The risk variants have been shown to vary substantially across populations and a genetic study in a heterogeneous population might shed a new light in the disease mechanism. This preliminary study aims to determine the frequency of the serotonin transporter gene polymorphism (5-HTTLPR) in the three main ethnic groups in Malaysia and its association with bipolar disorder.
The Malay people are an important ethnic composition in Southeast Asia, but their genetic make-up and population structure remain poorly studied. Here we conducted a genome-wide study of four geographical Malay populations: Peninsular Malaysian Malay (PMM), Singaporean Malay (SGM), Indonesian Malay (IDM) and Sri Lankan Malay (SLM). All the four Malay populations showed substantial admixture with multiple ancestries. We identified four major ancestral components in Malay populations: Austronesian (17%-62%), Proto-Malay (15%-31%), East Asian (4%-16%) and South Asian (3%-34%). Approximately 34% of the genetic makeup of SLM is of South Asian ancestry, resulting in its distinct genetic pattern compared with the other three Malay populations. Besides, substantial differentiation was observed between the Malay populations from the north and the south, and between those from the west and the east. In summary, this study revealed that the genetic identity of the Malays comprises a mixed entity of multiple ancestries represented by Austronesian, Proto-Malay, East Asian and South Asian, with most of the admixture events estimated to have occurred 175 to 1,500 years ago, which in turn suggests that geographical isolation and independent admixture have significantly shaped the genetic architectures and the diversity of the Malay populations.
There is a discrepancy between the results of 89 original studies and 15 meta-analyses investigating the association of MTHFR rs1801133 and rs1801131 polymorphisms with colorectal cancer (CRC) risk. We examined this hypothesis through meta-analyses of both loci and their diplotypes as well as evaluation of previous meta-analyses. The present meta-analysis showed that rs1801133 and rs1801131 might be CRC susceptibility variants in Americans and Australians and rs1801133 in Brazilians and Japanese. A strong linkage disequilibrium was observed between both loci and their diplotypes were associated with CRC risk. Evaluation of 15 meta-analyses showed a high discrepancy among their findings, mainly caused by population stratification of original studies and data analysis strategies in meta-analysis. Population stratification was more dominant in the studies from Australia, America and Brazil leading to false positive or negative results. In conclusion, these loci alone might modify the development of CRC in some ethnicities.
In this study we genotyped ABO, Rhesus, Kell, Kidd and Duffy blood group loci in DNA samples from 120 unrelated individuals representing four Malay subethnic groups living in Peninsular Malaysia (Banjar: n = 30, Jawa: n = 30, Mandailing: n = 30 and Kelantan: n = 30). Analyses were performed using commercial polymerase chain reaction-sequence specific primer (PCR-SSP) typing kits (BAG Health Care GmbH, Lich, Germany). Overall, the present study has successfully compiled blood group datasets for the four Malay subethnic groups and used the datasets for studying ancestry and health.
Hair distribution on the dorsum of phalanges of the hand was studied on 302 Chinese subjects (134 males and 168 females) randomly selected from the residents of Kota Bharu, Malaysia. Proximal phalangeal hair was seen on the dorsum of both hands in 99.3% of male subjects but in only 85.1% of female subjects. Chinese females showed a significantly lower (p < 0.05) incidence of proximal phalangeal hair on the hands than Chinese males. Comparison with other racial groups showed that Chinese females had significantly less (p < 0.05) hair on the proximal phalanges of the hands than Malay and African (Nigerian) females. The least common digital combination of proximal phalangeal hair in female subjects was the presence of proximal phalangeal hair only on the fourth digit (ring finger) and was noted in 0.6% of subjects. This has not been reported before. The frequency of middle phalangeal hair (MPH) distribution in Chinese falls between that in Malays and in Japanese which is probably explained by the fact that all these three racial groups originate from Asia. A study of digital combination of MPH in Chinese showed that the most common and the least common combinations in the Chinese differ considerably from those in other races. A total of 16 patterns of hair distribution was noted on the dorsum of the phalanges of the hands in Chinese subjects. Our study showed that though Chinese females had less digital hair on the hands than Chinese males, they showed a much larger variety of patterns of digital hair distribution than males.
In this study 200 Malay subjects (100 males and 100 females) were randomly selected from patients attending outpatient clinics of Hospital USM, Kelantan, Malaysia, to find out the incidence, density and direction of hair on the dorsum of phalanges of the hand. These features have not been studied so far in females nor has such a study been conducted in Malays. The probability of density of hair distribution among the digits of both hands showed significant correlation on proximal phalanges (p < 0.05) in both sexes. Significant correlation was not observed, however, in the middle phalangeal hair (MPH) of the hands. The direction of proximal phalangeal hair, from little finger to the thumb, showed significant changes from ulnar to radial in both sexes (p < 0.05). Identification of isolated digits, which is of medicolegal importance, would be more accurate if the direction and the density of hair on the digits are both considered together. MPH was present in 48% of males and in 33% of females studied. Comparisons with presence of MPH in other populations show that Malays are ethnically similar to other Asiatic populations.
Study site: utpatient clinics of Hospital USM, Kelantan, Malaysi
One hundred and two Southern Thai-Muslims (STM) from Nakhon Si Thammarat province were studied for HLA class I and II by SSP ARMS-PCR and PCR-SSO, respectively. The allele frequencies, haplotype frequencies, delta value and linkage disequilibrium between alleles were expressed. The most frequent alleles for HLA-A, HLA-B and HLA-C were A*24(02,03), A*11 (01,02), A*02(01,03,05-07,11): B*15(01,04-07,12,19,20), B*07(02-05), B*51(01-05)/B*52 (011,012); and Cw*07(01-03), Cw*04(01,02), Cw*08(01-03), respectively. The HLA class II alleles frequently found were DRB1*1202, DRB1*15021, DRB1*0701; DRB3*0301; DRB5* 0101; DQA1*0101, DQA1*0103, DQA1*0601; DQB1*0301, DQB1*0501, DQB1*0201; and DPB1*1301, DPB1*2301 and DPB1*0501. Two common HLA class I and II haplotypes with significant linkage disequilibrium were A*24 (02,03)-Cw*08 (01-03)-B*15 (01,04-07,12,19,20) -DRB1*1202 and A*33 (01,02)-Cw*0302-B*5801-DQB1*0201. The absence of B*27 and DRB1 *1401, the presence of A*2301 and high frequency of A*68 were observed in STM.
The HLA-A*02 subtyping in Thais was conducted and included in the 12th International Histocompatibility Workshop (12WS). A total of 81 randomized individuals previously serologically or DNA typed as A2 were studied for A2 subtypings. The subjects consisted of 32 Southern Thai-Muslims (STM) and 49 Central Thais (CT). The 12WS HLA-A*02 subtyping DNA typing kit was employed. The most common A*02 subtypes in STM were A*0203,*0201 and *0207 while they were A*0203, *0207 and *0201 in CT. A*0202, *0204, *0208, *0209, *0212, *0213, *0214, *0215, *0216 and *0217 were not found in both STM and CT. The 12WS data indicated that A*0201 was also the most frequent allele of A*2 among North-East Asians. A2 subtype study in 32 STM revealed that 2 in 8 of A*0201 showed the absence of bands at 813 bp and 705 bp with primer mix number 03A and 517A and weak reaction band with primer mix number 33A. In addition, 3 subjects with A*0201 variations have one nucleotide difference in exon 2 by sequence base typing (by MGJ. Tilanus) which will be reported separately.
Allele frequencies for the 15 STR loci in the AmpFlSTR Identifiler kit were determined and compared for the three main ethnic groups of the Malaysian population comprising 210 Malays, 219 Chinese and 209 Indians. Blood was placed on FTA paper and DNA was purified in-situ.
We report the prevalence and ethnic differences of autosomal-dominant cerebellar ataxia (ADCA) in Singapore. Amongst 204 patients with ataxia who underwent genetic testing for dentatorubral-pallidoluysian atrophy (DRPLA) and for spinocerebellar ataxias (SCA) 1, 2, 3, 6, 7, 8, 10 and 12, 58 (28.4%) patients from 36 families tested positive. SCA 3 was identified in 31 (53.4%) patients from 15 families, SCA 2 in 17 (29.3%) patients from 12 families and SCA 1 in four (6.9%) patients from four families. Other SCA subtypes were rare. SCA 2 was the only subtype identified amongst ethnic Malay and ethnic Indian families. The estimated prevalence of ADCA in Singaporean families was at least 1 : 27,000. Based on the history and ancestry of Singaporeans, our study supported a founder effect for specific SCA subtypes and the association of ethnicity-specific SCA subtypes. Our findings suggest that SCA 2 is relatively common amongst the Malay race and that priority testing for SCA 3 and SCA 2 for ethnic Chinese, and SCA 2 for ethnic Malay, may be cost effective and relevant for the region.
The D1S80 allele frequencies in 124 unrelated Malays from the Malaysian population were determined and 51 genotypes and 19 alleles were encountered. The D1S80 frequency distribution met Hardy-Weinberg expectations. The observed heterozygosity was 0.80 and the power of discrimination was 0.96.
Peninsular Malaysia is populated by the Malays, Chinese, Indians, and Orang Asli. We have analyzed 17 Y-STRs loci for 243 randomly unrelated individuals, which include 153 Malays (7 Acheh, 13 Champa, 11 Rawa, 9 Kedah, 23 Minang, 15 Bugis, 43 Kelantan, 14 Jawa, and 18 Bugis) and 90 Orang Asli [54 Semang (16 Kensiu, 13 Lanoh, 25 Bateq); 30 Senoi (21 Semai, 9 Che Wong); and 6 Proto-Malay (6 Orang Kanaq)] from selected settlements in Peninsular Malaysia using the AmpFlSTR Yfiler™ kit (Applied Biosystems™). The overall haplotype diversity is 0.9966, i.e., 0.9984 for the Malays and 0.9793 for the Orang Asli. A total of 158 haplotypes (65.02%) were individually unique. The p value and pairwise Rst analysis was calculated to show the genetic structure of the samples with other world populations (from YHRD website). Based on the Y-STR data, Champa, Acheh, Kedah, Minang, and Kelantan are clustered together. Lanoh and Kensiu (Semang) are very closely related, suggesting similar paternal ancestry. Jawa Malays and Indonesian Java, plus the Bugis Malays and Australian Aborigines shared high degree of paternal lineage affinity. This study presents data for very precious relict groups, who are the earliest inhabitants of Peninsular Malaysia.
Malays, Chinese and Indians from peninsular Malaysia; Ibans and Bidayuh from Sarawak state, Northern Borneo; and Bataks, Minangkabau and Javanese from North Sumatra, Indonesia, were subtyped for Gc (group-specific component) by polyacrylamide gel isoelectric focusing. All eight populations investigated were found to be polymorphic for three common alleles, Gc1F, Gc1S and Gc2.
In this study, 268 samples for unrelated males belonging to the five major human subpopulation groups in Ghana (Akan, Ewe, Mole-Dagbon, Ga-Dangme and Guang) were genetically characterised for 23 Y chromosome short tandem repeat (STR) loci using the Powerplex® Y23 STR kit. A total of 263 complete haplotypes were recorded of which 258 were unique. The haplotype diversity, discriminating capacity and match probability for the pooled population data were 0.9998, 0.9627 and 0.0039, respectively. The pairwise genetic distance (RST) for the Ghanaian datasets and other reference populations deposited in the Y-STR Haplotype Reference Database (YHRD) were estimated and mapped using multidimensional scaling (MDS) plot. The Guang and Ewe were significantly different from the Akan, Mole-Dagbon and Ga-Dangme. However, the five Ghanaian datasets were all plotted close together with other African populations in the MDS data mapping.
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.
The use of 21 autosomal STR loci for human identification has been gaining popularity throughout the world. It has been indicated that the forensic statistical parameters for supporting the use of 21 STR loci varied among different populations. Hitherto, such data for the diverse Malaysian populations remain unreported, rendering doubts in the court of law about its real ability for human identification in Malaysian population. Using the GlobalFiler™ Express PCR Amplification Kit, complete DNA profiles of 21 STR loci from buccal swabs of convicted Malaysian criminal (n = 570; 190 each for Malays, Chinese, and Indians) (by the year 2016-2017) were analyzed for their allele frequencies, exact test of Hardy-Weinberg equilibrium, observed and expected heterozygosity, power of discrimination, power of exclusion, match probability, and polymorphism information content. Most of the loci were found to be in the Hardy-Weinberg equilibrium after the Bonferroni correction. Being the most informative locus, SE33 demonstrated the highest power of discrimination and power of exclusion, indicating its usefulness to discriminate individuals. In contrast, TPOX had the lowest power of discrimination and power of exclusion, as well as being the less informative genetic locus for all Malaysian population studied here. The probabilities that two individuals would share the same DNA profiles among the Malaysian Malays, Chinese, and Indians, as well as in general Malaysian population, were 1.3713 × 10-25, 2.8822 × 10-25, 7.5668 × 10-26, and 1.0385 × 10-26, respectively. The results obtained here were found comparable with similar studies reported in other populations. Hence, its robustness for forensic human identification among the Malaysian populations is, therefore, statistically supported.