A map of copy number variations in Chinese populations.

It has been shown that the human genome contains extensive copy number variations (CNVs). Investigating the medical and evolutionary impacts of CNVs requires the knowledge of locations, sizes and frequency distribution of them within and between populations. However, CNV study of Chinese minorities,...

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Autores principales:	Haiyi Lou, Shilin Li, Yajun Yang, Longli Kang, Xin Zhang, Wenfei Jin, Bailin Wu, Li Jin, Shuhua Xu
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/2ede9c6450094eba80647c303aaab264
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spelling	oai:doaj.org-article:2ede9c6450094eba80647c303aaab2642021-11-18T07:34:49ZA map of copy number variations in Chinese populations.1932-620310.1371/journal.pone.0027341https://doaj.org/article/2ede9c6450094eba80647c303aaab2642011-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22087296/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203It has been shown that the human genome contains extensive copy number variations (CNVs). Investigating the medical and evolutionary impacts of CNVs requires the knowledge of locations, sizes and frequency distribution of them within and between populations. However, CNV study of Chinese minorities, which harbor the majority of genetic diversity of Chinese populations, has been underrepresented considering the same efforts in other populations. Here we constructed, to our knowledge, a first CNV map in seven Chinese populations representing the major linguistic groups in China with 1,440 CNV regions identified using Affymetrix SNP 6.0 Array. Considerable differences in distributions of CNV regions between populations and substantial population structures were observed. We showed that ∼35% of CNV regions identified in minority ethnic groups are not shared by Han Chinese population, indicating that the contribution of the minorities to genetic architecture of Chinese population could not be ignored. We further identified highly differentiated CNV regions between populations. For example, a common deletion in Dong and Zhuang (44.4% and 50%), which overlaps two keratin-associated protein genes contributing to the structure of hair fibers, was not observed in Han Chinese. Interestingly, the most differentiated CNV deletion between HapMap CEU and YRI containing CCL3L1 gene reported in previous studies was also the highest differentiated regions between Tibetan and other populations. Besides, by jointly analyzing CNVs and SNPs, we found a CNV region containing gene CTDSPL were in almost perfect linkage disequilibrium between flanking SNPs in Tibetan while not in other populations except HapMap CHD. Furthermore, we found the SNP taggability of CNVs in Chinese populations was much lower than that in European populations. Our results suggest the necessity of a full characterization of CNVs in Chinese populations, and the CNV map we constructed serves as a useful resource in further evolutionary and medical studies.Haiyi LouShilin LiYajun YangLongli KangXin ZhangWenfei JinBailin WuLi JinShuhua XuPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 11, p e27341 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Haiyi Lou Shilin Li Yajun Yang Longli Kang Xin Zhang Wenfei Jin Bailin Wu Li Jin Shuhua Xu A map of copy number variations in Chinese populations.
description	It has been shown that the human genome contains extensive copy number variations (CNVs). Investigating the medical and evolutionary impacts of CNVs requires the knowledge of locations, sizes and frequency distribution of them within and between populations. However, CNV study of Chinese minorities, which harbor the majority of genetic diversity of Chinese populations, has been underrepresented considering the same efforts in other populations. Here we constructed, to our knowledge, a first CNV map in seven Chinese populations representing the major linguistic groups in China with 1,440 CNV regions identified using Affymetrix SNP 6.0 Array. Considerable differences in distributions of CNV regions between populations and substantial population structures were observed. We showed that ∼35% of CNV regions identified in minority ethnic groups are not shared by Han Chinese population, indicating that the contribution of the minorities to genetic architecture of Chinese population could not be ignored. We further identified highly differentiated CNV regions between populations. For example, a common deletion in Dong and Zhuang (44.4% and 50%), which overlaps two keratin-associated protein genes contributing to the structure of hair fibers, was not observed in Han Chinese. Interestingly, the most differentiated CNV deletion between HapMap CEU and YRI containing CCL3L1 gene reported in previous studies was also the highest differentiated regions between Tibetan and other populations. Besides, by jointly analyzing CNVs and SNPs, we found a CNV region containing gene CTDSPL were in almost perfect linkage disequilibrium between flanking SNPs in Tibetan while not in other populations except HapMap CHD. Furthermore, we found the SNP taggability of CNVs in Chinese populations was much lower than that in European populations. Our results suggest the necessity of a full characterization of CNVs in Chinese populations, and the CNV map we constructed serves as a useful resource in further evolutionary and medical studies.
format	article
author	Haiyi Lou Shilin Li Yajun Yang Longli Kang Xin Zhang Wenfei Jin Bailin Wu Li Jin Shuhua Xu
author_facet	Haiyi Lou Shilin Li Yajun Yang Longli Kang Xin Zhang Wenfei Jin Bailin Wu Li Jin Shuhua Xu
author_sort	Haiyi Lou
title	A map of copy number variations in Chinese populations.
title_short	A map of copy number variations in Chinese populations.
title_full	A map of copy number variations in Chinese populations.
title_fullStr	A map of copy number variations in Chinese populations.
title_full_unstemmed	A map of copy number variations in Chinese populations.
title_sort	map of copy number variations in chinese populations.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/2ede9c6450094eba80647c303aaab264
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A map of copy number variations in Chinese populations.

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