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  1. Y-chromosome and mitochondrial DNA studies on the population structure of the Christmas Island community
    Wise CA, Sullivan SG, Black ML, Erber WN, Bittles AH
    Am. J. Phys. Anthropol., 2005 Nov;128(3):670-7.
    PMID: 15864813
    Christmas Island is a remote Australian territory located close to the main Indonesian island of Java. Y-chromosome and mitochondrial DNA (mtDNA) markers were used to investigate the genetic structure of the population, which comprises communities of mixed ethnic origin. Analysis of 12 Y-chromosome biallelic polymorphisms revealed a high level of gene diversity and haplotype frequencies that were consistent with source populations in southern China and Southeast Asia. mtDNA hypervariable segment I (HVS-I) sequences displayed high levels of haplotype diversity and nucleotide diversity that were comparable to various Asian populations. Genetic distances revealed extremely low mtDNA differentiation among Christmas Islanders and Asian populations. This was supported by the relatively high proportion of sequence types shared among these populations. The most common mtDNA haplogroups were M* and B, followed by D and F, which are prevalent in East/Southeast Asia. Christmas Islanders of European descent were characterized by the Eurasian haplogroup R*, and a limited degree of admixture was observed. In general, analysis of the genetic data indicated population affinities to southern Chinese (in particular from the Yunnan Province) and Southeast Asia (Thailand, Malaysia, and Cambodia), which was consistent with historical records of settlement. The combined use of these different marker systems provides a useful and appropriate model for the study of contemporary populations derived from different ethnic origins.
    Matched MeSH terms: Chromosomes, Human, Y/genetics*
  2. Association of azoospermia factor region deletions in infertile male subjects among Malaysians
    Hussein AA, Vasudevan R, Patimah I, Prashant N, Nora FA
    Andrologia, 2015 Mar;47(2):168-77.
    PMID: 24528375 DOI: 10.1111/and.12240
    Azoospermia factor region (AZF) deletions (AZFa, AZFb, AZFc and AZFd) in the Y chromosome were analysed in male infertility subjects in various populations with conflicting results. This study comprised of 54 infertile males and 63 fertile controls, and the frequency of AZFa, AZFb, AZFc and AZFd deletions were determined using conventional polymerase chain reaction (PCR) as well as real-time PCR-high resolution melting analysis-based methods. The results of this study showed that, three of 54 cases (5.55%) had AZF (a, b and c) deletions (two had AZFc and one had AZFa deletions). Four cases were found to have AZFd deletions (7.4%) with two of them being associated with AZFc deletions (P = 0.028). The frequency of AZF (a, b and c) deletions in Malaysian infertile male subjects was found to be comparable with other populations. AZFd deletions were found to be significant (P < 0.05) in male infertility and it may be associated with other types of AZF deletions.
    Matched MeSH terms: Chromosomes, Human, Y/genetics*
  3. Linkage between prostate cancer occurrence and Y-chromosomal DYS loci in Malaysian subjects
    Nargesi MM, Ismail P, Razack AH, Pasalar P, Nazemi A, Oshkoor SA, et al.
    Asian Pac J Cancer Prev, 2011;12(5):1265-8.
    PMID: 21875279
    PURPOSE: Prostate cancer differs markedly in incidence across ethnic groups. Since this disease is influenced by complex genetics, it is many genetic factors may affect the level of susceptibility to development of the disease. In this study, four Y-linked short tandem repeats (STRs), DYS388, DYS435, DYS437, and DYS439, were genotyped to compare Malaysian prostate cancer patients and normal control males.

    MATERIALS AND METHODS: A total of 175 subjects comprising 84 patients and 91 healthy individuals were recruited. Multiplex PCR was optimized to co-amplify DYS388, DYS435, DYS437, and DYS439 loci. All samples were genotyped for alleles of four DYS loci using a Genetic Analysis System.

    RESULTS: Of all DYS loci, allele 10 (A) of DYS388 had a significantly lower incidence of disease in compare with other alleles of this locus, while a higher incidence of disease was found among males who had either allele 12 (C) of DYS388 or allele 14 (E) of DYS439. Moreover, a total of 47 different haplotypes comprising different alleles of four DYS loci were found among the whole study samples, of which haplotypes AABC and CAAA showed a lower and higher frequency among cases than controls, respectively.

    CONCLUSIONS: It is likely that Malaysian males who belong to Y-lineages with either allele 12 of DYS388, allele 14 of DYS439, or haplotype CAAA are more susceptible to develop prostate cancer, while those belonging to lineages with allele 10 of DYS388 or haplotype AABC are more resistant to the disease.

    Matched MeSH terms: Chromosomes, Human, Y/genetics*
  4. Fulltext Mitochondrial and Y-chromosome diversity of the Tharus (Nepal): a reservoir of genetic variation
    Fornarino S, Pala M, Battaglia V, Maranta R, Achilli A, Modiano G, et al.
    BMC Evol. Biol., 2009;9:154.
    PMID: 19573232 DOI: 10.1186/1471-2148-9-154
    Central Asia and the Indian subcontinent represent an area considered as a source and a reservoir for human genetic diversity, with many markers taking root here, most of which are the ancestral state of eastern and western haplogroups, while others are local. Between these two regions, Terai (Nepal) is a pivotal passageway allowing, in different times, multiple population interactions, although because of its highly malarial environment, it was scarcely inhabited until a few decades ago, when malaria was eradicated. One of the oldest and the largest indigenous people of Terai is represented by the malaria resistant Tharus, whose gene pool could still retain traces of ancient complex interactions. Until now, however, investigations on their genetic structure have been scarce mainly identifying East Asian signatures.
    Matched MeSH terms: Chromosomes, Human, Y/genetics*
  5. 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: Chromosomes, Human, Y*
  6. Fulltext Y Chromosome Sequences Reveal a Short Beringian Standstill, Rapid Expansion, and early Population structure of Native American Founders
    Pinotti T, Bergström A, Geppert M, Bawn M, Ohasi D, Shi W, et al.
    Curr Biol, 2019 01 07;29(1):149-157.e3.
    PMID: 30581024 DOI: 10.1016/j.cub.2018.11.029
    The Americas were the last inhabitable continents to be occupied by humans, with a growing multidisciplinary consensus for entry 15-25 thousand years ago (kya) from northeast Asia via the former Beringia land bridge [1-4]. Autosomal DNA analyses have dated the separation of Native American ancestors from the Asian gene pool to 23 kya or later [5, 6] and mtDNA analyses to ∼25 kya [7], followed by isolation ("Beringian Standstill" [8, 9]) for 2.4-9 ky and then a rapid expansion throughout the Americas. Here, we present a calibrated sequence-based analysis of 222 Native American and relevant Eurasian Y chromosomes (24 new) from haplogroups Q and C [10], with four major conclusions. First, we identify three to four independent lineages as autochthonous and likely founders: the major Q-M3 and rarer Q-CTS1780 present throughout the Americas, the very rare C3-MPB373 in South America, and possibly the C3-P39/Z30536 in North America. Second, from the divergence times and Eurasian/American distribution of lineages, we estimate a Beringian Standstill duration of 2.7 ky or 4.6 ky, according to alternative models, and entry south of the ice sheet after 19.5 kya. Third, we describe the star-like expansion of Q-M848 (within Q-M3) starting at 15 kya [11] in the Americas, followed by establishment of substantial spatial structure in South America by 12 kya. Fourth, the deep branches of the Q-CTS1780 lineage present at low frequencies throughout the Americas today [12] may reflect a separate out-of-Beringia dispersal after the melting of the glaciers at the end of the Pleistocene.
    Matched MeSH terms: Chromosomes, Human, Y/genetics*
  7. 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: Chromosomes, Human, Y
  8. A distinct Y-STR haplotype for Amelogenin negative males characterized by a large Y(p)11.2 (DYS458-MSY1-AMEL-Y) deletion
    Chang YM, Perumal R, Keat PY, Yong RY, Kuehn DL, Burgoyne L
    Forensic Sci Int, 2007 Mar 2;166(2-3):115-20.
    PMID: 16765004
    The use of STR multiplexes with the incorporated gender marker Amelogenin is common practice in forensic DNA analysis. However, when a known male sample shows a dropout of the Amelogenin Y-allele, the STR system falsely genotypes it as a female. To date, our laboratory has observed 18 such cases: 12 from our Y-STR database and six from casework. A study on 980 male individuals in the Malaysian population using the AmpFlSTR Y-filer has revealed a distinct Y-chromosome haplotype associated with the Amelogenin nulls. Our results showed that whilst the Amelogenin nulls were noticeably absent among the Chinese, both the Indians and Malays exhibited such mutations at 3.2 and 0.6%, respectively. It was also found that the Amelogenin negative individuals predominantly belonged to the J2e lineage, suggesting the possibility of a common ancestor for at least some of these chromosomes. The null frequencies showed concordance with the data published in Chang et al. [Higher failures of Amelogenin sex test in an Indian population group, J. Forensic Sci. 48 (2003) 1309-1313] on a smaller Malaysian population of 338 males which used a Y-STR triplex. In the current study, apart from the absence of the Amelogenin Y-locus, a complete absence of the DYS458 locus in all the nulls was also observed. This study together with the 2003 study has indicated a similar deletion region exists on the Y(p)11.2 band in all the 18 Y-chromosomes. Using bioinformatics, this deletion has been mapped to a region of at least 1.13 Mb on the Y(p)11.2 encompassing the Amelogenin, MSY1 minisatellite and DYS458 locus. Further, the Y-filer haplotypes revealed an additional null at Y-GATA H4 in two of the Indian males presented here.
    Matched MeSH terms: Chromosomes, Human, Y*
  9. Haplotype diversity of 16 Y-chromosomal STRs in three main ethnic populations (Malays, Chinese and Indians) in Malaysia
    Chang YM, Perumal R, Keat PY, Kuehn DL
    Forensic Sci Int, 2007 Mar 22;167(1):70-6.
    PMID: 16457976
    We have analyzed 16 Y-STR loci (DYS456, DYS389I, DYS390, DYS389II, DYS458, DYS19, DYS385a/b, DYS393, DYS391, DYS439, DYS635 or Y-GATA C4, DYS392, Y-GATA H4, DYS437, DYS438 and DYS448) from the non-recombining region of the human Y-chromosome in 980 male individuals from three main ethnic populations in Malaysia (Malay, Chinese, Indian) using the AmpFlSTR((R)) Y-filertrade mark (Applied Biosystems, Foster City, CA). The observed 17-loci haplotypes and the individual allele frequencies for each locus were estimated, whilst the locus diversity, haplotype diversity and discrimination capacity were calculated in the three ethnic populations. Analysis of molecular variance indicated that 88.7% of the haplotypic variation is found within population and 11.3% is between populations (fixation index F(ST)=0.113, p=0.000). This study has revealed Y-chromosomes with null alleles at several Y-loci, namely DYS458, DYS392, DYS389I, DYS389II, DYS439, DYS448 and Y-GATA H4; and several occurrences of duplications at the highly polymorphic DYS385 loci. Some of these deleted loci were in regions of the Y(q) arm that have been implicated in the occurrence of male infertility.
    Matched MeSH terms: Chromosomes, Human, Y*
  10. Haplotype diversity of 17 Y-chromosomal STRs in three native Sarawak populations (Iban, Bidayuh and Melanau) in East Malaysia
    Chang YM, Swaran Y, Phoon YK, Sothirasan K, Sim HT, Lim KB, et al.
    Forensic Sci Int Genet, 2009 Jun;3(3):e77-80.
    PMID: 19414156 DOI: 10.1016/j.fsigen.2008.07.007
    17 Y-STRs (DYS456, DYS389I, DYS390, DYS389II, DYS458, DYS19, DYS385a/b, DYS393, DYS391, DYS439, DYS635 or Y-GATA C4, DYS392, Y-GATA H4, DYS437, DYS438 and DYS448) have been analyzed in 320 male individuals from Sarawak, an eastern state of Malaysia on the Borneo island using the AmpFlSTR Y-filer (Applied Biosystems, Foster City, CA). These individuals were from three indigenous ethnic groups in Sarawak comprising of 103 Ibans, 113 Bidayuhs and 104 Melanaus. The observed 17-loci haplotypes and the individual allele frequencies for each locus were estimated, whilst the locus diversity, haplotype diversity and discrimination capacity were calculated in the three groups. Analysis of molecular variance (AMOVA) indicated that 87.6% of the haplotypic variation was found within population and 12.4% between populations (fixation index F(ST)=0.124, p=0.000). This study has revealed that the indigenous populations in Sarawak are distinctly different to each other, and to the three major ethnic groups in Malaysia (Malays, Chinese and Indians), with the Melanaus having a strikingly high degree of shared haplotypes within. There are rare unusual variants and microvariants that were not present in Malaysian Malay, Chinese or Indian groups. In addition, occurrences of DYS385 duplications which were only noticeably present in Chinese group previously was also observed in the Iban group whilst null alleles were detected at several Y-loci (namely DYS19, DYS392, DYS389II and DYS448) in the Iban and Melanau groups.
    Matched MeSH terms: Chromosomes, Human, Y*
  11. Characterization of genetic sequence variation of 58 STR loci in four major population groups
    Novroski NMM, King JL, Churchill JD, Seah LH, Budowle B
    Forensic Sci Int Genet, 2016 11;25:214-226.
    PMID: 27697609 DOI: 10.1016/j.fsigen.2016.09.007
    Massively parallel sequencing (MPS) can identify sequence variation within short tandem repeat (STR) alleles as well as their nominal allele lengths that traditionally have been obtained by capillary electrophoresis. Using the MiSeq FGx Forensic Genomics System (Illumina), STRait Razor, and in-house excel workbooks, genetic variation was characterized within STR repeat and flanking regions of 27 autosomal, 7 X-chromosome and 24 Y-chromosome STR markers in 777 unrelated individuals from four population groups. Seven hundred and forty six autosomal, 227 X-chromosome, and 324 Y-chromosome STR alleles were identified by sequence compared with 357 autosomal, 107 X-chromosome, and 189 Y-chromosome STR alleles that were identified by length. Within the observed sequence variation, 227 autosomal, 156 X-chromosome, and 112 Y-chromosome novel alleles were identified and described. One hundred and seventy six autosomal, 123 X-chromosome, and 93 Y-chromosome sequence variants resided within STR repeat regions, and 86 autosomal, 39 X-chromosome, and 20 Y-chromosome variants were located in STR flanking regions. Three markers, D18S51, DXS10135, and DYS385a-b had 1, 4, and 1 alleles, respectively, which contained both a novel repeat region variant and a flanking sequence variant in the same nucleotide sequence. There were 50 markers that demonstrated a relative increase in diversity with the variant sequence alleles compared with those of traditional nominal length alleles. These population data illustrate the genetic variation that exists in the commonly used STR markers in the selected population samples and provide allele frequencies for statistical calculations related to STR profiling with MPS data.
    Matched MeSH terms: Chromosomes, Human, Y
  12. Fulltext Copy number variation arising from gene conversion on the human Y chromosome
    Shi W, Massaia A, Louzada S, Banerjee R, Hallast P, Chen Y, et al.
    Hum Genet, 2018 Jan;137(1):73-83.
    PMID: 29209947 DOI: 10.1007/s00439-017-1857-9
    We describe the variation in copy number of a ~ 10 kb region overlapping the long intergenic noncoding RNA (lincRNA) gene, TTTY22, within the IR3 inverted repeat on the short arm of the human Y chromosome, leading to individuals with 0-3 copies of this region in the general population. Variation of this CNV is common, with 266 individuals having 0 copies, 943 (including the reference sequence) having 1, 23 having 2 copies, and two having 3 copies, and was validated by breakpoint PCR, fibre-FISH, and 10× Genomics Chromium linked-read sequencing in subsets of 1234 individuals from the 1000 Genomes Project. Mapping the changes in copy number to the phylogeny of these Y chromosomes previously established by the Project identified at least 20 mutational events, and investigation of flanking paralogous sequence variants showed that the mutations involved flanking sequences in 18 of these, and could extend over > 30 kb of DNA. While either gene conversion or double crossover between misaligned sister chromatids could formally explain the 0-2 copy events, gene conversion is the more likely mechanism, and these events include the longest non-allelic gene conversion reported thus far. Chromosomes with three copies of this CNV have arisen just once in our data set via another mechanism: duplication of 420 kb that places the third copy 230 kb proximal to the existing proximal copy. Our results establish gene conversion as a previously under-appreciated mechanism of generating copy number changes in humans and reveal the exceptionally large size of the conversion events that can occur.
    Matched MeSH terms: Chromosomes, Human, Y/genetics*
  13. Fulltext Resolving the ancestry of Austronesian-speaking populations
    Soares PA, Trejaut JA, Rito T, Cavadas B, Hill C, Eng KK, et al.
    Hum Genet, 2016 Mar;135(3):309-26.
    PMID: 26781090 DOI: 10.1007/s00439-015-1620-z
    There are two very different interpretations of the prehistory of Island Southeast Asia (ISEA), with genetic evidence invoked in support of both. The "out-of-Taiwan" model proposes a major Late Holocene expansion of Neolithic Austronesian speakers from Taiwan. An alternative, proposing that Late Glacial/postglacial sea-level rises triggered largely autochthonous dispersals, accounts for some otherwise enigmatic genetic patterns, but fails to explain the Austronesian language dispersal. Combining mitochondrial DNA (mtDNA), Y-chromosome and genome-wide data, we performed the most comprehensive analysis of the region to date, obtaining highly consistent results across all three systems and allowing us to reconcile the models. We infer a primarily common ancestry for Taiwan/ISEA populations established before the Neolithic, but also detected clear signals of two minor Late Holocene migrations, probably representing Neolithic input from both Mainland Southeast Asia and South China, via Taiwan. This latter may therefore have mediated the Austronesian language dispersal, implying small-scale migration and language shift rather than large-scale expansion.
    Matched MeSH terms: Chromosomes, Human, Y/genetics
  14. Molecular characterization of a polymorphic 3-Mb deletion at chromosome Yp11.2 containing the AMELY locus in Singapore and Malaysia populations
    Yong RY, Gan LS, Chang YM, Yap EP
    Hum Genet, 2007 Nov;122(3-4):237-49.
    PMID: 17588179
    Amelogenin paralogs on Chromosome X (AMELX) and Y (AMELY) are commonly used sexing markers. Interstitial deletion of Yp involving the AMELY locus has previously been reported. The combined frequency of the AMELY null allele in Singapore and Malaysia populations is 2.7%, 0.6% in Indian and Malay ethnic groups respectively. It is absent among 541 Chinese screened. The null allele in this study belongs to 3 Y haplogroups; J2e1 (85.7%), F* (9.5%) and D* (4.8%). Low and high-resolution STS mapping, followed by sequence analysis of breakpoint junction confirmed a large deletion of 3 to 3.7-Mb located at the Yp11.2 region. Both breakpoints were located in TSPY repeat arrays, suggesting a non-allelic homologous recombination (NAHR) mechanism of deletion. All regional null samples shared identical breakpoint sequences according to their haplogroup affiliation, providing molecular evidence of a common ancestry origin for each haplogroup, and at least 3 independent deletion events recurred in history. The estimated ages based on Y-SNP and STR analysis were approximately 13.5 +/- 3.1 kyears and approximately 0.9 +/- 0.9 kyears for the J2e1 and F* mutations, respectively. A novel polymorphism G > A at Y-GATA-H4 locus in complete linkage disequilibrium with J2e1 null mutations is a more recent event. This work re-emphasizes the need to include other sexing markers for gender determination in certain regional populations. The frequency difference among global populations suggests it constitutes another structural variation locus of human chromosome Y. The breakpoint sequences provide further information to a better understanding of the NAHR mechanism and DNA rearrangements due to higher order genomic architecture.
    Matched MeSH terms: Chromosomes, Human, Y/genetics*
  15. Fulltext Evolutionary and functional analysis of RBMY1 gene copy number variation on the human Y chromosome
    Shi W, Louzada S, Grigorova M, Massaia A, Arciero E, Kibena L, et al.
    Hum Mol Genet, 2019 Aug 15;28(16):2785-2798.
    PMID: 31108506 DOI: 10.1093/hmg/ddz101
    Human RBMY1 genes are located in four variable-sized clusters on the Y chromosome, expressed in male germ cells and possibly associated with sperm motility. We have re-investigated the mutational background and evolutionary history of the RBMY1 copy number distribution in worldwide samples and its relevance to sperm parameters in an Estonian cohort of idiopathic male factor infertility subjects. We estimated approximate RBMY1 copy numbers in 1218 1000 Genomes Project phase 3 males from sequencing read-depth, then chose 14 for valid ation by multicolour fibre-FISH. These fibre-FISH samples provided accurate calibration standards for the entire panel and led to detailed insights into population variation and mutational mechanisms. RBMY1 copy number worldwide ranged from 3 to 13 with a mode of 8. The two larger proximal clusters were the most variable, and additional duplications, deletions and inversions were detected. Placing the copy number estimates onto the published Y-SNP-based phylogeny of the same samples suggested a minimum of 562 mutational changes, translating to a mutation rate of 2.20 × 10-3 (95% CI 1.94 × 10-3 to 2.48 × 10-3) per father-to-son Y-transmission, higher than many short tandem repeat (Y-STRs), and showed no evidence for selection for increased or decreased copy number, but possible copy number stabilizing selection. An analysis of RBMY1 copy numbers among 376 infertility subjects failed to replicate a previously reported association with sperm motility and showed no significant effect on sperm count and concentration, serum follicle stimulating hormone (FSH), luteinizing hormone (LH) and testosterone levels or testicular and semen volume. These results provide the first in-depth insights into the structural rearrangements underlying RBMY1 copy number variation across diverse human lineages.
    Matched MeSH terms: Chromosomes, Human, Y*
  16. Paternal lineage affinity of the Malay subethnic and Orang Asli populations in Peninsular Malaysia
    SharifahNany RahayuKarmilla S, Aedrianee AR, Nur Haslindawaty AR, Nur Azeelah A, Panneerchelvam S, Norazmi MN, et al.
    Int J Legal Med, 2018 Jul;132(4):1087-1090.
    PMID: 29052042 DOI: 10.1007/s00414-017-1697-0
    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.
    Matched MeSH terms: Chromosomes, Human, Y*
  17. Population data of 23 Y chromosome STR loci for the five major human subpopulations of Ghana
    Kofi AE, Hakim HM, Khan HO, Ismail SA, Ghansah A, David AA, et al.
    Int J Legal Med, 2020 Jul;134(4):1313-1315.
    PMID: 31154498 DOI: 10.1007/s00414-019-02099-w
    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.
    Matched MeSH terms: Chromosomes, Human, Y*
  18. Population data for 23 Y chromosome STR loci using the Powerplex® Y23 STR kit for the Kedayan population in Malaysia
    Hakim HM, Khan HO, Ismail SA, Lalung J, Kofi AE, Nelson BR, et al.
    Int J Legal Med, 2020 Jul;134(4):1335-1337.
    PMID: 31897667 DOI: 10.1007/s00414-019-02237-4
    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.
    Matched MeSH terms: Chromosomes, Human, Y*
  19. Higher failures of amelogenin sex test in an Indian population group
    Chang YM, Burgoyne LA, Both K
    J Forensic Sci, 2003 Nov;48(6):1309-13.
    PMID: 14640276
    The human sex test in forensic multiplexes is based on the amelogenin gene on both the X and Y chromosomes commonly used in sex genotyping. In this study of 338 male individuals in a Malaysian population comprising Malays, Chinese and Indians, using the AmpFlSTR Profiler Plus kit, the amelogenin test gave a significant proportion of null alleles in the Indian ethnic group (3.6% frequency) and 0.88% frequency in the Malay ethnic group due to a deletion of the gene on the Y chromosome. This sex test also failed in a forensic casework sample. Failure of the amelogenin test highlights the need for more reliable sex determination than is offered by the amelogenin locus in the Malay and Indian populations. The gender of the Indian-Malay amelogenin nulls was confirmed by the presence of three Y-STR alleles (DYS438, DYS390 and DYS439). For the Indian ethnic group, one of the Y-STR forms a stable haplotype with the amelogenin null. The amelogenin-deletion individuals also showed a null with a male-specific minisatellite MSY1, indicating that a very large deletion was involved that included the amelogenin and the MSY1 loci on the short arm of the Y chromosomes (Yp).
    Matched MeSH terms: Chromosomes, Human, Y
  20. Fulltext Ancestry of the Iban is predominantly Southeast Asian: genetic evidence from autosomal, mitochondrial, and Y chromosomes
    Simonson TS, Xing J, Barrett R, Jerah E, Loa P, Zhang Y, et al.
    PLoS One, 2011;6(1):e16338.
    PMID: 21305013 DOI: 10.1371/journal.pone.0016338
    Humans reached present-day Island Southeast Asia (ISEA) in one of the first major human migrations out of Africa. Population movements in the millennia following this initial settlement are thought to have greatly influenced the genetic makeup of current inhabitants, yet the extent attributed to different events is not clear. Recent studies suggest that south-to-north gene flow largely influenced present-day patterns of genetic variation in Southeast Asian populations and that late Pleistocene and early Holocene migrations from Southeast Asia are responsible for a substantial proportion of ISEA ancestry. Archaeological and linguistic evidence suggests that the ancestors of present-day inhabitants came mainly from north-to-south migrations from Taiwan and throughout ISEA approximately 4,000 years ago. We report a large-scale genetic analysis of human variation in the Iban population from the Malaysian state of Sarawak in northwestern Borneo, located in the center of ISEA. Genome-wide single-nucleotide polymorphism (SNP) markers analyzed here suggest that the Iban exhibit greatest genetic similarity to Indonesian and mainland Southeast Asian populations. The most common non-recombining Y (NRY) and mitochondrial (mt) DNA haplogroups present in the Iban are associated with populations of Southeast Asia. We conclude that migrations from Southeast Asia made a large contribution to Iban ancestry, although evidence of potential gene flow from Taiwan is also seen in uniparentally inherited marker data.
    Matched MeSH terms: Chromosomes, Human, Y*
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