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Article
Open AccessA systematic strategy for identifying causal single nucleotide polymorphisms and their target genes on Juvenile arthritis risk haplotypes
Although genome-wide association studies (GWAS) have identified multiple regions conferring genetic risk for juvenile idiopathic arthritis (JIA), we are still faced with the task of identifying the single nucl...
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Article
Open AccessMulticenter integrated analysis of noncoding CRISPRi screens
The ENCODE Consortium’s efforts to annotate noncoding cis-regulatory elements (CREs) have advanced our understanding of gene regulatory landscapes. Pooled, noncoding CRISPR screens offer a systematic approach to ...
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Article
Open AccessGenome-wide association study identifies human genetic variants associated with fatal outcome from Lassa fever
Infection with Lassa virus (LASV) can cause Lassa fever, a haemorrhagic illness with an estimated fatality rate of 29.7%, but causes no or mild symptoms in many individuals. Here, to investigate whether human ...
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Article
Open AccessWidespread perturbation of ETS factor binding sites in cancer
Although >90% of somatic mutations reside in non-coding regions, few have been reported as cancer drivers. To predict driver non-coding variants (NCVs), we present a transcription factor (TF)-aware burden test...
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Article
Prioritization of autoimmune disease-associated genetic variants that perturb regulatory element activity in T cells
Genome-wide association studies (GWASs) have uncovered hundreds of autoimmune disease-associated loci; however, the causal genetic variants within each locus are mostly unknown. Here, we perform high-throughpu...
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Article
Synthetic DNA spike-ins (SDSIs) enable sample tracking and detection of inter-sample contamination in SARS-CoV-2 sequencing workflows
The global spread and continued evolution of SARS-CoV-2 has driven an unprecedented surge in viral genomic surveillance. Amplicon-based sequencing methods provide a sensitive, low-cost and rapid approach but s...
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Author Correction: Direct characterization of cis-regulatory elements and functional dissection of complex genetic associations using HCR–FlowFISH
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Article
Open AccessFunctional characterization of T2D-associated SNP effects on baseline and ER stress-responsive β cell transcriptional activation
Genome-wide association studies (GWAS) have linked single nucleotide polymorphisms (SNPs) at >250 loci in the human genome to type 2 diabetes (T2D) risk. For each locus, identifying the functional variant(s) a...
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Article
Direct characterization of cis-regulatory elements and functional dissection of complex genetic associations using HCR–FlowFISH
Effective interpretation of genome function and genetic variation requires a shift from epigenetic map** of cis-regulatory elements (CREs) to characterization of endogenous function. We developed hybridization ...
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Article
Open AccessPrioritizing disease and trait causal variants at the TNFAIP3 locus using functional and genomic features
Genome-wide association studies have associated thousands of genetic variants with complex traits and diseases, but pinpointing the causal variant(s) among those in tight linkage disequilibrium with each assoc...
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Article
Genome-wide identification of microRNAs regulating cholesterol and triglyceride homeostasis
From a systematic analysis of genome-wide association studies of blood lipid levels, Wagschal et al. identify several miRNAs that target key proteins involved in cholesterol and lipid metabolism, including the LD...
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Article
Open AccessEnhanced methods for unbiased deep sequencing of Lassa and Ebola RNA viruses from clinical and biological samples
We have developed a robust RNA sequencing method for generating complete de novo assemblies with intra-host variant calls of Lassa and Ebola virus genomes in clinical and biological samples. Our method uses targe...
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Article
Open AccessGenetic structure of community acquired methicillin-resistant Staphylococcus aureus USA300
Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) is a significant bacterial pathogen that poses considerable clinical and public health challenges. The majority of the CA-MRSA disease...
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Article
Open AccessWhole genome sequencing analysis of Plasmodium vivax using whole genome capture
Malaria caused by Plasmodium vivax is an experimentally neglected severe disease with a substantial burden on human health. Because of technical limitations, little is known about the biology of this important hu...
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Article
The importance of phase information for human genomics
This Opinion article argues that capturing phase information in human genomics studies is crucial for important aims such as understanding how genotype contributes to phenotypes. existing approaches for phasin...
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Article
The next phase in human genetics
Experimental haploty** of whole genomes is now feasible, enabling new studies aimed at linking sequence variation to human phenotypes and disease susceptibility.
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Article
Open AccessGenomic acquisition of a capsular polysaccharide virulence cluster by non-pathogenic Burkholderia isolates
Burkholderia thailandensis is a non-pathogenic environmental saprophyte closely related to Burkholderia pseudomallei, the causative agent of the often fatal animal and human disease melioidosis. To study B. thail...
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Article
Correction: Corrigendum: Microdroplet-based PCR enrichment for large-scale targeted sequencing
Nat. Biotechnol. 27, 1025–1031 (2009); published online 1 November 2009; corrected after print 11 November 2009 In the version of this article initially published, the email address for K.A.F. should have been...
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Article
Microdroplet-based PCR enrichment for large-scale targeted sequencing
In many sequencing applications, it is sufficient to sequence selected portions of a genome rather than the complete genome. Tewhey et al. describe an approach for massively parallel genome targeting that relies ...
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Article
Open AccessEnrichment of sequencing targets from the human genome by solution hybridization
To exploit fully the potential of current sequencing technologies for population-based studies, one must enrich for loci from the human genome. Here we evaluate the hybridization-based approach by using oligon...
