A genetic Study of the Ghanaian Population Using 15 Autosomal STR Loci.

Autosomal short tandem repeat (STR) population data collected from a well characterized population are needed to correctly assigning the weight of DNA profiles in the courtroom and widely used for ancestral analyses. In this study, allele frequencies for the 15 autosomal short tandem repeat (STR) loci included in the AmpFlSTR® Identifiler® plus kit (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, VWA, TPOX, D18S51, D5S818, FGA) were obtained by genotyping 332 unrelated individuals of Ghanaian origin. Statistical tests on STR genotype data showed no significant departure from Hardy-Weinberg equilibrium (HWE). The overall match probability, combined power of exclusion and combined power of discrimination for these loci were 1 in 3.85 × 1017, 0.99999893 and 0.99999998, respectively. Polymorphic information content (PIC) greater than 0.70 was observed for all loci except TH01 and D13S317. These statistical parameters confirm that this combination of loci is valuable for forensic identification and parentage analysis. Our results were also compared with those for 20 other human populations analyzed for the same set of markers. We observed that the Ghanaian population grouped with other African populations in two-dimensional principal coordinate (PCO) and a neighbor-joining (N-J) data mapping and placed closest to Nigerians. This observation reflects cultural similarities and geographical factors, coupled with the long history of migration and trading activities between Ghana and Nigeria. Our report provides what we believe to be the first published autosomal STR data for the general Ghanaian population using 15 loci genotyped using the AmpFlSTR® Identifiler® plus kit methodology. Our data show that the loci tested have sufficient power to be used reliably for DNA profiling in forensic casework and help to elucidate the genetic history of people living in the country.

Correction to: Paternal lineage affinity of the Malay subethnic and Orang Asli populations in Peninsular Malaysia.

The original version of this article contains an error. The Author Abd Rashid Nur Haslindawaty has been added as to the above author group as third author. The original article was corrected.

Paternal lineage affinity of the Malay subethnic and Orang Asli populations in Peninsular Malaysia.

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.

Human Leukocyte Antigen-G Gene Polymorphism in Peninsular Malaysia: A Preliminary Report.

Introduction: Expression of the nonclassical human leukocyte antigen (HLA)-G gene is upregulated in placenta during pregnancy. In other cells, HLA-G is upregulated during parasitic infections and allergic reactions. Polymorphism at the HLA-G gene locus has been reported for many populations, but so far not for any ethnic groups in Malaysia. In this survey, we screened for genetic variation in HLA-G genes from representative Malay, Chinese, and Indian individuals living in Peninsular Malaysia. Materials and Methods: Blood samples were obtained with informed consent, and ethnicity classes were assigned based on self-declared pedigree information. Exons 2, 3, and 4 of the HLA-G gene were amplified by polymerase chain reaction and subjected to Sanger sequencing. Results: The most common genotype in Malays and Indians was found to be HLA-G*01:01:01:01/01:01:01:01 with frequencies of 0.206 and 0.167, respectively, whereas the HLA-G*01:01:03:01/01:01:01:01 genotype was the one most frequently observed in Chinese (0.221). Based on this study, HLA-G*01:01:01:01 (0.427-0.448) is the most frequent HLA-G allele in the all three ethnic groups. In contrast, HLA-G*01:01:02:01 (0.186) was observed as the second most frequent HLA-G allele in Malays and HLA-G*01:04:01 in Chinese and Indians, (0.188-0.198, respectively). Several minor HLA-G alleles were detected at low frequency in Malays, Chinese, or Indians (HLA-G*01:01:05, 01:01:09, 01:04:02, and 01:04:03). These have only rarely, if ever, been reported in other population groups. Subsequent statistical analysis including using principal coordinate data mapping showed the Malays, Chinese, and Indians are distinct but quite closely related to one another as compared with other population groups from across Europe and Africa. Conclusion: The HLA-G population data collected in this study showed that the ancestrally unrelated Malays, Chinese, and Indians are genetically distinct. This new database provides a foundation for further studies to capture HLA-G allelic diversity in uncharacterized populations of Malaysia and for future attempts to identify their roles in disease resistance and susceptibility.

Sequence polymorphisms of mtDNA HV1, HV2, and HV3 regions in the Malay population of Peninsular Malaysia.

The uniparentally inherited mitochondrial DNA (mtDNA) is in the limelight for the past two decades, in studies relating to demographic history of mankind and in forensic kinship testing. In this study, human mtDNA hypervariable segments 1, 2, and 3 (HV1, HV2, and HV3) were analyzed in 248 unrelated Malay individuals in Peninsular Malaysia. Combined analyses of HV1, HV2, and HV3 revealed a total of 180 mtDNA haplotypes with 149 unique haplotypes and 31 haplotypes occurring in more than one individual. The genetic diversity was estimated to be 99.47%, and the probability of any two individuals sharing the same mtDNA haplotype was 0.93%. The most frequent mtDNA haplotype (73, 146, 150, 195, 263, 315.1C, 16140, 16182C, 16183C, 16189, 16217, 16274, and 16335) was shared by 11 (4.44%) individuals. The nucleotide diversity and mean of pair-wise differences were found to be 0.036063 ± 0.020101 and 12.544022 ± 6.230486, respectively.