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Human Platelet Antigen Allelic Diversity in Peninsular Malaysia

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Human Platelet Antigen Allelic Diversity in Peninsular Malaysia O RIGINAL R EP O RT Human platelet antigen allelic diversity in Peninsular Malaysia W.U.W. Syafawati, Z. Zefarina, Z. Zafarina, M.N. Hassan, M.N. Norazmi, S. Panneerchelvam, G.K. Chambers, and H.A. Edinur Human platelet antigens (HPAs) are polymorphic and each one containing six subgroups (Department of Orang Asli immunogenic glycoproteins encoded by biallelic genes on human Affairs, Malaysia: http://www.jakoa.gov.my): Semang (Batek, chromosome 17 (HPA-1 to -4 and HPA-6 to -11), chromosome Jahai, Kensiu, Kintak, Lanoh, and Mendriq), Senoi (Semai, 5 (HPA-5), and chromosome 6 (HPA-15) and expressed on the surface of platelets. In the present study, we typed seven HPA Temiar, Semoq Beri, Jahut, Che Wong, and Meh Meri), and loci (HPA-1 to -6 and HPA-15) by polymerase chain reaction Proto-Malays (Orang Kanaq, Kuala, Seletar, Jakun, Semelai, using sequence-specific primer and sequence-based typing in 166 and Temuan). blood samples representing three Orang Asli groups (Semang, Senoi, and Proto-Malays) that inhabit Peninsular Malaysia. The Semang inhabit northern parts of Peninsular Malaysia Combined with previous HPA data collected for Malay subethnic and are physically of small body size with dark skin and frizzy groups, Malays, Chinese, and Indians, our analyses showed high hair. The Semang are hunter-gatherers and numerically genetic diversity in Peninsular Malaysia, which is consistent with the smallest of all the Orang Asli groups. They arrived in multiple settlements of the region by several founding ancestors (Semang, Senoi, and Proto-Malays) in the last 50,000 years. The Peninsular Malaysia about 50,000 years ago and together gene pools of these ancient populations were then further shaped with Australian Aborigines and Papuans17 are associated with by various evolutionary pressures such as repeated founder those earliest modern humans who migrated out of Africa. effects, natural selection, and admixture with the relatively The Senoi, who inhabit the foothills and lowlands of northern recent arrivals such as Chinese, Indians, and Malay subethnic groups. Medical consequences of this genetic complexity are and central regions of Peninsular Malaysia, are estimated to also discussed, including the risks of platelet alloimmunization have arrived about 8,000 years ago and are the largest group of associated with random platelet transfusion and gestation. Orang Asli. The light-skinned and relatively tall Senoi people Immunohematology 2016;32:143–160. are linked to Austro-Asiatic agriculturists who originated from mainland Southeast Asia or South China. In contrast, Proto- Key Words: human platelet antigen, Orang Asli, Semang, Malays arrived quite recently in Peninsular Malaysia (~4,000 Senoi, Proto-Malays, Peninsular Malaysia years ago).18 They are believed to be descendants of Neolithic Austronesian voyagers who migrated out of Taiwan to islands Human platelet antigens (HPAs) are expressed on the of Southeast Asia, and Near and Remote Oceania.19 It is from surface of platelets. They are polymorphic and immunogenic this Orang Asli group that the admixed Deutero-Malays later glycoproteins encoded by the biallelic genes on human emerged. Their contemporary gene pool now contains recent chromosomes 17 (HPA-1 to -4 and HPA-6 to -11), 5 (HPA-5), minor admixture from other residents in Malaysia, including and 6 (HPA-15).1,2 HPAs are clinically relevant in transfusion Chinese and Indians.20 and gestation, since incompatibility can cause posttransfusion Overall, our present study on HPA in representative OA purpura (PTP),3 platelet transfusion refractoriness (PTR),4 groups/subgroups complements earlier studies on Malays,16 and neonatal alloimmune thrombocytopenia (NAIT).5 Chinese,16 Indians,16 and Malay subethnic groups15 and thus Collections of HPA data have been reported for many provides more fully extensive documentation of HPA allelic populations, including Europeans,6–8 Asians,9–13 Africans,1 spectra in Peninsular Malaysia for the first time. These data and Amerindians.14 Knowledge about local distributions of sets can now be subjected to a small-scale meta-analysis HPAs is useful for population and disease studies as well as for study of ancestry and used to estimate the risks of platelet estimating the risk of platelet alloimmunization. In Peninsular alloimmunization associated with random platelet transfusion Malaysia, HPA data have been collected and reported for Malay and gestation. We present the findings from this investigation subethnic groups,15 Malays,16 Chinese,16 and Indians,16 but and our comments on their significance. not for the minority indigenous peoples collectively known as Orang Asli. They are represented by three major groups with IMMUNOHEMATOLOGY, Volume 32, Number 4, 2016 143 W.U.W. Syafawati et al. Materials and Methods samples using specific discriminating oligonucleotide primers (forward: 5´-GAATATGGATCAATATGCAGTA-3´; reverse: Blood Samples 5´-AAAAGACAAAGCCAAGGA-3´) and PCR cycling condi- A total of 166 blood samples were obtained with informed tions reported by Xu et al.21 The amplified PCR products were consent from all three Orang Asli groups: Semang (Batek: then purified (QIAquick PCR Purification, QIAGEN) and N = 27, Che Wong: N = 26, and Kensiu: N = 36), Senoi (Lanoh: analyzed using agarose gel electrophoresis. The remaining N = 25 and Semai: N = 41), and Proto-Malays (Orang Kanaq: aliquots of purified PCR amplicons were sent to the DNA N = 11). The Orang Asli study samples were then split into sequencing service provided by 1st BASE Biochemicals, smaller subsamples of unrelated (u) individuals; uBatek Singapore, (Applied Biosystems 3730xl DNA analyzer, Foster (N = 17), uChe Wong (N = 14), uKensiu (N = 21), uLanoh (N = City, CA). 13), uSemai (N = 34), and uProto-Malays (N = 7). All volunteers were self-declared as having three generations lacking any Statistical Analyses admixture with other ethnicities. This study was reviewed and Allele and genotype frequencies were determined using approved by the human ethics committee of the University the following formula: Sains Malaysia [reference no. USM/JEPeM/1406217 and USM/PPP/ethics committee/2012(19)]. genotype frequency = number of genotype observed/ number of individuals and allele frequency = DNA Extraction number of allele observed/2 (number of individuals) DNA from blood samples were extracted using a kit (QIAamp DNA Mini Kit, QIAGEN, Hilden, Germany). χ2 tests were used for evaluating Hardy-Weinberg Extractions were performed according to the manufacturer’s equilibrium (HWE) in Orang Asli using the formula: instructions. The eluted DNA was quantified by spectrophotometry (NanoDrop 2000c Spectrophotometer, χ2 = ∑ [(O – E) 2/E] Thermo Scientific, Waltham, MA) and stored at –20°C until further use. where O and E are observed and expected number of genotypes, respectively. Significant departure from HWE is considered Sequence-Specific Primer Genotyping of HPA-1 to -6 at a p value <0.05.22 Genetic differentiation between pairs of and HPA-15 Loci Orang Asli subgroups and between Orang Asli and previously The polymerase chain reaction using sequence- studied Malay subethnic groups,15 Malays,16 Chinese,16 and specific primer (PCR-SSP) genotyping protocols, including Indians16 were evaluated using Fischer’s exact test in a software oligonucleotide primers and thermal cycling parameters, program (SPSS, SPSS Inc., Chicago, IL). Two data sets were reported by Kupatawintu et al.11 and Feng et al.,12 were used considered significantly different at a p value <0.05. Genetic to genotype HPA-1, -2, -4, -5, and -15, and HPA-3 and -6, relationships between Orang Asli subgroups, Malay subethnic respectively. The amplified products and DNA size markers groups, and other reference populations were studied were separated by using stained 2 percent agarose gels (SYBR using principal coordinate analysis software (Multivariate Safe, Life Technologies Corp., Singapore) and visualized using Statistical Software Package 3, Kovach Computing Services, a digital gel documentation system (Vilber Lourmat Software, Pentraeth, Isle of Anglesey, UK). The HPA frequency data VILBER, Eberhardzell, Germany). All HPA allelic scoring was for reference populations were obtained from published made by comparing band patterns for amplified HPA allele- resources6–9,13,15,16,23,24 and the IPD-HPA database.1 The specific products with a DNA size standard. probability of transfusion and pregnancy alloimmunization were calculated using the formula established by De La Vega Sequence-Based Typing of HPA-15 Elena et al.14 Our PCR-SSP typing showed an extremely high frequency of HPA-15b/b genotype in Orang Asli. Indeed, the HPA- Results 15b allele is fixed in Batek. Thus, we randomly selected 20 samples and genotyped the HPA-15 locus using sequence- The HPA genotype data for Orang Asli and their smaller based typing (SBT) as part of our verification procedure. subsamples of unrelated (u) individuals are shown in Tables 1 The HPA-15 locus was amplified from these selected DNA and 2, respectively. No significant departures from HWE were 144 IMMUNOHEMATOLOGY, Volume 32, Number 4, 2016 HPA diversity in Peninsular Malaysia Table 1. HPA genotype profiles and Hardy-Weinberg equilibrium estimations for Orang Asli subgroups Batek (N = 27) Che Wong (N = 26) Kensiu (N = 36) Lanoh (N = 25) Semai (N = 40) Orang Kanaq (N = 11) HPA O E p O E p O E p O E p O E p O E p 1a/1a 1.000 1.000 NA 1.000 1.000 NA 0.917 0.918 0.794 1.000 1.000 NA 0.976 0.976 0.937 1.000 1.000 NA 1a/1b 0.000 0.000 0.000 0.000 0.083 0.080
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