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Structural variation across 138,134 samples in the TOPMed consortium

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....

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Autores principales: Jun, Goo, English, Adam C, Metcalf, Ginger A, Yang, Jianzhi, Chaisson, Mark JP, Pankratz, Nathan, Menon, Vipin K, Salerno, William J, Krasheninina, Olga, Smith, Albert V, Lane, John A, Blackwell, Tom, Kang, Hyun Min, Salvi, Sejal, Meng, Qingchang, Shen, Hua, Pasham, Divya, Bhamidipati, Sravya, Kottapalli, Kavya, Arnett, Donna K., Ashley-Koch, Allison, Auer, Paul L., Beutel, Kathleen M, Bis, Joshua C., Blangero, John, Bowden, Donald W., Brody, Jennifer A., Cade, Brian E., Chen, Yii-Der Ida, Cho, Michael H., Curran, Joanne E., Fornage, Myriam, Freedman, Barry I., Fingerlin, Tasha, Gelb, Bruce D., Hou, Lifang, Hung, Yi-Jen, Kane, John P, Kaplan, Robert, Kim, Wonji, Loos, Ruth J.F., Marcus, Gregory M, Mathias, Rasika A., McGarvey, Stephen T., Montgomery, Courtney, Naseri, Take, Nouraie, S. Mehdi, Preuss, Michael H., Palmer, Nicholette D., Peyser, Patricia A., Raffield, Laura M., Ratan, Aakrosh, Redline, Susan, Reupena, Sefuiva, Rotter, Jerome I., Rich, Stephen S., Rienstra, Michiel, Ruczinski, Ingo, Sankaran, Vijay G., Schwartz, David A., Seidman, Christine E., Seidman, Jonathan G., Silverman, Edwin K., Smith, Jennifer A., Stilp, Adrienne, Taylor, Kent D., Telen, Marilyn J., Weiss, Scott T., Williams, L. Keoki, Wu, Baojun, Yanek, Lisa R., Zhang, Yingze, Lasky-Su, Jessica, Gingras, Marie Claude, Dutcher, Susan K., Eichler, Evan E., Gabriel, Stacey, Germer, Soren, Kim, Ryan, Viaud-Martinez, Karine A., Nickerson, Deborah A., Luo, James, Reiner, Alex, Gibbs, Richard A, Boerwinkle, Eric, Abecasis, Goncalo, Sedlazeck, Fritz J
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Cold Spring Harbor Laboratory 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9900832/
https://www.ncbi.nlm.nih.gov/pubmed/36747810
http://dx.doi.org/10.1101/2023.01.25.525428
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author Jun, Goo
English, Adam C
Metcalf, Ginger A
Yang, Jianzhi
Chaisson, Mark JP
Pankratz, Nathan
Menon, Vipin K
Salerno, William J
Krasheninina, Olga
Smith, Albert V
Lane, John A
Blackwell, Tom
Kang, Hyun Min
Salvi, Sejal
Meng, Qingchang
Shen, Hua
Pasham, Divya
Bhamidipati, Sravya
Kottapalli, Kavya
Arnett, Donna K.
Ashley-Koch, Allison
Auer, Paul L.
Beutel, Kathleen M
Bis, Joshua C.
Blangero, John
Bowden, Donald W.
Brody, Jennifer A.
Cade, Brian E.
Chen, Yii-Der Ida
Cho, Michael H.
Curran, Joanne E.
Fornage, Myriam
Freedman, Barry I.
Fingerlin, Tasha
Gelb, Bruce D.
Hou, Lifang
Hung, Yi-Jen
Kane, John P
Kaplan, Robert
Kim, Wonji
Loos, Ruth J.F.
Marcus, Gregory M
Mathias, Rasika A.
McGarvey, Stephen T.
Montgomery, Courtney
Naseri, Take
Nouraie, S. Mehdi
Preuss, Michael H.
Palmer, Nicholette D.
Peyser, Patricia A.
Raffield, Laura M.
Ratan, Aakrosh
Redline, Susan
Reupena, Sefuiva
Rotter, Jerome I.
Rich, Stephen S.
Rienstra, Michiel
Ruczinski, Ingo
Sankaran, Vijay G.
Schwartz, David A.
Seidman, Christine E.
Seidman, Jonathan G.
Silverman, Edwin K.
Smith, Jennifer A.
Stilp, Adrienne
Taylor, Kent D.
Telen, Marilyn J.
Weiss, Scott T.
Williams, L. Keoki
Wu, Baojun
Yanek, Lisa R.
Zhang, Yingze
Lasky-Su, Jessica
Gingras, Marie Claude
Dutcher, Susan K.
Eichler, Evan E.
Gabriel, Stacey
Germer, Soren
Kim, Ryan
Viaud-Martinez, Karine A.
Nickerson, Deborah A.
Luo, James
Reiner, Alex
Gibbs, Richard A
Boerwinkle, Eric
Abecasis, Goncalo
Sedlazeck, Fritz J
author_facet Jun, Goo
English, Adam C
Metcalf, Ginger A
Yang, Jianzhi
Chaisson, Mark JP
Pankratz, Nathan
Menon, Vipin K
Salerno, William J
Krasheninina, Olga
Smith, Albert V
Lane, John A
Blackwell, Tom
Kang, Hyun Min
Salvi, Sejal
Meng, Qingchang
Shen, Hua
Pasham, Divya
Bhamidipati, Sravya
Kottapalli, Kavya
Arnett, Donna K.
Ashley-Koch, Allison
Auer, Paul L.
Beutel, Kathleen M
Bis, Joshua C.
Blangero, John
Bowden, Donald W.
Brody, Jennifer A.
Cade, Brian E.
Chen, Yii-Der Ida
Cho, Michael H.
Curran, Joanne E.
Fornage, Myriam
Freedman, Barry I.
Fingerlin, Tasha
Gelb, Bruce D.
Hou, Lifang
Hung, Yi-Jen
Kane, John P
Kaplan, Robert
Kim, Wonji
Loos, Ruth J.F.
Marcus, Gregory M
Mathias, Rasika A.
McGarvey, Stephen T.
Montgomery, Courtney
Naseri, Take
Nouraie, S. Mehdi
Preuss, Michael H.
Palmer, Nicholette D.
Peyser, Patricia A.
Raffield, Laura M.
Ratan, Aakrosh
Redline, Susan
Reupena, Sefuiva
Rotter, Jerome I.
Rich, Stephen S.
Rienstra, Michiel
Ruczinski, Ingo
Sankaran, Vijay G.
Schwartz, David A.
Seidman, Christine E.
Seidman, Jonathan G.
Silverman, Edwin K.
Smith, Jennifer A.
Stilp, Adrienne
Taylor, Kent D.
Telen, Marilyn J.
Weiss, Scott T.
Williams, L. Keoki
Wu, Baojun
Yanek, Lisa R.
Zhang, Yingze
Lasky-Su, Jessica
Gingras, Marie Claude
Dutcher, Susan K.
Eichler, Evan E.
Gabriel, Stacey
Germer, Soren
Kim, Ryan
Viaud-Martinez, Karine A.
Nickerson, Deborah A.
Luo, James
Reiner, Alex
Gibbs, Richard A
Boerwinkle, Eric
Abecasis, Goncalo
Sedlazeck, Fritz J
author_sort Jun, Goo
collection PubMed
description 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 hemotologic 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.
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spelling pubmed-99008322023-02-07 Structural variation across 138,134 samples in the TOPMed consortium Jun, Goo English, Adam C Metcalf, Ginger A Yang, Jianzhi Chaisson, Mark JP Pankratz, Nathan Menon, Vipin K Salerno, William J Krasheninina, Olga Smith, Albert V Lane, John A Blackwell, Tom Kang, Hyun Min Salvi, Sejal Meng, Qingchang Shen, Hua Pasham, Divya Bhamidipati, Sravya Kottapalli, Kavya Arnett, Donna K. Ashley-Koch, Allison Auer, Paul L. Beutel, Kathleen M Bis, Joshua C. Blangero, John Bowden, Donald W. Brody, Jennifer A. Cade, Brian E. Chen, Yii-Der Ida Cho, Michael H. Curran, Joanne E. Fornage, Myriam Freedman, Barry I. Fingerlin, Tasha Gelb, Bruce D. Hou, Lifang Hung, Yi-Jen Kane, John P Kaplan, Robert Kim, Wonji Loos, Ruth J.F. Marcus, Gregory M Mathias, Rasika A. McGarvey, Stephen T. Montgomery, Courtney Naseri, Take Nouraie, S. Mehdi Preuss, Michael H. Palmer, Nicholette D. Peyser, Patricia A. Raffield, Laura M. Ratan, Aakrosh Redline, Susan Reupena, Sefuiva Rotter, Jerome I. Rich, Stephen S. Rienstra, Michiel Ruczinski, Ingo Sankaran, Vijay G. Schwartz, David A. Seidman, Christine E. Seidman, Jonathan G. Silverman, Edwin K. Smith, Jennifer A. Stilp, Adrienne Taylor, Kent D. Telen, Marilyn J. Weiss, Scott T. Williams, L. Keoki Wu, Baojun Yanek, Lisa R. Zhang, Yingze Lasky-Su, Jessica Gingras, Marie Claude Dutcher, Susan K. Eichler, Evan E. Gabriel, Stacey Germer, Soren Kim, Ryan Viaud-Martinez, Karine A. Nickerson, Deborah A. Luo, James Reiner, Alex Gibbs, Richard A Boerwinkle, Eric Abecasis, Goncalo Sedlazeck, Fritz J bioRxiv Article 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 hemotologic 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. Cold Spring Harbor Laboratory 2023-01-25 /pmc/articles/PMC9900832/ /pubmed/36747810 http://dx.doi.org/10.1101/2023.01.25.525428 Text en https://creativecommons.org/licenses/by-nd/4.0/This work is licensed under a Creative Commons Attribution-NoDerivatives 4.0 International License (https://creativecommons.org/licenses/by-nd/4.0/) , which allows reusers to copy and distribute the material in any medium or format in unadapted form only, and only so long as attribution is given to the creator. The license allows for commercial use.
spellingShingle Article
Jun, Goo
English, Adam C
Metcalf, Ginger A
Yang, Jianzhi
Chaisson, Mark JP
Pankratz, Nathan
Menon, Vipin K
Salerno, William J
Krasheninina, Olga
Smith, Albert V
Lane, John A
Blackwell, Tom
Kang, Hyun Min
Salvi, Sejal
Meng, Qingchang
Shen, Hua
Pasham, Divya
Bhamidipati, Sravya
Kottapalli, Kavya
Arnett, Donna K.
Ashley-Koch, Allison
Auer, Paul L.
Beutel, Kathleen M
Bis, Joshua C.
Blangero, John
Bowden, Donald W.
Brody, Jennifer A.
Cade, Brian E.
Chen, Yii-Der Ida
Cho, Michael H.
Curran, Joanne E.
Fornage, Myriam
Freedman, Barry I.
Fingerlin, Tasha
Gelb, Bruce D.
Hou, Lifang
Hung, Yi-Jen
Kane, John P
Kaplan, Robert
Kim, Wonji
Loos, Ruth J.F.
Marcus, Gregory M
Mathias, Rasika A.
McGarvey, Stephen T.
Montgomery, Courtney
Naseri, Take
Nouraie, S. Mehdi
Preuss, Michael H.
Palmer, Nicholette D.
Peyser, Patricia A.
Raffield, Laura M.
Ratan, Aakrosh
Redline, Susan
Reupena, Sefuiva
Rotter, Jerome I.
Rich, Stephen S.
Rienstra, Michiel
Ruczinski, Ingo
Sankaran, Vijay G.
Schwartz, David A.
Seidman, Christine E.
Seidman, Jonathan G.
Silverman, Edwin K.
Smith, Jennifer A.
Stilp, Adrienne
Taylor, Kent D.
Telen, Marilyn J.
Weiss, Scott T.
Williams, L. Keoki
Wu, Baojun
Yanek, Lisa R.
Zhang, Yingze
Lasky-Su, Jessica
Gingras, Marie Claude
Dutcher, Susan K.
Eichler, Evan E.
Gabriel, Stacey
Germer, Soren
Kim, Ryan
Viaud-Martinez, Karine A.
Nickerson, Deborah A.
Luo, James
Reiner, Alex
Gibbs, Richard A
Boerwinkle, Eric
Abecasis, Goncalo
Sedlazeck, Fritz J
Structural variation across 138,134 samples in the TOPMed consortium
title Structural variation across 138,134 samples in the TOPMed consortium
title_full Structural variation across 138,134 samples in the TOPMed consortium
title_fullStr Structural variation across 138,134 samples in the TOPMed consortium
title_full_unstemmed Structural variation across 138,134 samples in the TOPMed consortium
title_short Structural variation across 138,134 samples in the TOPMed consortium
title_sort structural variation across 138,134 samples in the topmed consortium
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9900832/
https://www.ncbi.nlm.nih.gov/pubmed/36747810
http://dx.doi.org/10.1101/2023.01.25.525428
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