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Huang, Le; Rosen, Jonathan D.; Sun, Quan; Chen, Jiawen; Wheeler, Marsha M.; Zhou, Ying; Min, Yuan-I; Kooperberg, Charles; Conomos, Matthew P.; Stilp, Adrienne M.; Rich, Stephen S.; Rotter, Jerome I.; Manichaikul, Ani; Loos, Ruth J.F.; Kenny, Eimear E.; Blackwell, Thomas W.; Smith, Albert V.; Jun, Goo; Sedlazeck, Fritz J.; Metcalf, Ginger; Boerwinkle, Eric; Raffield, Laura M.; Reiner, Alex P.; Auer, Paul L.; Li, Yun
American journal of human genetics, 06/2022, Letnik: 109, Številka: 6Journal Article
Current publicly available tools that allow rapid exploration of linkage disequilibrium (LD) between markers (e.g., HaploReg and LDlink) are based on whole-genome sequence (WGS) data from 2,504 individuals in the 1000 Genomes Project. Here, we present TOP-LD, an online tool to explore LD inferred with high-coverage (∼30×) WGS data from 15,578 individuals in the NHLBI Trans-Omics for Precision Medicine (TOPMed) program. TOP-LD provides a significant upgrade compared to current LD tools, as the TOPMed WGS data provide a more comprehensive representation of genetic variation than the 1000 Genomes data, particularly for rare variants and in the specific populations that we analyzed. For example, TOP-LD encompasses LD information for 150.3, 62.2, and 36.7 million variants for European, African, and East Asian ancestral samples, respectively, offering 2.6- to 9.1-fold increase in variant coverage compared to HaploReg 4.0 or LDlink. In addition, TOP-LD includes tens of thousands of structural variants (SVs). We demonstrate the value of TOP-LD in fine-mapping at the GGT1 locus associated with gamma glutamyltransferase in the African ancestry participants in UK Biobank. Beyond fine-mapping, TOP-LD can facilitate a wide range of applications that are based on summary statistics and estimates of LD. TOP-LD is freely available online.
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JCR | SNIP | JCR | SNIP | JCR | SNIP | JCR | SNIP |
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Povezave do osebnih bibliografij avtorjev | Povezave do podatkov o raziskovalcih v sistemu SICRIS |
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Vir: Osebne bibliografije
in: SICRIS
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