12 Result(s)
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Karthik A Jagadeesh
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Polygenic architecture of rare coding variation across 394,783 exomes
Both common and rare genetic variants influence complex traits and common diseases. Genome-wide association studies have identified thousands of common-variant associations, and more recently, large-scale exom...
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Open AccessPublisher Correction: SAIGE-GENE+ improves the efficiency and accuracy of set-based rare variant association tests
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Open AccessSAIGE-GENE+ improves the efficiency and accuracy of set-based rare variant association tests
Several biobanks, including UK Biobank (UKBB), are generating large-scale sequencing data. An existing method, SAIGE-GENE, performs well when testing variants with minor allele frequency (MAF) ≤ 1%, but inflat...
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Polygenic enrichment distinguishes disease associations of individual cells in single-cell RNA-seq data
Single-cell RNA sequencing (scRNA-seq) provides unique insights into the pathology and cellular origin of disease. We introduce single-cell disease relevance score (scDRS), an approach that links scRNA-seq wit...
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Identifying disease-critical cell types and cellular processes by integrating single-cell RNA-sequencing and human genetics
Genome-wide association studies provide a powerful means of identifying loci and genes contributing to disease, but in many cases, the related cell types/states through which genes confer disease risk remain u...
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Single-nucleus and spatial transcriptome profiling of pancreatic cancer identifies multicellular dynamics associated with neoadjuvant treatment
Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal and treatment-refractory cancer. Molecular stratification in pancreatic cancer remains rudimentary and does not yet inform clinical management or ther...
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Combining SNP-to-gene linking strategies to identify disease genes and assess disease omnigenicity
Disease-associated single-nucleotide polymorphisms (SNPs) generally do not implicate target genes, as most disease SNPs are regulatory. Many SNP-to-gene (S2G) linking strategies have been developed to link reg...
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COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets
COVID-19, which is caused by SARS-CoV-2, can result in acute respiratory distress syndrome and multiple organ failure1–4, but little is known about its pathophysiology. Here we generated single-cell atlases of 24...
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Avoiding genetic racial profiling in criminal DNA profile databases
DNA profiling has become an essential tool for crime solving and prevention, and CODIS (Combined DNA Index System) criminal investigation databases have flourished at the national, state and even local level. ...
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Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics
Angiotensin-converting enzyme 2 (ACE2) and accessory proteases (TMPRSS2 and CTSL) are needed for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) cellular entry, and their expression may shed light...
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S-CAP extends pathogenicity prediction to genetic variants that affect RNA splicing
Exome analysis of patients with a likely monogenic disease does not identify a causal variant in over half of cases. Splice-disrupting mutations make up the second largest class of known disease-causing mutati...
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M-CAP eliminates a majority of variants of uncertain significance in clinical exomes at high sensitivity
Gill Bejerano and colleagues present M-CAP, a classifier that estimates variant pathogenicity in clinical exome data sets. They show that M-CAP outperforms other existing methods at all thresholds and correctl...
