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Kevin-Tey WF, Wen WX, Bee PC, Eng HS, Ho KW, Tan SM, Anuar NA, Pung YF, Zain SM. KIR genotype and haplotype frequencies in the multi-ethnic population of Malaysia. Hum Immunol 2023; 84:172-185. [PMID: 36517321 DOI: 10.1016/j.humimm.2022.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 11/10/2022] [Accepted: 11/24/2022] [Indexed: 12/14/2022]
Abstract
Killer cell immunoglobulin-like receptors (KIR) genotype and haplotype frequencies have been reported to vary distinctly between populations, which in turn contributes to variation in the alloreactivity of natural killer (NK) cells. Utilizing the diverse KIR genes to identify suitable transplant donors would prove challenging in multi-ethnic countries, even more in resource-limited countries where KIR genotyping has not been established. In this study, we determined the KIR genotypes from 124 unrelated Malaysians consisting of the Malays, Chinese, Indians, and aboriginal people through polymerase chain reaction sequence-specific primer (PCR-SSP) genotyping and employing an expectation-maximization (EM) algorithm to assign haplotypes based on pre-established reference haplotypes. A total of 27 distinct KIR haplotypes were discerned with higher frequencies of haplotype A (55.2%) than haplotype B (44.8%). The most frequent haplotypes were cA01:tA01 (55.2%), cB01:tB01 (18.1%), and cB02:tA01 (13.3%), while the least frequent haplotypes were cB03:tB01 (1.2%), cB04:tB03 (0.4%), and cB03:tA01 (0.4%). Several haplotypes were identified to be unique to a specific ethnic group. The genotype with the highest frequency was genotype AB (71.8%), followed by AA (19.4%), and BB (8.9%). The Indians exhibited the lowest genotype AA but the highest genotype BB, whereas genotype BB was absent in the aboriginal people. Despite the limitations, the genotype and haplotypes in the Malaysian population were successfully highlighted. The identification of ethnic-specific KIR genotypes and haplotypes provides the first step to utilizing KIR in identifying suitable transplant donors to further improve the transplant outcome in the Malaysian population.
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Affiliation(s)
- Wen Fei Kevin-Tey
- Department of Pharmacology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Wei Xiong Wen
- Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Ping Chong Bee
- Department of Medicine, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Hooi Sian Eng
- Division of Nephrology, University Malaya Medical Centre, Kuala Lumpur, Malaysia
| | - Kim Wah Ho
- Department of Haematology, Hospital Ampang, Kuala Lumpur, Malaysia
| | - Sen Mui Tan
- Department of Haematology, Hospital Ampang, Kuala Lumpur, Malaysia
| | - Nur Adila Anuar
- Department of Medicine, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Yuh Fen Pung
- Division of Biomedical Science, University of Nottingham Malaysia, Semenyih, Malaysia
| | - Shamsul Mohd Zain
- Department of Pharmacology, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia.
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Hajar CGN, Md Akhir S, Zefarina Z, Riffin NSM, Tuan Mohammad TH, Hassan MN, Aziz MY, Pati S, Chambers GK, Kari ZA, Edinur HA, Che Mat NF. Distribution of 22 Single Nucleotide Polymorphisms in 13 Cytokine Genes in Malays, Chinese, and Indians in Peninsular Malaysia. Genet Test Mol Biomarkers 2022; 26:449-456. [PMID: 36166739 DOI: 10.1089/gtmb.2022.0107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Introduction: Cytokines are cell signaling glycoproteins that are particularly important in immunity and inflammatory responses. Therefore, variations, such as single nucleotide polymorphisms (SNPs), in genes encoding for cytokines may have important consequences for their roles in health. Materials and Methods: A total of 222 unrelated, healthy, and un-admixed Malays (n = 97), Chinese (n = 77), and Indians (n = 48) with a median age of 30 years old (range 21-50) were typed for 22 cytokine gene SNPs: IL-1α -889 T/C, IL-1β (-511 T/C, +3962 T/C), IL-1R pst1 1970 T/C, IL-1RA mspa1 11100 T/C, IL-4Rα +1902 G/A, IL-12 - 1188 C/A, IFN-γ +874 A/T, TGF-β (cdn 10 C/T, cdn 25 G/C), TNF-α (-308 A/G, -238 A/G) IL-2 (+166 G/T, -330 T/G), IL-4 (-1098 T/G, -590 T/C, -33 T/C), IL-6 (-174 C/G, nt565 G/A), and IL-10 (-1082 G/A, -819 C/T, -592 A/C). This involved using well-established polymerase chain reaction procedures with sequence-specific primers and restriction fragment length polymorphism methods. Results: The majority of the screened cytokine gene SNPs are polymorphic in all three ethnicities. Exceptions include TGF-β cdn 25 (G/C), IL-1β +3962 (T/C), and TNF-α -238 (A/G), which were all observed to be monomorphic in Malays, Chinese and Indians. Many of the analyzed cytokine gene SNP genotypes deviated from Hardy-Weinberg equilibrium and the three ethnic study groups were all well-separated from reference Asian, African and European populations in a principal component analysis plot. Conclusion: We successfully typed 22 SNPs in 13 cytokine genes from genetic material collected from unrelated and un-admixed Malay, Chinese and Indian individuals in Peninsular Malaysia. These new cytokine gene population datasets reveal interesting contrasts with other populations.
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Affiliation(s)
- Che Ghazali Norul Hajar
- Forensic Science Programme, School of Health Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
- Transfusion Medicine Unit, Hospital Universiti Sains Malaysia, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Suhaida Md Akhir
- Biomedicine Science Programme, School of Health Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Zulkafli Zefarina
- Transfusion Medicine Unit, Hospital Universiti Sains Malaysia, Universiti Sains Malaysia, Kelantan, Malaysia
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
| | | | | | - Mohd Nazri Hassan
- Transfusion Medicine Unit, Hospital Universiti Sains Malaysia, Universiti Sains Malaysia, Kelantan, Malaysia
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Mohd Yusmaidie Aziz
- Integrative Medicine Cluster, Advanced Medical and Dental Institute, Universiti Sains Malaysia, Pulau Pinang, Malaysia
| | | | | | - Zulhisyam Abdul Kari
- Faculty of Agro Based Industry, Universiti Malaysia Kelantan, Kelantan, Malaysia
| | - Hisham Atan Edinur
- Forensic Science Programme, School of Health Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
- Transfusion Medicine Unit, Hospital Universiti Sains Malaysia, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Nor Fazila Che Mat
- Transfusion Medicine Unit, Hospital Universiti Sains Malaysia, Universiti Sains Malaysia, Kelantan, Malaysia
- Biomedicine Science Programme, School of Health Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
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3
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Hoh BP, Deng L, Xu S. The Peopling and Migration History of the Natives in Peninsular Malaysia and Borneo: A Glimpse on the Studies Over the Past 100 years. Front Genet 2022; 13:767018. [PMID: 35154269 PMCID: PMC8829068 DOI: 10.3389/fgene.2022.767018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 01/07/2022] [Indexed: 12/05/2022] Open
Abstract
Southeast Asia (SEA) has one of the longest records of modern human habitation out-of-Africa. Located at the crossroad of the mainland and islands of SEA, Peninsular Malaysia is an important piece of puzzle to the map of peopling and migration history in Asia, a question that is of interest to many anthropologists, archeologists, and population geneticists. This review aims to revisit our understanding to the population genetics of the natives from Peninsular Malaysia and Borneo over the past century based on the chronology of the technology advancement: 1) Anthropological and Physical Characterization; 2) Blood Group Markers; 3) Protein Markers; 4) Mitochondrial and Autosomal DNA Markers; and 5) Whole Genome Analysis. Subsequently some missing gaps of the study are identified. In the later part of this review, challenges of studying the population genetics of natives will be elaborated. Finally, we conclude our review by reiterating the importance of unveiling migration history and genetic diversity of the indigenous populations as a steppingstone towards comprehending disease evolution and etiology.
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Affiliation(s)
- Boon-Peng Hoh
- Faculty of Medicine and Health Sciences, UCSI University, UCSI Hospital, Port Dickson, Malaysia
- *Correspondence: Boon-Peng Hoh,
| | - Lian Deng
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
| | - Shuhua Xu
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- Department of Liver Surgery and Transplantation Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Jiangsu Key Laboratory of Phylogenomics and Comparative Genomics, School of Life Sciences, Jiangsu Normal University, Xuzhou, China
- Henan Institute of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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4
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Sukri A, Noorizhab MNF, Teh LK, Salleh MZ. Insight of the mitochondrial genomes of the Orang Asli and Malays: The heterogeneity and the disease-associated variants. Mitochondrion 2021; 62:74-84. [PMID: 34748985 DOI: 10.1016/j.mito.2021.10.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 10/27/2021] [Accepted: 10/28/2021] [Indexed: 11/27/2022]
Abstract
Orang Asli are the oldest inhabitants in Peninsular Malaysia that forms as a national minority while the Malays are the majority. The study aimed to screen the mitochondrial genomes of the Orang Asli and the Malays to discover the disease-associated variants. A total of 99 Orang Asli from six tribes (Bateq, Cheq Wong, Orang Kanaq, Kensiu, Lanoh, and Semai) were recruited. Mitochondrial genome sequencing was conducted using a next-generation sequencing platform. Furthermore, we retrieved mitochondrial DNA sequences from the Malays for comparison. The clinical significance, pathogenicity prediction and frequency of variants were determined using online tools. Variants associated with mitochondrial diseases were detected in the 2 populations. A high frequency of variants associated with mitochondrial diseases, breast cancer, prostate cancer, and cervical cancer were detected in the Orang Asli and modern Malays. As medicine evolves to adopt prediction and prevention of diseases, this study highlights the need for intervention to adopt genomics medicine to strategise better healthcare management as a way forward for Precision Health.
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Affiliation(s)
- Asif Sukri
- Integrative Pharmacogenomics Institute, Universiti Teknologi MARA Cawangan Selangor, Puncak Alam Campus, 42300 Puncak Alam, Selangor, Malaysia
| | - Mohd Nur Fakhruzzaman Noorizhab
- Integrative Pharmacogenomics Institute, Universiti Teknologi MARA Cawangan Selangor, Puncak Alam Campus, 42300 Puncak Alam, Selangor, Malaysia; Faculty of Pharmacy, Universiti Teknologi MARA Cawangan Selangor, Puncak Alam Campus, 42300 Puncak Alam, Selangor, Malaysia
| | - Lay Kek Teh
- Integrative Pharmacogenomics Institute, Universiti Teknologi MARA Cawangan Selangor, Puncak Alam Campus, 42300 Puncak Alam, Selangor, Malaysia; Faculty of Pharmacy, Universiti Teknologi MARA Cawangan Selangor, Puncak Alam Campus, 42300 Puncak Alam, Selangor, Malaysia
| | - Mohd Zaki Salleh
- Integrative Pharmacogenomics Institute, Universiti Teknologi MARA Cawangan Selangor, Puncak Alam Campus, 42300 Puncak Alam, Selangor, Malaysia.
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5
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Tao S, Kichula KM, Harrison GF, Farias TDJ, Palmer WH, Leaton LA, Hajar CGN, Zefarina Z, Edinur HA, Zhu F, Norman PJ. The combinatorial diversity of KIR and HLA class I allotypes in Peninsular Malaysia. Immunology 2021; 162:389-404. [PMID: 33283280 PMCID: PMC7968402 DOI: 10.1111/imm.13289] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/18/2020] [Accepted: 11/21/2020] [Indexed: 12/16/2022] Open
Abstract
Killer cell immunoglobulin-like receptors (KIRs) interact with polymorphic human leucocyte antigen (HLA) class I molecules, modulating natural killer (NK) cell functions and affecting both the susceptibility and outcome of immune-mediated diseases. The KIR locus is highly diverse in gene content, copy number and allelic polymorphism within individuals and across geographical populations. To analyse currently under-represented Asian and Pacific populations, we investigated the combinatorial diversity of KIR and HLA class I in 92 unrelated Malay and 75 Malaysian Chinese individuals from the Malay Peninsula. We identified substantial allelic and structural diversity of the KIR locus in both populations and characterized novel variations at each analysis level. The Malay population is more diverse than Malay Chinese, likely representing a unique history including admixture with immigrating populations spanning several thousand years. Characterizing the Malay population are KIR haplotypes with large structural variants present in 10% individuals, and KIR and HLA alleles previously identified in Austronesian populations. Despite the differences in ancestries, the proportion of HLA allotypes that serve as KIR ligands is similar in each population. The exception is a significantly reduced frequency of interactions of KIR2DL1 with C2+ HLA-C in the Malaysian Chinese group, caused by the low frequency of C2+ HLA. One likely implication is a greater protection from preeclampsia, a pregnancy disorder associated with KIR2DL1, which shows higher incidence in the Malay than in the Malaysian Chinese. This first complete, high-resolution, characterization of combinatorial diversity of KIR and HLA in Malaysians will form a valuable reference for future clinical and population studies.
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Affiliation(s)
- Sudan Tao
- Division of Biomedical Informatics and Personalized MedicineDepartment of Immunology and MicrobiologyUniversity of Colorado Anschutz Medical CampusAuroraCOUSA
- Blood Center of Zhejiang ProvinceKey Laboratory of Blood Safety Research of Zhejiang ProvinceHangzhouZhejiangChina
| | - Katherine M. Kichula
- Division of Biomedical Informatics and Personalized MedicineDepartment of Immunology and MicrobiologyUniversity of Colorado Anschutz Medical CampusAuroraCOUSA
| | - Genelle F. Harrison
- Division of Biomedical Informatics and Personalized MedicineDepartment of Immunology and MicrobiologyUniversity of Colorado Anschutz Medical CampusAuroraCOUSA
| | - Ticiana Della Justina Farias
- Division of Biomedical Informatics and Personalized MedicineDepartment of Immunology and MicrobiologyUniversity of Colorado Anschutz Medical CampusAuroraCOUSA
| | - William H. Palmer
- Division of Biomedical Informatics and Personalized MedicineDepartment of Immunology and MicrobiologyUniversity of Colorado Anschutz Medical CampusAuroraCOUSA
| | - Laura Ann Leaton
- Division of Biomedical Informatics and Personalized MedicineDepartment of Immunology and MicrobiologyUniversity of Colorado Anschutz Medical CampusAuroraCOUSA
| | | | - Zulkafli Zefarina
- School of Medical SciencesUniversiti Sains Malaysia, Health CampusKelantanMalaysia
| | - Hisham Atan Edinur
- School of Health SciencesUniversiti Sains Malaysia, Health CampusKelantanMalaysia
| | - Faming Zhu
- Blood Center of Zhejiang ProvinceKey Laboratory of Blood Safety Research of Zhejiang ProvinceHangzhouZhejiangChina
| | - Paul J. Norman
- Division of Biomedical Informatics and Personalized MedicineDepartment of Immunology and MicrobiologyUniversity of Colorado Anschutz Medical CampusAuroraCOUSA
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6
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Hajar CGN, Zefarina Z, Md. Riffin NS, Tuan Mohammad TH, Hassan MN, Poonachi P, Safuan S, ElGhazali G, Chambers GK, Edinur HA. Extended blood group profiles for Malays, Chinese, and Indians in Peninsular Malaysia. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2020. [DOI: 10.1186/s43042-020-00096-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Blood group antigens are immunogenic polymorphic molecules presented on the surface of RBCs. This study aimed to determine extended blood group profiles (ABO, Rhesus, Kell, Kidd, Duffy, MNS, Cartwright, Dombrock, Colton, Lutheran, and Vel) in Malays, Chinese, and Indians in Peninsular Malaysia.
Results
Here, ABO Type O, DCCee, MNs, and Fy (a+b−) were the most frequent major blood group phenotypes in all three ethnic groups. Other minor blood group systems distributed differently across these ethnic groups, except for the Kell, Lutheran, Cartwright, and Vel blood group systems, where only K−k+, Lu (8+14), Yt (a+b−), and Vel (+) phenotypes were observed. Exact tests of population differentiation generally showed no significant differences between Malays included in the present study vs. other ethnically similar datasets from previous surveys. However, many significant differences were recorded in comparison between blood group datasets from ethnically unrelated populations (Malays vs. Chinese vs. Indians) especially for Rhesus, Kidd, and Duffy blood group systems. A Principal component analysis (PCA) plot showed that population groups from the Peninsular Malaysia map closely together as compared with population groups from other geographical regions.
Conclusions
Overall, our present study has successfully provided an extended blood group profiles for Malays, Chinese, and Indians in Peninsular Malaysia. These new blood group datasets can be used as guidelines for donor recruitment and as reference standards for studying diseases associated with blood group systems.
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7
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Siamoglou S, Koromina M, Moy FM, Mitropoulou C, Patrinos GP, Vasileiou K. What Do Students in Pharmacy and Medicine Think About Pharmacogenomics and Personalized Medicine Education? Awareness, Attitudes, and Perceptions in Malaysian Health Sciences. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2020; 25:52-59. [PMID: 33170085 DOI: 10.1089/omi.2020.0178] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
This study reports on the attitudes and perceptions toward pharmacogenomics (PGx) and personalized medicine (PM) education among pharmacy and medical students in Malaysian health sciences. Importantly, the survey was developed through a codesign approach, with field pretesting/design with users before the actual survey, and based on collaboration between institutions in Greece and Malaysia. The study addressed eight key areas of interest to education in health sciences: (1) General awareness about genetics and PGx, (2) Attitude toward genetic testing usefulness, (3) Benefits of direct-to-consumer personal genome testing as a "diagnostic" tool, (4) Concerns (risks) about genetics, (5) Effectiveness of genetic testing in PM, (6) Benefits of PGx on disease management, (7) Benefits of PGx on drug management, and (8) Attitudes toward genetic testing public endorsement. We observed that Malaysian students appear aware of the term PGx, but there are areas of critical knowledge gap such as the need for greater familiarity with the concept of PGx implementation science, and the availability of genetic testing in clinical practice. This is one of the first studies on perceptions and attitudes toward PGx testing in Southeast Asia. The present findings provide a map of the views and perspectives of medicine and pharmacy students regarding PGx and implementation of PM in Malaysia and should assist toward facilitating the integration of genomics into the medical decision-making process. To this end, it is necessary to enhance collaboration between universities, health care institutions, and governing bodies to incorporate further training and additional education topics related to PGx and genetic testing. This is the first study that assesses the level of PGx and genomics knowledge of pharmacy and medicine students in Southeast Asia, Malaysia in particular, and thus paves the way to guide future global PGx implementation science.
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Affiliation(s)
- Stavroula Siamoglou
- Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece
| | - Maria Koromina
- Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece
| | - Foong-Ming Moy
- Department of Social and Preventive Medicine, Faculty of Medicine, Julius Centre University of Malaya, Kuala Lumpur, Malaysia
| | | | - George P Patrinos
- Department of Pharmacy, School of Health Sciences, University of Patras, Patras, Greece.,Department of Pathology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates.,Zayed Bin Sultan Center for Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
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8
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Hakim HM, Khan HO, Ismail SA, Lalung J, Kofi AE, Abdullah MT, Chambers GK, Edinur HA. Dataset on 21 autosomal and two sex determining short tandem repeat loci in the Kedayan population in Borneo, Malaysia. Data Brief 2020; 31:105909. [PMID: 32642519 PMCID: PMC7334294 DOI: 10.1016/j.dib.2020.105909] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/16/2020] [Accepted: 06/17/2020] [Indexed: 11/30/2022] Open
Abstract
This data article provides population frequencies for 21 autosomal and two sex determining short tandem repeat (STR) loci in unrelated Kedayan individuals. This article is related to the research paper entitled “Forensic parameters and ancestral fraction in the Kedayan population inferred using 21 autosomal STR loci” [1] where these same data were subjected to ancestry and forensic analyses. We have collected 200 blood samples consisting of 128 male and 72 female volunteer representatives from Kedayan people residing in various parts of Borneo. All 23 STR loci were simultaneously amplified using Globalfiler™ Express PCR and amplicons were separated using an ABI 3500xl Genetic Analyzer. The STR allele calls at each locus were called using GeneMapperⓇ ID-X Software v1.4, while several algorithms in Arlequin software version 3.5 were used to estimate Hardy–Weinberg equilibrium (HWE) and linkage disequilibrium (LD) between pairs of STR loci.
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Affiliation(s)
- Hashom Mohd Hakim
- DNA Databank Division (D13), Criminal Investigation Department, Royal Malaysian Police, 43200, Cheras, Selangor, Malaysia.,School of Industrial Technology, Universiti Sains Malaysia, 11800, Pulau Pinang, Malaysia
| | - Hussein Omar Khan
- DNA Databank Division (D13), Criminal Investigation Department, Royal Malaysian Police, 43200, Cheras, Selangor, Malaysia
| | - Siti Afifah Ismail
- DNA Databank Division (D13), Criminal Investigation Department, Royal Malaysian Police, 43200, Cheras, Selangor, Malaysia
| | - Japareng Lalung
- School of Industrial Technology, Universiti Sains Malaysia, 11800, Pulau Pinang, Malaysia
| | - Abban Edward Kofi
- Forensic Science Programme, School of Health Sciences, Universiti Sains Malaysia, Health Campus, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Mohd Tajuddin Abdullah
- Institute of Tropical Biodiversity and Sustainable Development, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia
| | - Geoffrey Keith Chambers
- School of Biological Sciences, Victoria University of Wellington, P.O. Box 600, Wellington, New Zealand
| | - Hisham Atan Edinur
- Forensic Science Programme, School of Health Sciences, Universiti Sains Malaysia, Health Campus, 16150 Kubang Kerian, Kelantan, Malaysia.,Institute of Tropical Biodiversity and Sustainable Development, Universiti Malaysia Terengganu, 21030 Kuala Nerus, Terengganu, Malaysia.,Environmental Futures Research Institute, Griffith University, Nathan, Queensland 4111, Australia
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9
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Hajar CGN, Zefarina Z, Md Riffin NS, Mohammad THT, Hassan MN, Dafalla AM, ElGhazali G, Chambers GK, Edinur HA. Human Platelet Antigen Datasets for Malays, Chinese, and Indians in Peninsular Malaysia. Ann Lab Med 2020; 40:493-499. [PMID: 32539307 PMCID: PMC7295964 DOI: 10.3343/alm.2020.40.6.493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/07/2020] [Accepted: 05/21/2020] [Indexed: 12/05/2022] Open
Affiliation(s)
- Che Ghazali Norul Hajar
- School of Health Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian, Kelantan, Malaysia
| | - Zulkafli Zefarina
- Hospital Universiti Sains Malaysia, Universiti Sains Malaysia, Kubang Kerian, Kelantan, Malaysia
| | | | | | - Mohd Nazri Hassan
- Hospital Universiti Sains Malaysia, Universiti Sains Malaysia, Kubang Kerian, Kelantan, Malaysia
| | - Ameer Mohamed Dafalla
- HLA Laboratory, National Cancer Institute, University of Gezira, Wad Medani, Sudan, United Arab Emirates
| | - Gehad ElGhazali
- Department of Immunology, Pathology and Laboratory Medicine Services, Sheikh Khalifa Medical City, Abu Dhabi, United Arab Emirates
| | | | - Hisham Atan Edinur
- School of Health Sciences, Universiti Sains Malaysia, Health Campus, Kubang Kerian, Kelantan, Malaysia
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10
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Jamaluddin J, Mohd Khair NK, Vinodamaney SD, Othman Z, Abubakar S. Copy number variation of CCL3L1 among three major ethnic groups in Malaysia. BMC Genet 2020; 21:1. [PMID: 31900126 PMCID: PMC6942282 DOI: 10.1186/s12863-019-0803-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Accepted: 12/17/2019] [Indexed: 11/30/2022] Open
Abstract
Background C-C motif Chemokine Ligand 3 Like 1 (CCL3L1) is a multiallelic copy number variable, which plays a crucial role in immunoregulatory and hosts defense through the production of macrophage inflammatory protein (MIP)-1α. Variable range of the CCL3L1 copies from 0 to 14 copies have been documented in several different populations. However, there is still lack of report on the range of CCL3L1 copy number exclusively among Malaysians who are a multi-ethnic population. Thus, this study aims to extensively examine the distribution of CCL3L1 copy number in the three major populations from Malaysia namely Malay, Chinese and Indian. A diploid copy number of CCL3L1 for 393 Malaysians (Malay = 178, Indian = 90, and Chinese = 125) was quantified using Paralogue Ratio Tests (PRTs) and then validated with microsatellites analysis. Results To our knowledge, this is the first report on the CCL3L1 copy number that has been attempted among Malaysians and the Chinese ethnic group exhibits a diverse pattern of CCL3L1 distribution copy number from the Malay and Indian (p < 0.0001). The CCL3L1 ranged from 0 to 8 copies for both the Malay and Indian ethnic groups while 0 to 10 copies for the Chinese ethnic. Consequently, the CCL3L1 copy number among major ethnic groups in the Malaysian population is found to be significantly varied when compared to the European population (p < 0.0001). The mean/median reported for the Malay, Chinese, Indian, and European are 2.759/2.869, 3.453/3.290, 2.437/1.970 and 2.001/1.940 respectively. Conclusion This study reveals the existence of genetic variation of CCL3L1 in the Malaysian population, and suggests by examining genetic diversity on the ethnicity, and specific geographical region could help in reconstructing human evolutionary history and for the prediction of disease risk related to the CCL3L1 copy number.
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Affiliation(s)
- Jalilah Jamaluddin
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM, 43400, Serdang, Selangor, Malaysia
| | - Nur Khairina Mohd Khair
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM, 43400, Serdang, Selangor, Malaysia
| | - Shameni Devi Vinodamaney
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM, 43400, Serdang, Selangor, Malaysia
| | - Zulkefley Othman
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM, 43400, Serdang, Selangor, Malaysia
| | - Suhaili Abubakar
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM, 43400, Serdang, Selangor, Malaysia.
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Hakim HM, Khan HO, Ismail SA, Lalung J, Kofi AE, Nelson BR, Abdullah MT, Chambers GK, Edinur HA. Population data for 23 Y chromosome STR loci using the Powerplex® Y23 STR kit for the Kedayan population in Malaysia. Int J Legal Med 2020; 134:1335-1337. [PMID: 31897667 DOI: 10.1007/s00414-019-02237-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 12/11/2019] [Indexed: 11/25/2022]
Abstract
Genetic polymorphisms at 23 Y chromosome short tandem repeat (STRs) loci included in the Powerplex® Y23 PCR kit were successfully scored in 128 unrelated Kedayan individuals living in Sabah, East Malaysia. Complete haplotypes were recorded for all individuals and included 92 different types with 72 being unique to single male subjects. Three important forensic statistics were calculated from these data; haplotype diversity = 0.993, discriminating capacity = 0.719, and match probability = 0.015. The Kedayan appear to be most closely related to Malays and Filipinos in a multidimensional scaling plot and are separated from other mainland Asia populations including Thais and Hakka Han. These new data for Kedayan have been deposited in the YHRD database (accession number: YA004621). Our statistical analyses showed the reliability of Y-STR loci for geographically extended use in forensic casework and for studying human population history.
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Affiliation(s)
- Hashom Mohd Hakim
- DNA Databank Division (D13), Criminal Investigation Department, Royal Malaysia Police, 43200, Cheras, Selangor, Malaysia.
- School of Industrial Technology, Universiti Sains Malaysia, Jalan Sungai 2, 11800, Gelugor, Pulau Pinang, Malaysia.
| | - Hussein Omar Khan
- DNA Databank Division (D13), Criminal Investigation Department, Royal Malaysia Police, 43200, Cheras, Selangor, Malaysia
| | - Siti Afifah Ismail
- DNA Databank Division (D13), Criminal Investigation Department, Royal Malaysia Police, 43200, Cheras, Selangor, Malaysia
| | - Japareng Lalung
- School of Industrial Technology, Universiti Sains Malaysia, Jalan Sungai 2, 11800, Gelugor, Pulau Pinang, Malaysia
| | - Abban Edward Kofi
- Forensic Science Programme, School of Health Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia
| | - Bryan Raveen Nelson
- Institute of Tropical Biodiversity and Sustainable Development, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia
| | - Mohd Tajuddin Abdullah
- Institute of Tropical Biodiversity and Sustainable Development, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia
| | - Geoffrey Keith Chambers
- School of Biological Sciences, Victoria University of Wellington, P.O. Box 600, Wellington, New Zealand
| | - Hisham Atan Edinur
- Forensic Science Programme, School of Health Sciences, Universiti Sains Malaysia, Health Campus, 16150, Kubang Kerian, Kelantan, Malaysia.
- Institute of Tropical Biodiversity and Sustainable Development, Universiti Malaysia Terengganu, 21030, Kuala Nerus, Terengganu, Malaysia.
- Environmental Futures Research Institute, Griffith University, Nathan, Queensland, 4111, Australia.
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Hajar CGN, Zulkafli Z, Md Riffin NS, Tuan Mohammad TH, Safuan S, Nelson BR, Abdullah MT, Chambers GK, Edinur HA. Human neutrophil antigen frequency data for Malays, Chinese and Indians. Transfus Apher Sci 2019; 59:102651. [PMID: 31606336 DOI: 10.1016/j.transci.2019.09.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 09/27/2019] [Indexed: 10/25/2022]
Abstract
BACKGROUND Human neutrophil antigens (HNAs) are implicated in several clinical disorders and their allelic variations have been reported for many populations. This new study was aimed to report the genotype and alleles frequencies of HNA-1, -3, -4 and -5 loci in Malays, Chinese and Indians in Peninsular Malaysia. METHODS A total of 222 blood samples were collected from healthy, unrelated Malay, Chinese and Indian individuals. Their HNA-1, -3 and -4 and HNA-5 loci were genotyped using polymerase chain reaction-sequence specific primer (PCR-SSP) or PCR-restriction fragment length polymorphism (RFLP) assays. RESULTS All HNA loci are polymorphic, except for HNA -4. Geneotypes HNA-1a/1b, -3a/3b and -4a/4a were observed most frequently at these three loci in all three ethnic groups. In contrast, HNA-5a/5b and -5a/5a were observed as the predominant genotypes in Malays vs. Chinese and Indians, respectively. The Malays, Chinese and Indians shared HNA -3a (0.505-0.527), HNA -4a (1.000) and -5a (0.676-0.854) as the most frequent alleles. However, HNA-1a was found to be the most common in Malays (0.506) and Chinese (0.504) and HNA-1b for Indians (0.525). CONCLUSION Combined with HNA data that have been published for Malay subethnic and Orang Asli groups, this study provides the first fully comprehensive HNA dataset for populations to be found in Peninsular Malaysia. Overall, our findings provide further evidence of genetic complexity in the region. This now publicly available HNA dataset can be used as a reliable reference source for improving medical outcomes.
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Affiliation(s)
- Che Ghazali Norul Hajar
- School of Health Sciences, Universiti Sains Malaysia, Kelantan, Malaysia; Hospital Universiti Sains Malaysia, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Zefarina Zulkafli
- Hospital Universiti Sains Malaysia, Universiti Sains Malaysia, Kelantan, Malaysia; School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
| | | | | | - Sabreena Safuan
- School of Health Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Bryan Raveen Nelson
- Institute of Tropical Biodiversity and Sustainable Development, Universiti Malaysia Terengganu, Terengganu, Malaysia
| | - Mohd Tajuddin Abdullah
- Institute of Tropical Biodiversity and Sustainable Development, Universiti Malaysia Terengganu, Terengganu, Malaysia
| | | | - Hisham Atan Edinur
- School of Health Sciences, Universiti Sains Malaysia, Health Campus, Kelantan, Malaysia.
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Palittapongarnpim P, Ajawatanawong P, Viratyosin W, Smittipat N, Disratthakit A, Mahasirimongkol S, Yanai H, Yamada N, Nedsuwan S, Imasanguan W, Kantipong P, Chaiyasirinroje B, Wongyai J, Toyo-Oka L, Phelan J, Parkhill J, Clark TG, Hibberd ML, Ruengchai W, Palittapongarnpim P, Juthayothin T, Tongsima S, Tokunaga K. Evidence for Host-Bacterial Co-evolution via Genome Sequence Analysis of 480 Thai Mycobacterium tuberculosis Lineage 1 Isolates. Sci Rep 2018; 8:11597. [PMID: 30072734 PMCID: PMC6072702 DOI: 10.1038/s41598-018-29986-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 07/20/2018] [Indexed: 12/19/2022] Open
Abstract
Tuberculosis presents a global health challenge. Mycobacterium tuberculosis is divided into several lineages, each with a different geographical distribution. M. tuberculosis lineage 1 (L1) is common in the high-burden areas in East Africa and Southeast Asia. Although the founder effect contributes significantly to the phylogeographic profile, co-evolution between the host and M. tuberculosis may also play a role. Here, we reported the genomic analysis of 480 L1 isolates from patients in northern Thailand. The studied bacterial population was genetically diverse, allowing the identification of a total of 18 sublineages distributed into three major clades. The majority of isolates belonged to L1.1 followed by L1.2.1 and L1.2.2. Comparison of the single nucleotide variant (SNV) phylogenetic tree and the clades defined by spoligotyping revealed some monophyletic clades representing EAI2_MNL, EAI2_NTM and EAI6_BGD1 spoligotypes. Our work demonstrates that ambiguity in spoligotype assignment could be partially resolved if the entire DR region is investigated. Using the information to map L1 diversity across Southeast Asia highlighted differences in the dominant strain-types in each individual country, despite extensive interactions between populations over time. This finding supported the hypothesis that there is co-evolution between the bacteria and the host, and have implications for tuberculosis disease control.
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Affiliation(s)
- Prasit Palittapongarnpim
- Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, Thailand.
- National Centre for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Phahonyothin Road, Pathumthani, Thailand.
| | - Pravech Ajawatanawong
- Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, Thailand
| | - Wasna Viratyosin
- National Centre for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Phahonyothin Road, Pathumthani, Thailand
| | - Nat Smittipat
- National Centre for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Phahonyothin Road, Pathumthani, Thailand
| | - Areeya Disratthakit
- Department of Medical Sciences, Ministry of Public Health, Tiwanon Road, Nonthaburi, Thailand
| | | | - Hideki Yanai
- TB-HIV Research Foundation, Chiangrai, Thailand
- Fukujuji Hospital, Japan Anti-tuberculosis Association (JATA), Kiyose, Japan
| | - Norio Yamada
- Research Institute of Tuberculosis, JATA, Kiyose, Japan
| | - Supalert Nedsuwan
- Chiangrai Prachanukroh Hospital, Ministry of Public Health, Chiangrai, Thailand
| | - Worarat Imasanguan
- Chiangrai Prachanukroh Hospital, Ministry of Public Health, Chiangrai, Thailand
| | - Pacharee Kantipong
- Chiangrai Prachanukroh Hospital, Ministry of Public Health, Chiangrai, Thailand
| | | | | | - Licht Toyo-Oka
- Department of Human Genetics, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
| | - Jody Phelan
- London School of Hygiene and Tropical Medicine, London, UK
| | | | - Taane G Clark
- London School of Hygiene and Tropical Medicine, London, UK
| | | | - Wuthiwat Ruengchai
- Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, Thailand
| | | | - Tada Juthayothin
- National Centre for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Phahonyothin Road, Pathumthani, Thailand
| | - Sissades Tongsima
- National Centre for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Phahonyothin Road, Pathumthani, Thailand
| | - Katsushi Tokunaga
- Department of Human Genetics, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan
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SharifahNany RahayuKarmilla S, Aedrianee AR, Nur Haslindawaty AR, Nur Azeelah A, Panneerchelvam S, Norazmi MN, Zafarina Z. Paternal lineage affinity of the Malay subethnic and Orang Asli populations in Peninsular Malaysia. Int J Legal Med 2017; 132:1087-1090. [DOI: 10.1007/s00414-017-1697-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 09/20/2017] [Indexed: 10/18/2022]
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