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TOP-LD: A tool to explore linkage disequilibrium with TOPMed whole-genome sequence data.
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.
Afiliación
  • Huang L; Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
  • Rosen JD; Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
  • Sun Q; Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
  • Chen J; Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
  • Wheeler MM; Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA.
  • Zhou Y; Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
  • Min YI; Department of Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA.
  • Kooperberg C; Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
  • Conomos MP; Department of Biostatistics, University of Washington, Seattle, WA 98105, USA.
  • Stilp AM; Department of Biostatistics, University of Washington, Seattle, WA 98105, USA.
  • Rich SS; Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA 22908, USA.
  • Rotter JI; The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA.
  • Manichaikul A; Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA 22908, USA.
  • Loos RJF; The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA; Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.
  • Kenny EE; The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA.
  • Blackwell TW; TOPMed Informatics Research Center, University of Michigan, Department of Biostatistics, Ann Arbor, MI 48109, USA.
  • Smith AV; TOPMed Informatics Research Center, University of Michigan, Department of Biostatistics, Ann Arbor, MI 48109, USA.
  • Jun G; Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
  • Sedlazeck FJ; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.
  • Metcalf G; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.
  • Boerwinkle E; Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
  • Raffield LM; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
  • Reiner AP; Department of Epidemiology, University of Washington, Seattle, WA 98195, USA; Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
  • Auer PL; Division of Biostatistics, Institute for Health and Equity, and Cancer Center, Medical College of Wisconsin, Milwaukee, WI 53226, USA. Electronic address: pauer@mcw.edu.
  • Li Y; Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, U
Am J Hum Genet ; 109(6): 1175-1181, 2022 06 02.
Article en En | MEDLINE | ID: mdl-35504290
ABSTRACT
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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Texto completo: 1 Colección: 01-internacional Banco de datos: MEDLINE Asunto principal: Estudio de Asociación del Genoma Completo / Medicina de Precisión Límite: Humans Idioma: En Revista: Am J Hum Genet Año: 2022 Tipo del documento: Article País de afiliación: Estados Unidos
Texto completo
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Colección: 01-internacional Banco de datos: MEDLINE Asunto principal: Estudio de Asociación del Genoma Completo / Medicina de Precisión Límite: Humans Idioma: En Revista: Am J Hum Genet Año: 2022 Tipo del documento: Article País de afiliación: Estados Unidos