarthy et al.   Genome Medicine

Reducing INDEL calling errors in whole genome and exome sequencing data

(2014) Han Fang et al.   Genome Medicine

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

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

Improved exome prioritization of disease genes through cross-species phenotype comparison

(2013) P. N. Robinson et al.   GENOME RESEARCH

eXtasy: variant prioritization by genomic data fusion

(2013) Alejandro Sifrim et al.   NATURE METHODS

RefSeq: an update on mammalian reference sequences

(2013) Kim D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

APPRIS: annotation of principal and alternative splice isoforms

(2012) Jose Manuel Rodriguez et al.   NUCLEIC ACIDS RESEARCH

Complete Khoisan and Bantu genomes from southern Africa

(2010) Stephan C. Schuster et al.   NATURE

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding

(2009) K. J. McKernan et al.   GENOME RESEARCH

Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm

(2009) Prateek Kumar et al.   Nature Protocols