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Can I read TOP-LD: A tool to explore linkage disequilibrium with TOPMed whole-genome sequence data on EtoBox?
TOP-LD: A tool to explore linkage disequilibrium with TOPMed whole-genome sequence data by Le Huang; Jonathan D. Rosen; Quan Sun; Jiawen Chen; Marsha M. Wheeler; Ying Zhou; Yuan-I Min; Charles Kooperberg; Matthew P. Conomos; Adrienne M. Stilp; Stephen S. Rich; Jerome I. Rotter; Ani Manichaikul; Ruth J.F. Loos; Eimear E. Kenny; Thomas W. Blackwell; Albert V. Smith; Goo Jun; Fritz J. Sedlazeck; Ginger Metcalf; Eric Boerwinkle; Laura M. Raffield; Alex P. Reiner; Paul L. Auer; Yun Li is a Biochemistry, Genetics and Molecular Biology article available to read on EtoBox.
What is TOP-LD: A tool to explore linkage disequilibrium with TOPMed whole-genome sequence data about?
## Summary 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. Beyon
Who reads TOP-LD: A tool to explore linkage disequilibrium with TOPMed whole-genome sequence data?
It is typically read by researchers, students, and practitioners in Biochemistry, Genetics and Molecular Biology.
- Author
- Le Huang; Jonathan D. Rosen; Quan Sun; Jiawen Chen; Marsha M. Wheeler; Ying Zhou; Yuan-I Min; Charles Kooperberg; Matthew P. Conomos; Adrienne M. Stilp; Stephen S. Rich; Jerome I. Rotter; Ani Manichaikul; Ruth J.F. Loos; Eimear E. Kenny; Thomas W. Blackwell; Albert V. Smith; Goo Jun; Fritz J. Sedlazeck; Ginger Metcalf; Eric Boerwinkle; Laura M. Raffield; Alex P. Reiner; Paul L. Auer; Yun Li
- Publisher
- Elsevier BV
- Published
- 2022
- Language
- EN
- Field
- Biochemistry, Genetics and Molecular Biology (Life Sciences)