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Open AccessGenomic analysis of 116 autism families strengthens known risk genes and highlights promising candidates
Autism spectrum disorder (ASD) is a complex neurodevelopmental condition with a strong genetic component in which rare variants contribute significantly to risk. We performed whole genome and/or exome sequenci...
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Open AccessAuthor Correction: Nasal airway transcriptome-wide association study of asthma reveals genetically driven mucus pathobiology
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Open AccessPangenome-based genome inference allows efficient and accurate genoty** across a wide spectrum of variant classes
Typical genoty** workflows map reads to a reference genome before identifying genetic variants. Generating such alignments introduces reference biases and comes with substantial computational burden. Further...
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Open AccessNasal airway transcriptome-wide association study of asthma reveals genetically driven mucus pathobiology
To identify genetic determinants of airway dysfunction, we performed a transcriptome-wide association study for asthma by combining RNA-seq data from the nasal airway epithelium of 681 children, with UK Bioban...
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Recent ultra-rare inherited variants implicate new autism candidate risk genes
Autism is a highly heritable complex disorder in which de novo mutation (DNM) variation contributes significantly to risk. Using whole-genome sequencing data from 3,474 families, we investigate another source ...
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Open AccessCoding and noncoding variants in EBF3 are involved in HADDS and simplex autism
Previous research in autism and other neurodevelopmental disorders (NDDs) has indicated an important contribution of protein-coding (coding) de novo variants (DNVs) within specific genes. The role of de novo n...
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Open AccessSequencing of 53,831 diverse genomes from the NHLBI TOPMed Program
The Trans-Omics for Precision Medicine (TOPMed) programme seeks to elucidate the genetic architecture and biology of heart, lung, blood and sleep disorders, with the ultimate goal of improving diagnosis, treat...
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Open AccessType 2 and interferon inflammation regulate SARS-CoV-2 entry factor expression in the airway epithelium
Coronavirus disease 2019 (COVID-19) is caused by SARS-CoV-2, an emerging virus that utilizes host proteins ACE2 and TMPRSS2 as entry factors. Understanding the factors affecting the pattern and levels of expre...
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Map** and characterization of structural variation in 17,795 human genomes
A key goal of whole-genome sequencing for studies of human genetics is to interrogate all forms of variation, including single-nucleotide variants, small insertion or deletion (indel) variants and structural v...
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Open AccessDeep whole-genome sequencing of 3 cancer cell lines on 2 sequencing platforms
To test the performance of a new sequencing platform, develop an updated somatic calling pipeline and establish a reference for future benchmarking experiments, we performed whole-genome sequencing of 3 common...
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Open AccessCorrection to: Sequencing and curation strategies for identifying candidate glioblastoma treatments
Following publication of the original article [1], it was reported that the given name of the fourteenth author was incorrectly published. The incorrect and the correct names are given below.
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Open AccessSequencing and curation strategies for identifying candidate glioblastoma treatments
Prompted by the revolution in high-throughput sequencing and its potential impact for treating cancer patients, we initiated a clinical research study to compare the ability of different sequencing assays and ...
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Open AccessFunctional equivalence of genome sequencing analysis pipelines enables harmonized variant calling across human genetics projects
Hundreds of thousands of human whole genome sequencing (WGS) datasets will be generated over the next few years. These data are more valuable in aggregate: joint analysis of genomes from many sources increases...
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Open AccessGenome-wide somatic variant calling using localized colored de Bruijn graphs
Reliable detection of somatic variations is of critical importance in cancer research. Here we present Lancet, an accurate and sensitive somatic variant caller, which detects SNVs and indels by jointly analyzi...
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Indel variant analysis of short-read sequencing data with Scalpel
Fang et al. describe a computational protocol to accurately call indels from whole-genome and whole-exome sequencing data using Scalpel. Important issues for indel identification, such as short repeat regions and...
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Open AccessV-Phaser 2: variant inference for viral populations
Massively parallel sequencing offers the possibility of revolutionizing the study of viral populations by providing ultra deep sequencing (tens to hundreds of thousand fold coverage) of complete viral genomes....
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Mutations causing medullary cystic kidney disease type 1 lie in a large VNTR in MUC1 missed by massively parallel sequencing
Anthony Bleyer, Eric Lander, Mark Daly and colleagues show that frameshift mutations in a large VNTR of MUC1 cause medullary cystic kidney disease type 1. Their discovery sheds light on the biology of this diseas...
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Open AccessDe novo assembly of highly diverse viral populations
Extensive genetic diversity in viral populations within infected hosts and the divergence of variants from existing reference genomes impede the analysis of deep viral sequencing data. A de novo population consen...
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Open AccessNovel origins of copy number variation in the dog genome
Copy number variants (CNVs) account for substantial variation between genomes and are a major source of normal and pathogenic phenotypic differences. The dog is an ideal model to investigate mutational mechani...
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Structural haplotypes and recent evolution of the human 17q21.31 region
Steven McCarroll and colleagues use a population genetics approach to identify nine different structural forms of the 17q21.31 inversion region. They show that duplications have arisen independently on both an...
