Displaying publications 21 - 40 of 283 in total

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  1. Fulltext Classical Human Leukocyte Antigen Alleles and C4 Haplotypes Are Not Significantly Associated With Depression
    Glanville KP, Coleman JRI, Hanscombe KB, Euesden J, Choi SW, Purves KL, et al.
    Biol Psychiatry, 2020 Mar 01;87(5):419-430.
    PMID: 31570195 DOI: 10.1016/j.biopsych.2019.06.031
    BACKGROUND: The prevalence of depression is higher in individuals with autoimmune diseases, but the mechanisms underlying the observed comorbidities are unknown. Shared genetic etiology is a plausible explanation for the overlap, and in this study we tested whether genetic variation in the major histocompatibility complex (MHC), which is associated with risk for autoimmune diseases, is also associated with risk for depression.

    METHODS: We fine-mapped the classical MHC (chr6: 29.6-33.1 Mb), imputing 216 human leukocyte antigen (HLA) alleles and 4 complement component 4 (C4) haplotypes in studies from the Psychiatric Genomics Consortium Major Depressive Disorder Working Group and the UK Biobank. The total sample size was 45,149 depression cases and 86,698 controls. We tested for association between depression status and imputed MHC variants, applying both a region-wide significance threshold (3.9 × 10-6) and a candidate threshold (1.6 × 10-4).

    RESULTS: No HLA alleles or C4 haplotypes were associated with depression at the region-wide threshold. HLA-B*08:01 was associated with modest protection for depression at the candidate threshold for testing in HLA genes in the meta-analysis (odds ratio = 0.98, 95% confidence interval = 0.97-0.99).

    CONCLUSIONS: We found no evidence that an increased risk for depression was conferred by HLA alleles, which play a major role in the genetic susceptibility to autoimmune diseases, or C4 haplotypes, which are strongly associated with schizophrenia. These results suggest that any HLA or C4 variants associated with depression either are rare or have very modest effect sizes.

    Matched MeSH terms: Haplotypes
  2. Fulltext Genetic structure of the snakehead murrel, Channa striata (channidae) based on the cytochrome c oxidase subunit I gene: Influence of historical and geomorphological factors
    Jamsari AF, Jamaluddin JA, Pau TM, Siti-Azizah MN
    Genet Mol Biol, 2011 01;34(1):152-60.
    PMID: 21637559 DOI: 10.1590/S1415-47572011000100026
    Nucleotide sequences of a partial cytochrome c oxidase subunit I gene were used to assess the manner in which historical processes and geomorphological effects may have influenced genetic structuring and phylogeographic patterns in Channa striata. Assaying was based on individuals from twelve populations in four river systems, which were separated into two regions, the eastern and western, of the biodiversely rich state of Perak in central Peninsular Malaysia. In 238 specimens, a total of 368-bp sequences with ten polymorphic sites and eleven unique haplotypes were detected. Data on all the twelve populations revealed incomplete divergence due to past historical coalescence and the short period of separation. Nevertheless, SAMOVA and F(ST) revealed geographical structuring existed to a certain extent in both regions. For the eastern region, the data also showed that the upstream populations were genetically significantly different compared to the mid- and downstream ones. It is inferred that physical barriers and historical processes played a dominant role in structuring the genetic dispersal of the species. A further inference is that the Grik, Tanjung Rambutan and Sungkai are potential candidates for conservation and aquaculture programmes since they contained most of the total diversity in this area.
    Matched MeSH terms: Haplotypes
  3. Population genetic analysis of oceanic paddle crab (varuna litterata) in Thailand
    Uthamas Suppapan, Jamjun Pechsiri, Sompong O-thong, Arunrat Vanichanon, Pradit Sangthong, Verakiat Supmee
    Sains Malaysiana, 2017;46:2251-2261.
    Population genetic structure of Varuna litterata living along the coast of Thailand were examined in this study. The samples were collected from 3 coastal regions: The Andaman sea (Satun, Trang, Phang Nga), the lower Gulf of Thailand (Pattani, Songkhla, Nakhon Si Thammarat) and the upper Gulf of Thailand (Petchburi, Samut Songkram, Rayong, Trat). Intraspecific variation was determined based on partial sequences of the cytochrome oxidase subunits I gene. A total of 182 samples were collected but only 32 haplotypes were obtained from these samples. An excess of rare haplotypes indicated that the female effective population size of V. litterata living along the coast of Thailand is large. Estimated values of haplotype diversity and nucleotide diversity were 0.790 and 0.003, respectively. The AMOVA (analysis of molecular variance) and phylogenetic analysis results showed that based on genetic variation, the population of this organism was found to have 2 genetically different populations: The Andaman sea population and the Gulf of Thailand population. Genetic exchange of V. litterata among populations inhabiting along the coast of Thailand could be described by the stepping stone model. The results of neutrality tests, both Tajima's D and Fu's Fs statistics, yielded negative values (-1.992 and -26.877, respectively) and statistically significant deviation from the neutrality, indicating that the V. litterata living along the Thailand coast had experienced population expansion. Mismatch distribution analysis indicated that a possible expansion occurred 211,428 years ago during the Pleistocene glaciations period.
    Matched MeSH terms: Haplotypes
  4. Fulltext Hidden genetic diversity in snakeskin gourami, Trichopodus pectoralis (Perciformes, Osphronemidae), inferred from the mitochondrial DNA CO1 gene
    Tan MP, Amornsakun T, Siti Azizah MN, Habib A, Sung YY, Danish-Daniel M
    Mitochondrial DNA B Resour, 2019 Sep 12;4(2):2966-2969.
    PMID: 33365813 DOI: 10.1080/23802359.2019.1662741
    Eighty-four specimens collected from 13 populations from Malaysia, Thailand, and Vietnam were analysed, revealing 21 putative haplotypes with overall estimated haplotype and nucleotide diversities of 0.79 and 0.0079, respectively. High levels of diversity and an absence of founder effects were observed among populations in peninsular Malaysia. In contrast, populations from Sarawak exhibited low genetic diversity, which is a typical sign of colonies introduced from a single source. Historical translocation of Trichopodus pectoralis from Thailand to Malaysia, as well as to the Philippines, Indonesia, and Myanmar was apparent. Historical introduction of T. pectoralis from Vietnam was also detected in peninsular Malaysia.
    Matched MeSH terms: Haplotypes
  5. New scenario for speciation in the benthic dinoflagellate genus Coolia (Dinophyceae)
    Leaw CP, Tan TH, Lim HC, Teng ST, Yong HL, Smith KF, et al.
    Harmful Algae, 2016 05;55:137-149.
    PMID: 28073527 DOI: 10.1016/j.hal.2016.02.010
    In this study, inter- and intraspecific genetic diversity within the marine harmful dinoflagellate genus Coolia Meunier was evaluated using isolates obtained from the tropics to subtropics in both Pacific and Atlantic Ocean basins. The aim was to assess the phylogeographic history of the genus and to clarify the validity of established species including Coolia malayensis. Phylogenetic analysis of the D1-D2 LSU rDNA sequences identified six major lineages (L1-L6) corresponding to the morphospecies Coolia malayensis (L1), C. monotis (L2), C. santacroce (L3), C. palmyrensis (L4), C. tropicalis (L5), and C. canariensis (L6). A median joining network (MJN) of C. malayensis ITS2 rDNA sequences revealed a total of 16 haplotypes; however, no spatial genetic differentiation among populations was observed. These MJN results in conjunction with CBC analysis, rDNA phylogenies and geographical distribution analyses confirm C. malayensis as a distinct species which is globally distributed in the tropical to warm-temperate regions. A molecular clock analysis using ITS2 rDNA revealed the evolutionary history of Coolia dated back to the Mesozoic, and supports the hypothesis that historical vicariant events in the early Cenozoic drove the allopatric differentiation of C. malayensis and C. monotis.
    Matched MeSH terms: Haplotypes
  6. Fulltext Genetic association study of PDLIM5 and HTR2A variants in Malaysian subjects diagnosed with bipolar disorder; a genetic modelling approach
    Mohd Aizat Zain, Nor Zuraida Zainal, Sharmilla Kanagasundram, Zahurin Mohamed
    Neuroscience Research Notes, 2018;1(1):11-20.
    MyJurnal
    Genetic hereditary has been implicated in bipolar disorder pathogenesis. The PDLIM5 and HTR2A genes have been investigated for its association with bipolar disorder in various populations, however, the results have been conflicting. In this study, we investigate the association between bipolar disorder and the two genes of interest, PDLIM5 and HTR2A genes. We recruited 253 bipolar disorder patients (75 Malays, 104 Chinese, and 74 Indians) and 505 control individuals (198 Malays, 155 Chinese, and 152 Indians) from three ethnic groups within Malaysian population. We genotyped for 3 SNPs of the PDLIM5 (rs2433320, rs2433322 and rs2438146) and 3 SNPs of the HTR2A (rs6313, rs2070040 and rs6311). Significant associations between bipolar disorder and each of the 3 SNPs of PDLIM5 in Malays, Indians and pooled samples. However, only rs2438146 remains significant in the Malays as co-dominant (T/T vs. C/C, p=0.004, OR=0.128, 95%CI=0.031-0.524) and recessive genetic models (T/T vs. C/T+C/C, p=0.003, OR=0.122, 95%CI=0.030-0.494) after applying conservative Bonferroni correction. Haplotype analysis of 3 SNPs of PDLIM5 also showed a significant association with bipolar disorder. No association was observed between bipolar disorder and each of the 3 SNPs of HTR2A in any of the ethnicities. We conclude that PDLIM5 polymorphisms are associated with bipolar disorder in the pooled analysis. After stratification to different ethnic groups, the association remains significant in the Malay and Indian groups. The association is also supported by the significant association in haplotype analysis of PDLIM5. We also conclude there is no association between the HTR2A polymorphisms in the Malaysian population.
    Matched MeSH terms: Haplotypes
  7. Microsatellite DYS385 polymorphism among the Tai and Mon-Khmer speaking populations of Northern Thailand
    Jatupol Kampuansai, Siriwadee Chomdej
    Sains Malaysiana, 2015;44:1453-1459.
    Microsatellite DYS385 is a highly polymorphic marker in the Y chromosome. It has been used for investigating population genetic structure and personal identification in various ethnic groups of the world. This research aimed to analyze the microsatellite DYS385 polymorphism among 9 Tai and 11 Mon-Khmer speaking populations of northern Thailand. Fiftysix different haplotypes were found in 453 samples from 20 populations. Haplotype diversities and discrimination powers of populations belonging to the Tai linguistic family was higher than those of the Mon-Khmer group. Genetic affinities based on DYS385 variation do not conform to linguistic classification but a fraction of genetic divergence patterns can be explained by geographic distances.
    Matched MeSH terms: Haplotypes
  8. Fulltext Genetic assessment of the internal transcribed spacer region (ITS1.2) in Mangifera indica L. landraces
    Fazeli-Nasab B, Sayyed RZ, Farsi M, Ansari S, El-Enshasy HA
    Physiol Mol Biol Plants, 2020 Jan;26(1):107-117.
    PMID: 32158124 DOI: 10.1007/s12298-019-00732-x
    Mango (Mangifera indica) is one of the most important tropical fruits in the world. Twenty-two genotypes of native mangoes from different regions of southern Iran (Hormozgan and Kerman) were collected and analyzed for the ribosomal genes. GC content was found to be 55.5%. Fu and Li's D* test statistic (0.437), Fu and Li's F* test statistic (0.500) and Tajima's D (1.801) were positive and nonsignificant. A total of 769 positions were identified (319 with insertion or deletion including 250 polymorphic and 69 monomorphic loci; 450 loci without any insertion or deletion including 35 Singletons and 22 haplotypes). Nucleotide diversity of 0.309 and a high genetic differentiation including Chi square of 79.8; P value of 0.3605 and df value of 76 was observed among mango genotypes studied. The numerical value of the ratio dN/dS (0.45) indicated a pure selection in the examined gene and the absence of any key changes. Cluster analysis differentiated the mango used in this research (M. indica L.) into two genotypes but could not differentiate their geographical locations. The results of this study indicated that a high genetic distance exists between HajiGholam (Manojan) and Arbabi (Rodan) genotypes and showed higher genetic diversity in mango of Rodan region. Results of present study suggested that for successful breeding, the genotypes of Rodan region mango especially Arbabi mango can be used as a gene donor and ITS can be a suitable tool for genetic evaluations of inter and intra species.
    Matched MeSH terms: Haplotypes
  9. Intra- and inter-specific variation of four acetes species (crustacea: decapoda: sergestidae) sampled along the west coast of peninsular Malaysia
    Boon Yee Wong, Taranjeet Kaur Awtar Singh, Gideon Khoo, Han Kiat Alan Ong
    Sains Malaysiana, 2017;46:2393-2416.
    The intra- and inter-specific variation of Acetes shrimps were evaluated based on samples collected from in-shore catches and off-shore trawling around the west coast of Peninsular Malaysia. Species captured were identified as Acetes indicus, A. serrulatus, A. japonicus and A. sibogae. A region of the mitochondrial cytochrome c oxidase subunit I (COI) gene comprising 552 base pairs (bp) was amplified from 159 Acetes specimens. The sequence alignment analysis generated phylogenetic trees which depicted the four major clades that were consistent with the species identified morphologically. These four species varied considerably for haplotype and nucleotide diversity, with A. indicus and A. serrulatus showing different demographic histories. Furthermore, the observation of two clades in the A. indicus and A. sibogae lineages, with relatively high levels of intraspecific divergence, suggests that cryptic diversity is possibly present in these two taxa. This study has contributed to the knowledge of the distribution patterns and molecular phylogenetics of four Acetes spp. in the Straits of Malacca.
    Matched MeSH terms: Haplotypes
  10. Fulltext Population Genetics in Malaysia and Japanese Populations Using Power Plex Y23 System
    Nakamura Y, Samejima M, Minaguchi K, Nambiar P, Hashimoto M
    Bull. Tokyo Dent. Coll., 2020 Jul 04;61(2):83-94.
    PMID: 32522936 DOI: 10.2209/tdcpublication.2019-0023
    Population flow between Southeast Asian countries and Japan continues to gather pace. Accordingly, the number of foreigners involved in incidents in Japan has markedly increased, which means that forensic dentistry is now increasingly being faced with the need to analyze DNA from persons of non-Japanese extraction. The DNA test currently used for personal identification mainly utilizes short tandem repeats (STRs) on autosomal chromosomes and the Y-chromosome. This test was developed for use in personal identification, not for distinguishing among races; nonetheless, the standard method for personal identification is often used because the procedure has been established. To determine the degree to which racial differences can be distinguished by standard DNA analysis, 23 STRs located on the Y chromosome were investigated in 218 Malay and 426 Japanese males. The frequencies of each STR were calculated in the two populations. The difference in the power of discrimination between the Malay and Japanese populations ranged from a minimum of 0.01 to a maximum of 0.27; the difference in polymorphic information content ranged from 0.01 (minimum) to 0.23 (maximum). No major differences were noted in the polymorphisms in these two Mongoloid populations, but the distributions of the 17 STRs differed significantly. Short tandem repeat types demonstrating a likelihood of racial differences were identified in 14 of the STRs. Race-specific STR types were identified in 10 STRs. These results suggest that the likelihood of Malay or Japanese genetic background can be judged based on Y-chromosome STR test results.
    Matched MeSH terms: Haplotypes
  11. Fulltext Polymorphism of 11 Y Chromosome Short Tandem Repeat Markers among Malaysian Aborigines
    Mohd Yussup SS, Marzukhi M, Md-Zain BM, Mamat K, Mohd Yusof FZ
    Evol Bioinform Online, 2017;13:1176934317735318.
    PMID: 29085238 DOI: 10.1177/1176934317735318
    The conventional technique such as patrilocality suggests some substantial effects on population diversity. With that, this particular study investigated the paternal line, specifically Scientific Working Group on DNA Analysis Methods (SWGDAM)-recommended Y-STR markers, namely, DYS19, DYS385, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS438, and DYS439. These markers were tested to compare 184 Orang Asli individuals from 3 tribes found in Peninsular Malaysia. As a result, the haplotype diversity and the discrimination capacity obtained were 0.9987 and 0.9076, respectively. Besides, the most diverse marker was DYS385b, whereas the least was DYS391. Furthermore, the Senoi and Proto-Malay tribes were found to be the most distant, whereas the Senoi and Negrito clans were almost similar to each other. In addition, the analysis of molecular variance analysis revealed 82% of variance within the population, but only 18% of difference between the tribes. Finally, the phylogenetic trees constructed using Neighbour Joining and UPGMA (Unweighted Pair Group Method with Arithmetic Mean) displayed several clusters that were tribe specific. With that, future studies are projected to analyse individuals based on more specific sub-tribes.
    Matched MeSH terms: Haplotypes
  12. Maternal lineage of Nicobari pig (Sus scrofa nicobaricus) correlated with migration of Nicobarese, a native tribal population of Andaman and Nicobar Islands, India
    De AK, Sawhney S, Ponraj P, Muthiyan R, Muniswamy K, Ravi SK, et al.
    Anim Biotechnol, 2023 Apr;34(2):156-165.
    PMID: 34310265 DOI: 10.1080/10495398.2021.1950742
    Nicobari pig is reared by Nicobarese, a native tribal population of Andaman and Nicobar Islands. Nicobari pig has maintained its genetic identity due to geographical isolation. This communication is the first report on maternal inheritance of Nicobari pigs. DNA polymorphism data showed seven haplotypes. D-loop sequence information and mitogenome analysis were able to earmark Nicobari pigs to Asian clade. The domestication process of pigs and its expansion pattern help to understand human migration pattern. Based on this hypothesis, this communication elucidates the probable origin of Nicobarese. Earlier studies indicated that Nicobarese had genetic affinities to races distributed in China, Malaysia and Thailand. Our data on maternal inheritance of Nicobari pig correlates with the data on migration of Nicobarese. Moreover, we could establish a novel connection of Nicobarese with people of Northeastern parts of India, Philippines and Vietnam through phylogenetic signal and geographical provenance of Nicobari pig. We further concluded that migration of Nicobarese happened during Western route of migration (WRM) ∼4000 years before present. Therefore, we propose one wave hypothesis of peopling of Nicobar based on our study and existence of Ausrtroasiatic language, Mon-Khmer in these islands.
    Matched MeSH terms: Haplotypes
  13. Fulltext Genetic and morphological analyses of Gracilaria firma and G. changii (Gracilariaceae, Rhodophyta), the commercially important agarophytes in western Pacific
    Ng PK, Lin SM, Lim PE, Hurtado AQ, Phang SM, Yow YY, et al.
    PLoS One, 2017;12(7):e0182176.
    PMID: 28759629 DOI: 10.1371/journal.pone.0182176
    Many studies classifying Gracilaria species for the exploitation of agarophytes and the development of the agar industry were conducted before the prevalence of molecular tools, resulting in the description of many species based solely on their morphology. Gracilaria firma and G. changii are among the commercially important agarophytes from the western Pacific; both feature branches with basal constrictions that taper toward acute apices. In this study, we contrasted the morpho-anatomical circumscriptions of the two traditionally described species with molecular data from samples that included representatives of G. changii collected from its type locality. Concerted molecular analyses using the rbcL and cox1 gene sequences, coupled with morphological observations of the collections from the western Pacific, revealed no inherent differences to support the treatment of the two entities as distinct taxa. We propose merging G. changii (a later synonym) into G. firma and recognize G. firma based on thallus branches with abrupt basal constrictions that gradually taper toward acute (or sometimes broken) apices, cystocarps consisting of small gonimoblast cells and inconspicuous multinucleate tubular nutritive cells issuing from gonimoblasts extending into the inner pericarp at the cystocarp floor, as well as deep spermatangial conceptacles of the verrucosa-type. The validation of specimens under different names as a single genetic species is useful to allow communication and knowledge transfer among groups from different fields. This study also revealed considerably low number of haplotypes and nucleotide diversity with apparent phylogeographic patterns for G. firma in the region. Populations from the Philippines and Taiwan were divergent from each other as well as from the populations from Malaysia, Thailand, Singapore and Vietnam. Establishment of baseline data on the genetic diversity of this commercially important agarophyte is relevant in the context of cultivation, as limited genetic diversity may jeopardize the potential for its genetic improvement over time.
    Matched MeSH terms: Haplotypes
  14. Mitochondrial genomics identifies major haplogroups in Aboriginal Australians
    van Holst Pellekaan SM, Ingman M, Roberts-Thomson J, Harding RM
    Am J Phys Anthropol, 2006 Oct;131(2):282-94.
    PMID: 16596590
    We classified diversity in eight new complete mitochondrial genome sequences and 41 partial sequences from living Aboriginal Australians into five haplogroups. Haplogroup AuB belongs to global lineage M, and AuA, AuC, AuD, and AuE to N. Within N, we recognize subdivisions, assigning AuA to haplogroup S, AuD to haplogroup O, AuC to P4, and AuE to P8. On available evidence, (S)AuA and (M)AuB are widespread in Australia. (P4)AuC is found in the Riverine region of western New South Wales, and was identified by others in northern Australia. (O)AuD and (P8)AuE were clearly identified only from central Australia. Our eight Australian full mt genome sequences, combined with 20 others (Ingman and Gyllensten 2003 Genome Res. 13:1600-1606) and compared with full mt genome sequences from regions to the north that include Papua New Guinea, Malaya, and Andaman and Nicobar Islands, show that ancestral connections between regions are deep and limited to clustering at the level of the N and M macrohaplogroups. The Australian-specific distribution of the five haplogroups identified indicates genetic isolation over a long period. Ancestral connections within Australia are deeper than those reflected by known linguistic or culturally based affinities. Applying a coalescence analysis to a gene tree for the coding regions of the eight genomic sequences, we made estimates of time depth that support a continuity of presence for the descendants of a founding population already established by 40,000 years ago.
    Matched MeSH terms: Haplotypes
  15. Fulltext Full-length sequence analysis of chloroquine resistance transporter gene in Plasmodium falciparum isolates from Sabah, Malaysia
    Tan LL, Lau TY, Timothy W, Prabakaran D
    ScientificWorldJournal, 2014;2014:935846.
    PMID: 25574497 DOI: 10.1155/2014/935846
    Chloroquine resistance (CQR) in falciparum malaria was identified to be associated with several mutations in the chloroquine resistance transporter gene (pfcrt) that encodes the transmembrane transporter in digestive vacuole membrane of the parasite. This study aimed to investigate the point mutations across the full-length pfcrt in Plasmodium falciparum isolates in Sabah, Malaysia. A total of 31 P. falciparum positive samples collected from Keningau, Kota Kinabalu, and Kudat, Sabah, were analyzed. pfcrt was PCR amplified and cloned prior to sequence analysis. This study showed that all the previously described 10 point mutations associated with CQR at codons 72, 74, 75, 76, 97, 220, 271, 326, 356, and 371 were found with different prevalence. Besides, two novel point mutations, I166V and H273N, were identified with 22.5% and 19.3%, respectively. Three haplotypes, namely, CVMNK (29%), CVIET (3.2%), and SVMNT (67.7%), were identified. High prevalence of SVMNT among P. falciparum isolates from Sabah showed that these isolates are closer to the P. falciparum isolates from Papua New Guinea rather than to the more proximal Southeast Asian CVIET haplotype. Full-length analysis of pfcrt showed that chloroquine resistant P. falciparum in Sabah is still prevalent despite the withdrawal of chloroquine usage since 1979.
    Matched MeSH terms: Haplotypes/genetics
  16. Fulltext Continental monophyly and molecular divergence of Peninsular Malaysia's Macaca fascicularis fascicularis
    Abdul-Latiff MA, Ruslin F, Faiq H, Hairul MS, Rovie-Ryan JJ, Abdul-Patah P, et al.
    Biomed Res Int, 2014;2014:897682.
    PMID: 25143948 DOI: 10.1155/2014/897682
    The phylogenetic relationships of long-tailed macaque (Macaca fascicularis fascicularis) populations distributed in Peninsular Malaysia in relation to other regions remain unknown. The aim of this study was to reveal the phylogeography and population genetics of Peninsular Malaysia's M. f. fascicularis based on the D-loop region of mitochondrial DNA. Sixty-five haplotypes were detected in all populations, with only Vietnam and Cambodia sharing four haplotypes. The minimum-spanning network projected a distant relationship between Peninsular Malaysian and insular populations. Genetic differentiation (F(ST), Nst) results suggested that the gene flow among Peninsular Malaysian and the other populations is very low. Phylogenetic tree reconstructions indicated a monophyletic clade of Malaysia's population with continental populations (NJ = 97%, MP = 76%, and Bayesian = 1.00 posterior probabilities). The results demonstrate that Peninsular Malaysia's M. f. fascicularis belonged to Indochinese populations as opposed to the previously claimed Sundaic populations. M. f. fascicularis groups are estimated to have colonized Peninsular Malaysia ~0.47 million years ago (MYA) directly from Indochina through seaways, by means of natural sea rafting, or through terrestrial radiation during continental shelf emersion. Here, the Isthmus of Kra played a central part as biogeographical barriers that then separated it from the remaining continental populations.
    Matched MeSH terms: Haplotypes/genetics
  17. Fulltext Genetic diversity, haplotypes and allele groups of Duffy binding protein (PkDBPαII) of Plasmodium knowlesi clinical isolates from Peninsular Malaysia
    Fong MY, Lau YL, Chang PY, Anthony CN
    Parasit Vectors, 2014;7:161.
    PMID: 24693997 DOI: 10.1186/1756-3305-7-161
    The monkey malaria parasite Plasmodium knowlesi is now recognized as the fifth species of Plasmodium that can cause human malaria. Like the region II of the Duffy binding protein of P. vivax (PvDBPII), the region II of the P. knowlesi Duffy binding protein (PkDBPαII) plays an essential role in the parasite's invasion into the host's erythrocyte. Numerous polymorphism studies have been carried out on PvDBPII, but none has been reported on PkDBPαII. In this study, the genetic diversity, haplotyes and allele groups of PkDBPαII of P. knowlesi clinical isolates from Peninsular Malaysia were investigated.
    Matched MeSH terms: Haplotypes*
  18. Fulltext An efficient clustering algorithm for partitioning Y-short tandem repeats data
    Seman A, Bakar ZA, Isa MN
    BMC Res Notes, 2012;5:557.
    PMID: 23039132 DOI: 10.1186/1756-0500-5-557
    Y-Short Tandem Repeats (Y-STR) data consist of many similar and almost similar objects. This characteristic of Y-STR data causes two problems with partitioning: non-unique centroids and local minima problems. As a result, the existing partitioning algorithms produce poor clustering results.
    Matched MeSH terms: Haplotypes*
  19. Fulltext PanSNPdb: the Pan-Asian SNP genotyping database
    Ngamphiw C, Assawamakin A, Xu S, Shaw PJ, Yang JO, Ghang H, et al.
    PLoS One, 2011;6(6):e21451.
    PMID: 21731755 DOI: 10.1371/journal.pone.0021451
    The HUGO Pan-Asian SNP consortium conducted the largest survey to date of human genetic diversity among Asians by sampling 1,719 unrelated individuals among 71 populations from China, India, Indonesia, Japan, Malaysia, the Philippines, Singapore, South Korea, Taiwan, and Thailand. We have constructed a database (PanSNPdb), which contains these data and various new analyses of them. PanSNPdb is a research resource in the analysis of the population structure of Asian peoples, including linkage disequilibrium patterns, haplotype distributions, and copy number variations. Furthermore, PanSNPdb provides an interactive comparison with other SNP and CNV databases, including HapMap3, JSNP, dbSNP and DGV and thus provides a comprehensive resource of human genetic diversity. The information is accessible via a widely accepted graphical interface used in many genetic variation databases. Unrestricted access to PanSNPdb and any associated files is available at: http://www4a.biotec.or.th/PASNP.
    Matched MeSH terms: Haplotypes/genetics*
  20. Asian population frequencies and haplotype distribution of killer cell immunoglobulin-like receptor (KIR) genes among Chinese, Malay, and Indian in Singapore
    Lee YC, Chan SH, Ren EC
    Immunogenetics, 2008 Nov;60(11):645-54.
    PMID: 18668235 DOI: 10.1007/s00251-008-0321-3
    Killer cell immunoglobulin-like receptors (KIR) gene frequencies have been shown to be distinctly different between populations and contribute to functional variation in the immune response. We have investigated KIR gene frequencies in 370 individuals representing three Asian populations in Singapore and report here the distribution of 14 KIR genes (2DL1, 2DL2, 2DL3, 2DL4, 2DL5, 2DS1, 2DS2, 2DS3, 2DS4, 2DS5, 3DL1, 3DL2, 3DL3, 3DS1) with two pseudogenes (2DP1, 3DP1) among Singapore Chinese (n = 210); Singapore Malay (n = 80), and Singapore Indian (n = 80). Four framework genes (KIR3DL3, 3DP1, 2DL4, 3DL2) and a nonframework pseudogene 2DP1 were detected in all samples while KIR2DS2, 2DL2, 2DL5, and 2DS5 had the greatest significant variation across the three populations. Fifteen significant linkage patterns, consistent with associations between genes of A and B haplotypes, were observed. Eighty-four distinct KIR profiles were determined in our populations, 38 of which had not been described in other populations. KIR haplotype studies were performed using nine Singapore Chinese families comprising 34 individuals. All genotypes could be resolved into corresponding pairs of existing haplotypes with eight distinct KIR genotypes and eight different haplotypes. The haplotype A2 with frequency of 63.9% was dominant in Singapore Chinese, comparable to that reported in Korean and Chinese Han. The A haplotypes predominate in Singapore Chinese, with ratio of A to B haplotypes of approximately 3:1. Comparison with KIR frequencies in other populations showed that Singapore Chinese shared similar distributions with Chinese Han, Japanese, and Korean; Singapore Indian was found to be comparable with North Indian Hindus while Singapore Malay resembled the Thai.
    Matched MeSH terms: Haplotypes/genetics
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