Discrepancies in angiotensin-1 converting enzyme (ACE) allele genetic susceptibility with disease etiology have been attributed to ethnic differences. We investigated ACE gene polymorphism of the multiethnic Malaysian population by utilizing nested polymerase chain reaction. Allelic frequency of 0.65 and 0.35 for I and D allele, respectively in the pooled population was comparable with other Asian populations. A significant association was found between the Malaysian ethnic groups and ACE I/D genotype. The II genotype was found at higher frequency among the Malays but a greater frequency of DD genotype among Indians.
The Prostaglandin F2alpha (PGF2alpha) receptor gene has been found to play an important role in reducing the intraocular pressure of the glaucomatous patients. Variations of the PGF2alpha receptor gene may be responsible for the differences in the response to an antiglaucoma drug, Latanoprost. A combined method of denaturing High Performance Liquid Chromatography (dHPLC) and sequencing was applied to detection of the PGF2alpha receptor gene variant among the 76 Malaysian patients with glaucoma, and a novel single nucleotide polymorphism (SNP), IVS -97A>T, was identified. According to the genotyping analysis, 36.8% of the subjects were heterozygous for the variant allele T, while 9.2% homozygous. The frequency of variant allele T was 0.28. Although with a limited number of samples, our data suggested that this polymorphism is common in the Malaysian patients with glaucoma.
Giant grouper (Epinephelus lanceolatus) is a commercially important species, but its wild population has recently been classified as vulnerable. This species has significant potential for use in aquaculture, though a greater understanding of population genetics is necessary for selective breeding programs to minimize kinship for genetically healthy individuals. High-throughput pyrosequencing of genomic DNA was used to identify and characterize novel tetra- and trinucleotide microsatellite markers in giant grouper from Sabah, Malaysia. In total, of 62,763 sequences containing simple sequence repeats (SSRs) were obtained, and 78 SSR loci were selected to possibly contain tetra- and trinucleotide repeats. Of these loci, 16 had tetra- and 8 had trinucleotide repeats, all of which exhibited polymorphisms within easily genotyped regions. A total of 143 alleles were identified with an average of 5.94 alleles per locus, with mean observed and expected heterozygosities of 0.648 and 0.620, respectively. Among of them, 15 microsatellite markers were identified without null alleles and with Hardy-Weinberg equilibrium. These alleles showed a combined non-exclusion probability of 0.01138. The probability of individual identification (PID) value combined with in descending order 12 microsatellite markers was 0.00008, which strongly suggests that the use of the microsatellite markers developed in this study in various combinations would result in a high resolution method for parentage analysis and individual identification. These markers could be used to establish a broodstock management program for giant grouper and to provide a foundation for genetic studies such as population structure, parentage analysis, and kinship selection.
Cytokines are involved in immune responses and the pathogenesis of various diseases. Allelic variations within the genes coding for various ∼30kDa cytokine protein/glycoproteins have been reported for many populations and have been the subjects of many ancestry and health analyses. In this study, we typed 22 single nucleotide polymorphisms (SNPs) in 13 cytokine genes of 165 Orang Asli individuals by using sequence specific primer-polymerase chain reaction (SSP-PCR) assay. The volunteers came from all across the Peninsular of Malaysia and belong to six Orang Asli subgroups; Batek, Kensiu, Lanoh, Che Wong, Semai and Orang Kanaq. Here we report our general findings and original genotype data and their associated analyses (Hardy-Weinberg proportions, estimation of allele and haplotype frequencies) can be found in the supplementary files and will be held at Allele Frequency Net Database (AFND).
A group of Taiwan aborigines, the Toroko, was typed for 21 classical genetic loci. This is part of an ongoing program aimed at a comprehensive study of Taiwan aborigines. In this first paper a short summary of historical, archeological, and anthropological data in the literature is made, and results of the present survey are compared with older results from other aborigine tribes. An analysis of other neighboring populations from southeast Asia has also been carried out in order to give a preliminary answer to the question of origin of Taiwanese aborigines. Fifteen populations were studied for 13 loci by tree analysis, principal components, and isolation by distance. Tree analysis and principal component analysis gave results in fairly good agreement and indicate three major population clusters: a northeast cluster (Ainu, Korea, Japan, and Ryukyu); a southeast cluster (south China, Thailand, Vietnam, Philippines, Taiwan, and Toroko); and a third cluster including Malaya and Borneo. The positions of Polynesia, Micronesia, and Melanesia are somewhat peripheral. Analysis of the tree shows some potential cases of convergence, perhaps owing to admixture, and of divergence. The analysis of isolation by distance shows that geographic propinquity is a reasonably good predictor of general similarity in this area.
1. A total of 8 samples from three natural populations and a laboratory strain of Aedes albopictus were analysed for glycerol-3-phosphate dehydrogenase phenotypes by means of horizontal starch-gel electrophoresis. 2. The electrophoretic phenotypes were governed by three codominant Gpd alleles. 3. There was low variability, with the heterozygosity in the variable samples ranging from 0.02 to 0.12. 4. The commonest allele in all the population samples was GpdB which encoded an electrophoretic band with intermediate mobility. 5. There was no temporal or spatial variation.
1. Three natural populations and a laboratory strain of Aedes albopictus were analysed for glucose phosphate isomerase by means of horizontal starch-gel electrophoresis. 2. The electrophoretic phenotypes were governed by five codominant Gpi alleles. 3. The commonest allele in all the four population samples was GpiC which encoded an electrophoretic band with intermediate mobility. 4. The distributions of GPI phenotypes were in accordance with Hardy-Weinberg expectations. 5. The four population samples could be differentiated by the presence of a unique Gpi allele or the absence of a particular Gpi allele.
A total of 870 subjects comprising 524 Chinese (from different dialect groups), 231 Malays and 115 Tamil Indians were investigated for the distribution of haptoglobin types and ABO blood groups. Haptoglobins were typed by PAG electrophoresis using discontinuous buffer system. The frequencies of Hp,1 Hp2 and Hp0 were found to be 0.330, 0.670 and 0.029 in Chinese; 0.298, 0.702 and 0.004 in Malays; and 0.167, 0.833 and 0.009 in Indians. The Hainanese had the highest frequency of Hp1 (0.375) followed by Cantonese (0.348), Teochew (0.333) and Hakkas (0.288). The distribution of all the phenotypes of haptoglobin was at equilibrium in all the population groups studied. No association of ABO blood groups was detected with the haptoglobin types. However, there was an excess of AB blood group in persons carrying Hp2 compared with those with Hp1.
In this study, we sequenced a partial segment of the mitochondrial control region from 21 proboscis monkeys of the Klias peninsula, the last large population remaining on the west coast of Sabah, Malaysia. Our results showed that this population retains substantial genetic variation, and subpopulations from different river systems in the central and southern portions of the Klias share multiple haplotypes. We also compared our data with previously generated sequences from 2 eastern populations of proboscis monkeys in Sabah and found little evidence of regional genetic structure. Based on these results, we argue that conservation efforts should focus on restoring connectivity between central and southern Klias peninsula proboscis monkeys and discuss future analyses needed to better understand the mitochondrial structure of proboscis monkeys in Sabah.
We investigated 12 X-chromosomal short tandem repeat (STR) polymorphisms in 283 unrelated Malay individuals (160 males and 123 females) living in and around Kuala Lumpur using the Investigator Argus X-12 kit. Heterozygosity among the present 12 X-STRs showed a distribution of from 55.3 to 93.5 %. The diversity values of the haplotypes constructed using four closely linked groups were all higher than 0.9865. A comparison of allelic frequency in each system and haplotype variation indicated that the nature of these X-STRs in the Malay population differed from that in East Asian, European, or African populations. Several microvariant alleles found in the Malay population were characterized and compared with known sequence data. The present data may be helpful in forensic casework such as personal identification and kinship testing in the Malay population in Malaysia.
Objective: The frequency of the HLA class II antigens (HLA DR, DQ and DP) were determined among Malay patients with systemic lupus erythematosus (SLE) to ascertain the role they play in disease susceptibility. Study design: Fifty-six Malay SLE patients on follow-up at the SLE Clinic of the National University of Malaysia Hospital, Kuala Lumpur were enrolled into the study. Controls were taken from healthy unrelated individuals, ethnically-matched. Materials and Methods: Five ml of anticoagulated blood was taken from each patient and control and DNA extracted. The HLADR, DQ and DP antigen/allele frequencies were determined by the technique of modified PCR-RFLP and statistical analysis done by Chi-square and Fischers exact test. Relative risk was determined by the odds ratio and significant p values were corrected for the number of antigens/alleles tested. Results: We found that the DR2 antigen was significantly increased among the patients (85.7%) as compared to controls (61%)(p corr=0.03, RR=3.83). As for HLA-DQA1, the allele most commonly found among the patients was *0102 (57 vs 49.2%). HLA-DQA1* 0601 was slightly decreased among the patients but this finding was insignificant. Both HLA-DQB1*0501 and 0601 were found to be increased among the patients even after correction of multiple comparisons made (p=0.0036, RR=4.56 and p=0.0048, RR=6.0, respectively). However, HLA-DQB1*0503 and 0301 was slightly decreased in the sle patients though not statistically significant. The frequency of HLA-DQB1*0201 was insignificantly increased among the patients. Limited studies on the DPB1 locus shows the uncertain role of this antigen in contributing to disease susceptibility. However, our analysis of the HLA-DPB1*0901 showed a slight increase among the patients as compared to controls but failed to remain significant after being corrected with number of comparisons made. All other HLA-DPB1 alleles exhibited similar frequencies between sle patients and controls. Conclusion: From this study we suggest that HLA DR2, DQB1*0501 and *0601 may be important genetic factors in conferring disease susceptibility in the Malay SLE population of Malaysia.
Objectives: To evaluate the frequency of HLA Class II antigens in Malays with SLE in order to determine their role in disease susceptibility and association with clinical manifestations.
Design: Cross-sectional study
Methods: Fifty-four SLE patients from Malay ethnic attending Physician Clinic at Hospital Universiti Sains Malaysia were enrolled into the study. Demographic and clinical findings were obtained from medical records. HLA typing of class II antigens were carried out using MicroSSP Class II generic (DRB/ DQB) from One Lambda Inc. Controls were from ethnically matched healthy individuals.
Results: A univariate analysis confirmed the association between HLA-DR15 with SLE compared to healthy control group; and was maintained using multiple logistic regression model (P corr = 0.002, adjusted OR = 5.513). There was a weak decrease of HLA-DR4 which was not significant after corrections for multiple comparisons made. DR7 was found to be significantly increased in patients with malar rash. There was positive association of DR15 with arthritis in patients compare to those without.
Conclusion: Our data support the role of HLA Class II genes in conferring SLE susceptibility.
Study site: Physician Clinic, Hospital Universiti Sains Malaysia (HUSM), Kelantan, Malaysia
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.
Introduction: Filipino β°-deletion is predominant among the β-thalassaemia patients in the indigenous population of Sabah, Malaysia particularly among the Kadazandusun. Individuals who co-inherit with α- and β-thalassaemia will demonstrate milder clinical symptoms with modified complete blood count (CBC) and Hb subtype parameters. HBS1L-MYB variants act as one of the key regulator of haematopoiesis and erythropoiesis and display strong association
with variation of HbF levels. Therefore, this study aims to evaluate the association between genetic variants in HBS1L-MYB with Hb subtypes level among Filipino β°-deletion carriers co-inherited with -α3.7 deletion. Methods: Filipino β°-deletion and -α3.7 deletion were identified using gap-polymerase chain reaction (PCR). A total of 34 subjects found with coinheritance of Filipino β°-deletion and -α3.7 deletion were subjected for HBS1L-MYB intergenic polymorphisms (HMIP) analysis. Hb subtypes level were quantified using BioRad Variant II Hb analyser. Genotyping of HBS1L-MYB variants rs9399137 and rs11759553 was done using own designed tetra primer ARMS-PCR. Results: The minor allele frequencies (MAF) of the two HMIP is found more than 0.05 (rs11759553, MAF=0.18 and rs9399137, MAF=0.15), indicating the significance of these variants among the study subjects. Significant difference was found between HbF level and HBS1L-MYB variant rs11759553 with p-value less than 0.05 (p=0.001). Subjects with homozygous genotype for rs11759553 (T/T) was found with higher HbF, followed by heterozygous (A/T) and wild type (A/A). rs11759553 and rs9399137 was found did not influence the level of HbA and HbA2. HMIP of rs11759553 and rs9399137 are found significant among Filipino β°-deletion carriers co-inherited with -α3.7deletion with its high minor allelic frequency and high HbF level. Strong association with HbF level was demonstrated when
coinheritance of rs11759553. Conclusion: This study demonstrates that there are significant associations between certain genetic variants in HBS1L-MYB with Hb subtypes level among Filipino β°-deletion carriers co-inherited with -α3.7 deletion.
Nine populations of three species of Nephotettix (Insecta: Hemiptera) from Peninsular Malaysia were analysed for nine enzymes comprising 11 loci. Nei's (Genetics 89, 583, 1978) genetic distance, D, between N. virescens and N. malayanus was 0.181, that between N. virescens and N. nigropictus was 0.283, and that between N. malayanus and N. nigropictus was 0.203. The genetic distance between N. nigropictus from rice plant and from the weed-grass L. hexandra at Universiti Pertanian Malaysia was 0.004 and their genetic identity was 0.996, thus indicating that this insect species fees on both host plants. The proportion of polymorphic loci and the observed heterozygosities were higher in N. nigropictus, with a wider range of host plants, than in N. virescens and N. malayanus, restricted to rice and L. hexandra, respectively.
Polymorphism in PAX9 (rs8004560), a gene responsible for craniofacial and tooth development, is often associated with Class II/Div2 malocclusion. This study aimed to detect the presence of PAX9 SNP (rs8004560) and to determine its genotype and allele distribution in Class II skeletal base malocclusion, contributed by retrognathic mandible, in the local Malaysian population. The association of PAX9 SNP (rs8004560) with Class II skeletal base malocclusion was also determined. A case control study was performed on 30 samples; 15 from Class II skeletal base malocclusion, and 15 from Class I skeletal base subject as control. Cephalometric measurements were performed prior to saliva samples collection. Genomic DNA was extracted from unstimulated saliva of all subjects, and the DNA was amplified using specific primers for marker rs8004560, followed by genotyping by sequencing. SHEsis online software was used to analyse Hardy-Weinberg Equilibrium (HWE) for cases and controls. Allelic and genotypic frequencies were compared between cases and controls. Significant difference in allele frequency was observed within the group whereby G allele was over-represented in the analysed population (p0.05). Although no genetic association between PAX9 SNP (rs8004560) with Class II skeletal base malocclusion was observed, significant difference in allele frequency observed might provide some indication in the involvement of PAX9 polymorphism in Class II skeletal base malocclusion contributed by retrognathic mandible. Further research utilising larger sample size will be required in order to determine the role of PAX9 gene in the aetiology of Class II skeletal base malocclusion observed in the local Malaysian population.