Understanding the genetic history of the Malay and Orang Asli populations in Peninsular Malaysia by killer cell immunolobulin-like receptors (KIR)

Extensive diversity of killer cell immunoglobulin-like receptor (KIR) genes among diverse populations has made these immune genes become a potential anthropological marker. The variations of KIR allotypes between two randomly selected individuals are also useful in individual identification. Here...

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Main Author:	Abidin, Nur Waliyuddin Hanis Zainal
Format:	Thesis
Language:	English
Published:	2018
Subjects:	R Medicine (General)
Online Access:	http://eprints.usm.my/47459/1/Dr.%20Nur%20Waliyuddin%20Hanis-24%20pages.pdf
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spelling	my-usm-ep.474592020-10-08T05:35:50Z Understanding the genetic history of the Malay and Orang Asli populations in Peninsular Malaysia by killer cell immunolobulin-like receptors (KIR) 2018 Abidin, Nur Waliyuddin Hanis Zainal R Medicine (General) Extensive diversity of killer cell immunoglobulin-like receptor (KIR) genes among diverse populations has made these immune genes become a potential anthropological marker. The variations of KIR allotypes between two randomly selected individuals are also useful in individual identification. Here, we genotyped KIR genes content and allelic polymorphisms for the first time for Malay and Orang Asli (OA) populations in Peninsular Malaysia using polymerase chain reactionsequence specific primers (PCR-SSP), next-generation sequencing (NGS) and finally optimized by Sanger typing method. A total of 333 individuals representing 10 Malay subethnic groups (Aceh, Banjar, Bugis, Jawa, Champa, Kedah, Kelantan, Mandailing, Minangkabau and Patani) and 167 individuals from six OA subgroups (Batek, Kensiu, Lanoh, Che Wong, Semai and Orang Kanaq) have participated in this research. Fourty KIR genotypes were observed among Malays and 25 genotypes in OA populations. Generally, the Malays having homogenous haplotype profile with slightly high frequencies of haplotype A, whereas OA are heterogeneous with various genotypes and wide range of haplotypes. Based on the principal component analysis, the Malay subethnic groups are located between the Chinese, Indian and Orang Asli populations. The Semang subgroups show genetic affinity toward the Australian Aborigines, Papuan, Indian and African populations. They shared several unique genotypes (AB6, BB71, BB73 and BB159) and have high frequencies ofHaplotype B, which could be speculated as general features of ancient populations. The Senoi demonstrated high frequency of haplotype A, and expressing hybrid phenotypes between Indo-China tribes and Semang population. In contrast, Orang Kanaq, the only Proto-Malay subgroup studied is significantly different from both related Taiwanese/Chinese and neighboring Malayo-Polynesian speaking populations and show evidence of becoming a distinct population. The NGS has successfully characterized 302 different allotypes of seven studied KIR genes among Malay and OA populations. KIR2DL1, KIR2DL4, and KIR3DL3 genes show less allelic variations and in favor on particular allele, which possibly being affected by natural selection and creates selective sweep. In addition, KIR2DS4, KIR3DL1, KIR3DL2 and KIR2DL3 are highly polymorphic genes with considerable number of alleles discovered, suggesting that these genes evolved on balanced selection. The KIR3DL2 gene could be the best marker for population studies, as it comprises signature alleles (KIR3DL2001 and 002) that support the theory of modern human migration. Comprehensive datasets generated from this research demonstrate the value of KIR genes content and allelic polymorphisms in elucidating genetic relationships between the Malays and OA with other world populations. 2018 Thesis http://eprints.usm.my/47459/ http://eprints.usm.my/47459/1/Dr.%20Nur%20Waliyuddin%20Hanis-24%20pages.pdf application/pdf en public masters Universiti Sains Malaysia Pusat Pengajian Sains Perubatan
institution	Universiti Sains Malaysia
collection	USM Institutional Repository
language	English
topic	R Medicine (General)
spellingShingle	R Medicine (General) Abidin, Nur Waliyuddin Hanis Zainal Understanding the genetic history of the Malay and Orang Asli populations in Peninsular Malaysia by killer cell immunolobulin-like receptors (KIR)
description	Extensive diversity of killer cell immunoglobulin-like receptor (KIR) genes among diverse populations has made these immune genes become a potential anthropological marker. The variations of KIR allotypes between two randomly selected individuals are also useful in individual identification. Here, we genotyped KIR genes content and allelic polymorphisms for the first time for Malay and Orang Asli (OA) populations in Peninsular Malaysia using polymerase chain reactionsequence specific primers (PCR-SSP), next-generation sequencing (NGS) and finally optimized by Sanger typing method. A total of 333 individuals representing 10 Malay subethnic groups (Aceh, Banjar, Bugis, Jawa, Champa, Kedah, Kelantan, Mandailing, Minangkabau and Patani) and 167 individuals from six OA subgroups (Batek, Kensiu, Lanoh, Che Wong, Semai and Orang Kanaq) have participated in this research. Fourty KIR genotypes were observed among Malays and 25 genotypes in OA populations. Generally, the Malays having homogenous haplotype profile with slightly high frequencies of haplotype A, whereas OA are heterogeneous with various genotypes and wide range of haplotypes. Based on the principal component analysis, the Malay subethnic groups are located between the Chinese, Indian and Orang Asli populations. The Semang subgroups show genetic affinity toward the Australian Aborigines, Papuan, Indian and African populations. They shared several unique genotypes (AB6, BB71, BB73 and BB159) and have high frequencies ofHaplotype B, which could be speculated as general features of ancient populations. The Senoi demonstrated high frequency of haplotype A, and expressing hybrid phenotypes between Indo-China tribes and Semang population. In contrast, Orang Kanaq, the only Proto-Malay subgroup studied is significantly different from both related Taiwanese/Chinese and neighboring Malayo-Polynesian speaking populations and show evidence of becoming a distinct population. The NGS has successfully characterized 302 different allotypes of seven studied KIR genes among Malay and OA populations. KIR2DL1, KIR2DL4, and KIR3DL3 genes show less allelic variations and in favor on particular allele, which possibly being affected by natural selection and creates selective sweep. In addition, KIR2DS4, KIR3DL1, KIR3DL2 and KIR2DL3 are highly polymorphic genes with considerable number of alleles discovered, suggesting that these genes evolved on balanced selection. The KIR3DL2 gene could be the best marker for population studies, as it comprises signature alleles (KIR3DL2001 and 002) that support the theory of modern human migration. Comprehensive datasets generated from this research demonstrate the value of KIR genes content and allelic polymorphisms in elucidating genetic relationships between the Malays and OA with other world populations.
format	Thesis
qualification_level	Master's degree
author	Abidin, Nur Waliyuddin Hanis Zainal
author_facet	Abidin, Nur Waliyuddin Hanis Zainal
author_sort	Abidin, Nur Waliyuddin Hanis Zainal
title	Understanding the genetic history of the Malay and Orang Asli populations in Peninsular Malaysia by killer cell immunolobulin-like receptors (KIR)
title_short	Understanding the genetic history of the Malay and Orang Asli populations in Peninsular Malaysia by killer cell immunolobulin-like receptors (KIR)
title_full	Understanding the genetic history of the Malay and Orang Asli populations in Peninsular Malaysia by killer cell immunolobulin-like receptors (KIR)
title_fullStr	Understanding the genetic history of the Malay and Orang Asli populations in Peninsular Malaysia by killer cell immunolobulin-like receptors (KIR)
title_full_unstemmed	Understanding the genetic history of the Malay and Orang Asli populations in Peninsular Malaysia by killer cell immunolobulin-like receptors (KIR)
title_sort	understanding the genetic history of the malay and orang asli populations in peninsular malaysia by killer cell immunolobulin-like receptors (kir)
granting_institution	Universiti Sains Malaysia
granting_department	Pusat Pengajian Sains Perubatan
publishDate	2018
url	http://eprints.usm.my/47459/1/Dr.%20Nur%20Waliyuddin%20Hanis-24%20pages.pdf
_version_	1747821781879619584

Understanding the genetic history of the Malay and Orang Asli populations in Peninsular Malaysia by killer cell immunolobulin-like receptors (KIR)

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