Copy number variations of Orang Asli’ (Negrito) from Peninsular Malaysia / Siti Shuhada Mokhtar

Copy number variation (CNV) has been acknowledged as a major contributor to the human genome diversity. This variability covers approximately about 15% of the entire human genome. To date, it is reported that CNV plays an important role in the association of common and complex diseases and also in d...

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Main Author:	Mokhtar, Siti Shuhada
Format:	Thesis
Language:	English
Published:	2015
Online Access:	http://ir.uitm.edu.my/id/eprint/18374/ http://ir.uitm.edu.my/id/eprint/18374/2/TM_SITI%20SHUHADA%20MOKHTAR%20MD%2015_5.pdf

id	uitm-18374
recordtype	eprints
spelling	uitm-183742019-02-19T08:09:50Z http://ir.uitm.edu.my/id/eprint/18374/ Copy number variations of Orang Asli’ (Negrito) from Peninsular Malaysia / Siti Shuhada Mokhtar Mokhtar, Siti Shuhada Copy number variation (CNV) has been acknowledged as a major contributor to the human genome diversity. This variability covers approximately about 15% of the entire human genome. To date, it is reported that CNV plays an important role in the association of common and complex diseases and also in determining the phenotypes. Nevertheless, CNV data from diverse populations is still limited and not saturated especially population from South East Asia. This study represents the first investigation of CNV in the indigenous populations from Peninsular Malaysia, of particular interest, the Negrito. Ninety-seven Negrito samples were recruited, of which 50 unrelated Negrito samples were genotyped using the Affymetrix SNP 6.0 microarray. CNVs were then called by two independent algorithms namely, Genotyping Console and Nexus CNV. Subsequently the CNVs being called by both algorithms were considered stringent hence included to the subsequent analyses. A total of 643 stringent CNVs were identified, comprising 217 gains and 426 losses. These stringent CNVs were then matched with the publicly available datasets including DGV, HapMap3 and SGVP, and identified 57 putative novel and Negrito specific CNVs, consisting of 28 CNVRs. These included 15 gains and 13 losses. Analysis of gene ontology revealed that genes within these CNVs were enriched in the immune system (p <0.001). In view of the small population size, relative isolation and semi-nomadic lifestyles of this community, it is speculated that these CNVs may be attributed to recent local adaptation of Negritos from Peninsular Malaysia. Nonetheless other factors such as genetic drift should not be ruled out. This study offers a preliminary effort at an extent to which rare variants shape risk of common disease. More saturated CNV map is needed and should be carried out through large-scale next generation sequencing. 2015 Thesis NonPeerReviewed text en http://ir.uitm.edu.my/id/eprint/18374/2/TM_SITI%20SHUHADA%20MOKHTAR%20MD%2015_5.pdf Mokhtar, Siti Shuhada (2015) Copy number variations of Orang Asli’ (Negrito) from Peninsular Malaysia / Siti Shuhada Mokhtar. Masters thesis, Universiti Teknologi MARA.
repository_type	Digital Repository
institution_category	Local University
institution	Universiti Teknologi MARA
building	UiTM Institutional Repository
collection	Online Access
language	English
description	Copy number variation (CNV) has been acknowledged as a major contributor to the human genome diversity. This variability covers approximately about 15% of the entire human genome. To date, it is reported that CNV plays an important role in the association of common and complex diseases and also in determining the phenotypes. Nevertheless, CNV data from diverse populations is still limited and not saturated especially population from South East Asia. This study represents the first investigation of CNV in the indigenous populations from Peninsular Malaysia, of particular interest, the Negrito. Ninety-seven Negrito samples were recruited, of which 50 unrelated Negrito samples were genotyped using the Affymetrix SNP 6.0 microarray. CNVs were then called by two independent algorithms namely, Genotyping Console and Nexus CNV. Subsequently the CNVs being called by both algorithms were considered stringent hence included to the subsequent analyses. A total of 643 stringent CNVs were identified, comprising 217 gains and 426 losses. These stringent CNVs were then matched with the publicly available datasets including DGV, HapMap3 and SGVP, and identified 57 putative novel and Negrito specific CNVs, consisting of 28 CNVRs. These included 15 gains and 13 losses. Analysis of gene ontology revealed that genes within these CNVs were enriched in the immune system (p <0.001). In view of the small population size, relative isolation and semi-nomadic lifestyles of this community, it is speculated that these CNVs may be attributed to recent local adaptation of Negritos from Peninsular Malaysia. Nonetheless other factors such as genetic drift should not be ruled out. This study offers a preliminary effort at an extent to which rare variants shape risk of common disease. More saturated CNV map is needed and should be carried out through large-scale next generation sequencing.
format	Thesis
author	Mokhtar, Siti Shuhada
spellingShingle	Mokhtar, Siti Shuhada Copy number variations of Orang Asli’ (Negrito) from Peninsular Malaysia / Siti Shuhada Mokhtar
author_facet	Mokhtar, Siti Shuhada
author_sort	Mokhtar, Siti Shuhada
title	Copy number variations of Orang Asli’ (Negrito) from Peninsular Malaysia / Siti Shuhada Mokhtar
title_short	Copy number variations of Orang Asli’ (Negrito) from Peninsular Malaysia / Siti Shuhada Mokhtar
title_full	Copy number variations of Orang Asli’ (Negrito) from Peninsular Malaysia / Siti Shuhada Mokhtar
title_fullStr	Copy number variations of Orang Asli’ (Negrito) from Peninsular Malaysia / Siti Shuhada Mokhtar
title_full_unstemmed	Copy number variations of Orang Asli’ (Negrito) from Peninsular Malaysia / Siti Shuhada Mokhtar
title_sort	copy number variations of orang asli’ (negrito) from peninsular malaysia / siti shuhada mokhtar
publishDate	2015
url	http://ir.uitm.edu.my/id/eprint/18374/ http://ir.uitm.edu.my/id/eprint/18374/2/TM_SITI%20SHUHADA%20MOKHTAR%20MD%2015_5.pdf
first_indexed	2023-09-18T23:00:23Z
last_indexed	2023-09-18T23:00:23Z
_version_	1777418133064122368

Copy number variations of Orang Asli’ (Negrito) from Peninsular Malaysia / Siti Shuhada Mokhtar

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