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Structural variation across 138,134 samples in the TOPMed consortium.

Publication ,  Journal Article
Jun, G; English, AC; Metcalf, GA; Yang, J; Chaisson, MJ; Pankratz, N; Menon, VK; Salerno, WJ; Krasheninina, O; Smith, AV; Lane, JA; Kang, HM ...
Published in: Res Sq
February 3, 2023

Ever larger Structural Variant (SV) catalogs highlighting the diversity within and between populations help researchers better understand the links between SVs and disease. The identification of SVs from DNA sequence data is non-trivial and requires a balance between comprehensiveness and precision. Here we present a catalog of 355,667 SVs (59.34% novel) across autosomes and the X chromosome (50bp+) from 138,134 individuals in the diverse TOPMed consortium. We describe our methodologies for SV inference resulting in high variant quality and >90% allele concordance compared to long-read de-novo assemblies of well-characterized control samples. We demonstrate utility through significant associations between SVs and important various cardio-metabolic and hematologic traits. We have identified 690 SV hotspots and deserts and those that potentially impact the regulation of medically relevant genes. This catalog characterizes SVs across multiple populations and will serve as a valuable tool to understand the impact of SV on disease development and progression.

Duke Scholars

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Res Sq

DOI

Publication Date

February 3, 2023

Location

United States
 

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Jun, G., English, A. C., Metcalf, G. A., Yang, J., Chaisson, M. J., Pankratz, N., … Sedlazeck, F. J. (2023). Structural variation across 138,134 samples in the TOPMed consortium. Res Sq. https://doi.org/10.21203/rs.3.rs-2515453/v1
Jun, Goo, Adam C. English, Ginger A. Metcalf, Jianzhi Yang, Mark Jp Chaisson, Nathan Pankratz, Vipin K. Menon, et al. “Structural variation across 138,134 samples in the TOPMed consortium.Res Sq, February 3, 2023. https://doi.org/10.21203/rs.3.rs-2515453/v1.
Jun G, English AC, Metcalf GA, Yang J, Chaisson MJ, Pankratz N, et al. Structural variation across 138,134 samples in the TOPMed consortium. Res Sq. 2023 Feb 3;
Jun, Goo, et al. “Structural variation across 138,134 samples in the TOPMed consortium.Res Sq, Feb. 2023. Pubmed, doi:10.21203/rs.3.rs-2515453/v1.
Jun G, English AC, Metcalf GA, Yang J, Chaisson MJ, Pankratz N, Menon VK, Salerno WJ, Krasheninina O, Smith AV, Lane JA, Blackwell T, Kang HM, Salvi S, Meng Q, Shen H, Pasham D, Bhamidipati S, Kottapalli K, Arnett DK, Ashley-Koch A, Auer PL, Beutel KM, Bis JC, Blangero J, Bowden DW, Brody JA, Cade BE, Chen Y-DI, Cho MH, Curran JE, Fornage M, Freedman BI, Fingerlin T, Gelb BD, Hou L, Hung Y-J, Kane JP, Kaplan R, Kim W, Loos RJF, Marcus GM, Mathias RA, McGarvey ST, Montgomery C, Naseri T, Nouraie SM, Preuss MH, Palmer ND, Peyser PA, Raffield LM, Ratan A, Redline S, Reupena S, Rotter JI, Rich SS, Rienstra M, Ruczinski I, Sankaran VG, Schwartz DA, Seidman CE, Seidman JG, Silverman EK, Smith JA, Stilp A, Taylor KD, Telen MJ, Weiss ST, Williams LK, Wu B, Yanek LR, Zhang Y, Lasky-Su J, Gingras MC, Dutcher SK, Eichler EE, Gabriel S, Germer S, Kim R, Viaud-Martinez KA, Nickerson DA, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, Luo J, Reiner A, Gibbs RA, Boerwinkle E, Abecasis G, Sedlazeck FJ. Structural variation across 138,134 samples in the TOPMed consortium. Res Sq. 2023 Feb 3;

Published In

Res Sq

DOI

Publication Date

February 3, 2023

Location

United States