Novel population specific autosomal copy number variation and its functional analysis amongst Negritos from Peninsular Malaysia.

Copy number variation (CNV) has been recognized as a major contributor to human genome diversity. It plays an important role in determining phenotypes and has been associated with a number of common and complex diseases. However CNV data from diverse populations is still limited. Here we report the...

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Autores principales:	Siti Shuhada Mokhtar, Christian R Marshall, Maude E Phipps, Bhooma Thiruvahindrapuram, Anath C Lionel, Stephen W Scherer, Hoh Boon Peng
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/e4367fcc4bc249f391c65c94833a95dc
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spelling	oai:doaj.org-article:e4367fcc4bc249f391c65c94833a95dc2021-11-18T08:14:38ZNovel population specific autosomal copy number variation and its functional analysis amongst Negritos from Peninsular Malaysia.1932-620310.1371/journal.pone.0100371https://doaj.org/article/e4367fcc4bc249f391c65c94833a95dc2014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24956385/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Copy number variation (CNV) has been recognized as a major contributor to human genome diversity. It plays an important role in determining phenotypes and has been associated with a number of common and complex diseases. However CNV data from diverse populations is still limited. Here we report the first investigation of CNV in the indigenous populations from Peninsular Malaysia. We genotyped 34 Negrito genomes from Peninsular Malaysia using the Affymetrix SNP 6.0 microarray and identified 48 putative novel CNVs, consisting of 24 gains and 24 losses, of which 5 were identified in at least 2 unrelated samples. These CNVs appear unique to the Negrito population and were absent in the DGV, HapMap3 and Singapore Genome Variation Project (SGVP) datasets. Analysis of gene ontology revealed that genes within these CNVs were enriched in the immune system (GO:0002376), response to stimulus mechanisms (GO:0050896), the metabolic pathways (GO:0001852), as well as regulation of transcription (GO:0006355). Copy number gains in CNV regions (CNVRs) enriched with genes were significantly higher than the losses (P value <0.001). In view of the small population size, relative isolation and semi-nomadic lifestyles of this community, we speculate that these CNVs may be attributed to recent local adaptation of Negritos from Peninsular Malaysia.Siti Shuhada MokhtarChristian R MarshallMaude E PhippsBhooma ThiruvahindrapuramAnath C LionelStephen W SchererHoh Boon PengPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 6, p e100371 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Siti Shuhada Mokhtar Christian R Marshall Maude E Phipps Bhooma Thiruvahindrapuram Anath C Lionel Stephen W Scherer Hoh Boon Peng Novel population specific autosomal copy number variation and its functional analysis amongst Negritos from Peninsular Malaysia.
description	Copy number variation (CNV) has been recognized as a major contributor to human genome diversity. It plays an important role in determining phenotypes and has been associated with a number of common and complex diseases. However CNV data from diverse populations is still limited. Here we report the first investigation of CNV in the indigenous populations from Peninsular Malaysia. We genotyped 34 Negrito genomes from Peninsular Malaysia using the Affymetrix SNP 6.0 microarray and identified 48 putative novel CNVs, consisting of 24 gains and 24 losses, of which 5 were identified in at least 2 unrelated samples. These CNVs appear unique to the Negrito population and were absent in the DGV, HapMap3 and Singapore Genome Variation Project (SGVP) datasets. Analysis of gene ontology revealed that genes within these CNVs were enriched in the immune system (GO:0002376), response to stimulus mechanisms (GO:0050896), the metabolic pathways (GO:0001852), as well as regulation of transcription (GO:0006355). Copy number gains in CNV regions (CNVRs) enriched with genes were significantly higher than the losses (P value <0.001). In view of the small population size, relative isolation and semi-nomadic lifestyles of this community, we speculate that these CNVs may be attributed to recent local adaptation of Negritos from Peninsular Malaysia.
format	article
author	Siti Shuhada Mokhtar Christian R Marshall Maude E Phipps Bhooma Thiruvahindrapuram Anath C Lionel Stephen W Scherer Hoh Boon Peng
author_facet	Siti Shuhada Mokhtar Christian R Marshall Maude E Phipps Bhooma Thiruvahindrapuram Anath C Lionel Stephen W Scherer Hoh Boon Peng
author_sort	Siti Shuhada Mokhtar
title	Novel population specific autosomal copy number variation and its functional analysis amongst Negritos from Peninsular Malaysia.
title_short	Novel population specific autosomal copy number variation and its functional analysis amongst Negritos from Peninsular Malaysia.
title_full	Novel population specific autosomal copy number variation and its functional analysis amongst Negritos from Peninsular Malaysia.
title_fullStr	Novel population specific autosomal copy number variation and its functional analysis amongst Negritos from Peninsular Malaysia.
title_full_unstemmed	Novel population specific autosomal copy number variation and its functional analysis amongst Negritos from Peninsular Malaysia.
title_sort	novel population specific autosomal copy number variation and its functional analysis amongst negritos from peninsular malaysia.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/e4367fcc4bc249f391c65c94833a95dc
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Novel population specific autosomal copy number variation and its functional analysis amongst Negritos from Peninsular Malaysia.

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