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Reference exome data for Australian Aboriginal populations to support health-based research

Whole exome sequencing (WES) is a popular and successful technology which is widely used in both research and clinical settings. However, there is a paucity of reference data for Aboriginal Australians to underpin the translation of health-based genomic research. Here we provide a catalogue of varia...

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Autores principales: Weeks, Alexia L., D’Antoine, Heather A., McKinnon, Melita, Syn, Genevieve, Bessarab, Dawn, Brown, Ngiare, Tong, Steven Y. C., Reményi, Bo, Steer, Andrew, Gray, Lesley-Ann, Inouye, Michael, Carapetis, Jonathan R., Blackwell, Jenefer M., Lassmann, Timo
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7190730/
https://www.ncbi.nlm.nih.gov/pubmed/32350262
http://dx.doi.org/10.1038/s41597-020-0463-1
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author Weeks, Alexia L.
D’Antoine, Heather A.
McKinnon, Melita
Syn, Genevieve
Bessarab, Dawn
Brown, Ngiare
Tong, Steven Y. C.
Reményi, Bo
Steer, Andrew
Gray, Lesley-Ann
Inouye, Michael
Carapetis, Jonathan R.
Blackwell, Jenefer M.
Lassmann, Timo
author_facet Weeks, Alexia L.
D’Antoine, Heather A.
McKinnon, Melita
Syn, Genevieve
Bessarab, Dawn
Brown, Ngiare
Tong, Steven Y. C.
Reményi, Bo
Steer, Andrew
Gray, Lesley-Ann
Inouye, Michael
Carapetis, Jonathan R.
Blackwell, Jenefer M.
Lassmann, Timo
author_sort Weeks, Alexia L.
collection PubMed
description Whole exome sequencing (WES) is a popular and successful technology which is widely used in both research and clinical settings. However, there is a paucity of reference data for Aboriginal Australians to underpin the translation of health-based genomic research. Here we provide a catalogue of variants called after sequencing the exomes of 50 Aboriginal individuals from the Northern Territory (NT) of Australia and compare these to 72 previously published exomes from a Western Australian (WA) population of Martu origin. Sequence data for both NT and WA samples were processed using an ‘intersect-then-combine’ (ITC) approach, using GATK and SAMtools to call variants. A total of 289,829 variants were identified in at least one individual in the NT cohort and 248,374 variants in at least one individual in the WA cohort. Of these, 166,719 variants were present in both cohorts, whilst 123,110 variants were private to the NT cohort and 81,655 were private to the WA cohort. Our data set provides a useful reference point for genomic studies on Aboriginal Australians.
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spelling pubmed-71907302020-05-06 Reference exome data for Australian Aboriginal populations to support health-based research Weeks, Alexia L. D’Antoine, Heather A. McKinnon, Melita Syn, Genevieve Bessarab, Dawn Brown, Ngiare Tong, Steven Y. C. Reményi, Bo Steer, Andrew Gray, Lesley-Ann Inouye, Michael Carapetis, Jonathan R. Blackwell, Jenefer M. Lassmann, Timo Sci Data Data Descriptor Whole exome sequencing (WES) is a popular and successful technology which is widely used in both research and clinical settings. However, there is a paucity of reference data for Aboriginal Australians to underpin the translation of health-based genomic research. Here we provide a catalogue of variants called after sequencing the exomes of 50 Aboriginal individuals from the Northern Territory (NT) of Australia and compare these to 72 previously published exomes from a Western Australian (WA) population of Martu origin. Sequence data for both NT and WA samples were processed using an ‘intersect-then-combine’ (ITC) approach, using GATK and SAMtools to call variants. A total of 289,829 variants were identified in at least one individual in the NT cohort and 248,374 variants in at least one individual in the WA cohort. Of these, 166,719 variants were present in both cohorts, whilst 123,110 variants were private to the NT cohort and 81,655 were private to the WA cohort. Our data set provides a useful reference point for genomic studies on Aboriginal Australians. Nature Publishing Group UK 2020-04-29 /pmc/articles/PMC7190730/ /pubmed/32350262 http://dx.doi.org/10.1038/s41597-020-0463-1 Text en © The Author(s) 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver http://creativecommons.org/publicdomain/zero/1.0/ applies to the metadata files associated with this article.
spellingShingle Data Descriptor
Weeks, Alexia L.
D’Antoine, Heather A.
McKinnon, Melita
Syn, Genevieve
Bessarab, Dawn
Brown, Ngiare
Tong, Steven Y. C.
Reményi, Bo
Steer, Andrew
Gray, Lesley-Ann
Inouye, Michael
Carapetis, Jonathan R.
Blackwell, Jenefer M.
Lassmann, Timo
Reference exome data for Australian Aboriginal populations to support health-based research
title Reference exome data for Australian Aboriginal populations to support health-based research
title_full Reference exome data for Australian Aboriginal populations to support health-based research
title_fullStr Reference exome data for Australian Aboriginal populations to support health-based research
title_full_unstemmed Reference exome data for Australian Aboriginal populations to support health-based research
title_short Reference exome data for Australian Aboriginal populations to support health-based research
title_sort reference exome data for australian aboriginal populations to support health-based research
topic Data Descriptor
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7190730/
https://www.ncbi.nlm.nih.gov/pubmed/32350262
http://dx.doi.org/10.1038/s41597-020-0463-1
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