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HKG: an open genetic variant database of 205 Hong Kong cantonese exomes

HKG is the first fully accessible variant database for Hong Kong Cantonese, constructed from 205 novel whole-exome sequencing data. There has long been a research gap in the understanding of the genetic architecture of southern Chinese subgroups, including Hong Kong Cantonese. HKG detected 196 325 h...

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Autores principales: Ou, Min, Leung, Henry Chi-Ming, Leung, Amy Wing-Sze, Luk, Ho-Ming, Yan, Bin, Liu, Chi-Man, Tong, Tony Ming-For, Mok, Myth Tsz-Shun, Ko, Wallace Ming-Yuen, Law, Wai-Chun, Lam, Tak-Wah, Lo, Ivan Fai-Man, Luo, Ruibang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8826781/
https://www.ncbi.nlm.nih.gov/pubmed/35156024
http://dx.doi.org/10.1093/nargab/lqac005
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author Ou, Min
Leung, Henry Chi-Ming
Leung, Amy Wing-Sze
Luk, Ho-Ming
Yan, Bin
Liu, Chi-Man
Tong, Tony Ming-For
Mok, Myth Tsz-Shun
Ko, Wallace Ming-Yuen
Law, Wai-Chun
Lam, Tak-Wah
Lo, Ivan Fai-Man
Luo, Ruibang
author_facet Ou, Min
Leung, Henry Chi-Ming
Leung, Amy Wing-Sze
Luk, Ho-Ming
Yan, Bin
Liu, Chi-Man
Tong, Tony Ming-For
Mok, Myth Tsz-Shun
Ko, Wallace Ming-Yuen
Law, Wai-Chun
Lam, Tak-Wah
Lo, Ivan Fai-Man
Luo, Ruibang
author_sort Ou, Min
collection PubMed
description HKG is the first fully accessible variant database for Hong Kong Cantonese, constructed from 205 novel whole-exome sequencing data. There has long been a research gap in the understanding of the genetic architecture of southern Chinese subgroups, including Hong Kong Cantonese. HKG detected 196 325 high-quality variants with 5.93% being novel, and 25 472 variants were found to be unique in HKG compared to three Chinese populations sampled from 1000 Genomes (CHN). PCA illustrates the uniqueness of HKG in CHN, and the admixture study estimated the ancestral composition of HKG and CHN, with a gradient change from north to south, consistent with their geological distribution. ClinVar, CIViC and PharmGKB annotated 599 clinically significant variants and 360 putative loss-of-function variants, substantiating our understanding of population characteristics for future medical development. Among the novel variants, 96.57% were singleton and 6.85% were of high impact. With a good representation of Hong Kong Cantonese, we demonstrated better variant imputation using reference with the addition of HKG data, thus successfully filling the data gap in southern Chinese to facilitate the regional and global development of population genetics.
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spelling pubmed-88267812022-02-10 HKG: an open genetic variant database of 205 Hong Kong cantonese exomes Ou, Min Leung, Henry Chi-Ming Leung, Amy Wing-Sze Luk, Ho-Ming Yan, Bin Liu, Chi-Man Tong, Tony Ming-For Mok, Myth Tsz-Shun Ko, Wallace Ming-Yuen Law, Wai-Chun Lam, Tak-Wah Lo, Ivan Fai-Man Luo, Ruibang NAR Genom Bioinform Standard Article HKG is the first fully accessible variant database for Hong Kong Cantonese, constructed from 205 novel whole-exome sequencing data. There has long been a research gap in the understanding of the genetic architecture of southern Chinese subgroups, including Hong Kong Cantonese. HKG detected 196 325 high-quality variants with 5.93% being novel, and 25 472 variants were found to be unique in HKG compared to three Chinese populations sampled from 1000 Genomes (CHN). PCA illustrates the uniqueness of HKG in CHN, and the admixture study estimated the ancestral composition of HKG and CHN, with a gradient change from north to south, consistent with their geological distribution. ClinVar, CIViC and PharmGKB annotated 599 clinically significant variants and 360 putative loss-of-function variants, substantiating our understanding of population characteristics for future medical development. Among the novel variants, 96.57% were singleton and 6.85% were of high impact. With a good representation of Hong Kong Cantonese, we demonstrated better variant imputation using reference with the addition of HKG data, thus successfully filling the data gap in southern Chinese to facilitate the regional and global development of population genetics. Oxford University Press 2022-02-08 /pmc/articles/PMC8826781/ /pubmed/35156024 http://dx.doi.org/10.1093/nargab/lqac005 Text en © The Author(s) 2022. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Standard Article
Ou, Min
Leung, Henry Chi-Ming
Leung, Amy Wing-Sze
Luk, Ho-Ming
Yan, Bin
Liu, Chi-Man
Tong, Tony Ming-For
Mok, Myth Tsz-Shun
Ko, Wallace Ming-Yuen
Law, Wai-Chun
Lam, Tak-Wah
Lo, Ivan Fai-Man
Luo, Ruibang
HKG: an open genetic variant database of 205 Hong Kong cantonese exomes
title HKG: an open genetic variant database of 205 Hong Kong cantonese exomes
title_full HKG: an open genetic variant database of 205 Hong Kong cantonese exomes
title_fullStr HKG: an open genetic variant database of 205 Hong Kong cantonese exomes
title_full_unstemmed HKG: an open genetic variant database of 205 Hong Kong cantonese exomes
title_short HKG: an open genetic variant database of 205 Hong Kong cantonese exomes
title_sort hkg: an open genetic variant database of 205 hong kong cantonese exomes
topic Standard Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8826781/
https://www.ncbi.nlm.nih.gov/pubmed/35156024
http://dx.doi.org/10.1093/nargab/lqac005
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