Diversities of HLA-A, -B, -C, -DRB1 and -DQB1 loci in Chinese Kazak population and its genetic relatedness dissection with multiple populations: a comparative study.

Studying the allele and haplotype distributions of human leukocyte antigen (HLA) loci at 2nd-field level in different populations was important. Allele and haplotype frequencies of HLA-A, -B, -C, -DRB1 and -DQB1 loci in 110 unrelated healthy Kazak individuals living in Xinjiang (China) were analyzed using polymerase chain reaction sequence based typing. Thirty HLA-A, 48 HLA-B, 24 HLA-C, 34 HLA-DRB1 and 18 HLA-DQB1 alleles were detected at the 2nd-field level in the Kazak population. Frequencies of HLA alleles, genotypes, and haplotypes were calculated, and some exhibited significantly different distributions among different populations. A neighbor-joining (NJ) tree, heatmap, multidimensional scaling (MDS) and principal component analysis (PCA) were used to explore the genetic relationships between the Kazak population and 32 reference populations distributed in Asia, Africa, America and Europe using frequency data of HLA-A, -B, -C and -DRB1 loci. The NJ tree, heatmap, and MDS of the 33 populations were constructed based on pairwise DA values of populations obtained by the HLA-A, -B, -C and -DRB1 allele frequencies. Different PCA plots were constructed based on the allele frequencies of HLA-A, -B, -C and -DRB1 or estimated haplotypic frequencies of HLA-A, -B, -C loci. The data obtained in the present research can be used for research on HLA-related diseases or paternity relationships, and aid to finding the best matched donors in stem cell transplantation for Kazak individuals.

Ancestry informative DIP loci for dissecting genetic structure and ancestry proportions of Qinghai Tibetan and Tibet Tibetan groups.

Tibetans living in the Qing-Tibet plateau show unique genetic features since they are exposed to the high altitude environment. Accordingly, it is necessary for us to analyze genetic components of the Tibetan groups. Here, genetic structure and ancestry proportions of Tibet Tibetan and Qinghai Tibetan groups are dissected by using a previously published ancestral deletion/insertion polymorphisms (DIPs) panel. Genetic distributions of the analyzed DIPs in both Tibetan groups reveal that some DIPs show relatively balanced frequency distributions with the values ranging from 0.4 to 0.6, implying that these DIPs could be used as individual identification loci for forensic applications in both groups. Besides, the cumulative power of discrimination of the panel also reflects that the panel could serve as a valuable tool for forensic individual identifications in Tibet Tibetan and Qinghai Tibetan groups. Population genetic analyses including principal component analysis, DA genetic distances, phylogenetic tree, and genetic structure reveal that two studied Tibetan groups have closer genetic affiliations with East Asian populations. Genetic differentiation analyses of two Han populations, Xinjiang Uyghur and two Tibetan groups reveal that some DIP loci might be informative for differentiating Uyghurs from the other populations.

Genetic variation and forensic efficiency of autosomal insertion/deletion polymorphisms in Chinese Bai ethnic group: phylogenetic analysis to other populations.

Thirty insertion/deletion loci were utilized to study the genetic diversities of 125 bloodstain samples collected from Bai group in Yunnan Dali region, China. The observed heterozygosity and expected heterozygosity of the 30 loci ranged from 0.1520 to 0.5680, and 0.1927 to 0.4997, respectively. No deviations from Hardy-Weinberg equilibrium tests after Bonferroni correction were found at all 30 loci in Bai group. The cumulative probability of exclusion and combined discrimination power were 0.9859 and 0.9999999999887, respectively, which indicated the 30 loci could be used as complementary genetic markers for paternity testing and were qualified for personal identification in forensic cases. We found the studied Bai group had close relationships with Tibetan, Yi and Han groups from China by the population structure, principal component analysis, population differentiations, and phylogenetic reconstruction studies. Even so, for a better understanding of Bai ethnicity's genetic milieu, DNA genotyping at various genetic markers is necessary in future studies.

Chinese Xibe population genetic composition according to linkage groups of X-chromosomal STRs: population genetic variability and interpopulation comparisons.

BACKGROUND: The Xibe population is one of China's officially recognised populations and is now distributed separately from west to east in the northern part of China. X-chromosomal short tandem repeats have a special inheritance pattern, and could be used as complements in forensic application, especially for complex or deficiency cases. SUBJECTS AND METHODS: This study obtained the allelic and haplotypic frequencies of 19 X-STR loci in the Xibe population from Xinjiang Uygur Autonomous Region, China, and studied the genetic differentiations between the Xibe and other populations. RESULTS: The combined power of discrimination in females and males and mean exclusion chances in deficiency cases, normal trios and duo cases was at least 0.999 999 994. In the haplotypic study, the Xibe population showed a more similar pattern of haplotype distribution with Asian populations than populations from other continents, while allelic study also indicated a closer relationship between the Xibe and Asian populations. CONCLUSIONS: The 19 X-STR loci would be useful in forensic application in the studied population. The Xibe population showed a closer genetic relationship with Asian populations in the study, and more population data would be necessary for more detailed genetic relationship studies.

Genetic polymorphisms of 54 mitochondrial DNA SNP loci in Chinese Xibe ethnic minority group.

We analyzed the genetic polymorphisms of 54 mitochondrial DNA (mtDNA) variants in Chinese Xibe ethnic minority group. A total of 137 unrelated healthy volunteers from Chinese Xibe group were the objects of our study. Among the selected loci, there were 51 variable positions including transitions and transversions, and single nucleotide transitions were common (83.93%) versus transversions. These variations defined 64 different mtDNA haplotypes exclusive of (CA)n and 9 bp deletion variation. The haplotype diversity and discrimination power in Xibe population were 0.9800 ± 0.004 and 0.9699, respectively. Besides, we compared Xibe group with 18 other populations and reconstructed a phylogenetic tree using Neighbor-Joining method. The result revealed that Xibe group was a close to Xinjiang Han and Yanbian Korean groups. Our data also indicated that Xibe group has a close relationship with Daur and Ewenki groups, which is reflected by the history that Xibe was influenced by Daur and Ewenki groups during the development of these groups. In conclusion, the variants we studied are polymorphic and could be used as informative genetic markers for forensic and population genetic application.

Population genetic structure analysis and forensic evaluation of Xinjiang Uigur ethnic group on genomic deletion and insertion polymorphisms.

BACKGROUND: The Uigur ethnic minority is the largest ethnic group in the Xinjiang Uygur Autonomous Region of China, and valuable resource for the study of ethnogeny. The objective of this study was to estimate the genetic diversities and forensic parameters of 30 insertion-deletion loci in Uigur ethnic group from Xinjiang Uigur Autonomous Region of China and to analyze the genetic relationships between Xinjiang Uigur group and other previously published groups based on population data of these loci. RESULTS: All the tested loci were conformed to Hardy-Weinberg equilibrium after Bonferroni correction. The observed and expected heterozygosity ranged from 0.3750 to 0.5515; and 0.4057 to 0.5037, respectively. The combined power of discrimination and probability of exclusion in the group were 0.99999999999940 and 0.9963, respectively. We analyzed the D A distance, interpopulation differentiations and population structure, conducted principal component analysis and neighbor-joining tree based on our studied group and 21 reference groups. The present results indicated that the studied Xinjiang Uigur group (represented our samples from the whole territory of Xinjiang Uigur Autonomous Region) had a close relationships with Urumchi Uigur (represented previously reported samples from Urumchi of Xinjiang) and Kazak groups. CONCLUSIONS: The present study may provide novel biological information for the study of population genetics, and can also increase our understanding of the genetic relationships between Xinjiang Uigur group and other groups.

Study of genetic diversity of killer cell immunoglobulin-like receptor loci in the Tujia ethnic minority.

The aim of this study was to analyze the genetic profiles of 14 killer cell immunoglobulin-like receptor (KIR) genes and 2 pseudogenes of 124 individuals from Tujia ethnic minority residing in Enshi Tujia and Miao autonomous prefecture of Hubei province of China and investigate the genetic relationships between the Tujia ethnic minority and other reported groups for the first time. Sequence specific primer amplification (PCR-SSP) methods were used to genotype the 14 KIR genes and 2 pseudogenes. The observed carrier frequencies (OF) and the gene frequencies (GF) of the KIR genes were measured. Neighbor-joining (N-J) tree and the principal component analysis (PCA) plot were constructed. All individuals were typed positive for the three framework loci KIR3DL3, 2DL4 and 3DL2, as well as for pseudogene KIR3DP1. The gene frequencies of the other KIR genes ranged from 9% in KIR2DS2 to 98% in KIR2DP1 and KIR3DL1. The present study of the KIR genes may be a powerful tool for enriching the Chinese ethnical gene information resources of the KIR gene pool, as well as for the anthropological research.

Allele and haplotype diversity of new multiplex of 19 ChrX-STR loci in Han population from Guanzhong region (China).

X-chromosomal short tandem repeats (X-STRs) have been proved to be useful for some deficiency paternity cases in recent years. Here, we studied the genetic polymorphisms of 19 X-STR loci (DXS10148-DXS10135-DXS8378, DXS10159-DXS10162-DXS10164, DXS7132-DXS10079-DXS10074-DXS10075, DXS6809-DXS6789, DXS7424-DXS101, DXS10103-HPRTB-DXS10101 and DXS7423-DXS10134) in 252 male and 222 female individuals from Guanzhong Han population, China. No deviation for all 19 loci was observed from the Hardy-Weinberg equilibrium. The polymorphism information content values of the panel of 19 loci were more than 0.5 with the exception of the locus DXS7423. The combined power of discrimination were 0.9999999999999999999994340 in females and 0.9999999999997662 in males, respectively; and the combined mean exclusion chances were 0.999999993764 in duos and 0.999999999997444 in trios, respectively. The haplotype diversities for all the seven clusters of linked loci were more than 0.9. The results showed that the panel of 19 X-STR loci were powerful for forensic applications in Guanzhong Han population. Locus by locus population comparisons showed significant differences at more than seven loci between Guanzhong Han population and the groups from North America, Europe and Africa.

Genetic analysis of 15 mtDNA SNP loci in Chinese Yi ethnic group using SNaPshot minisequencing.

SNaPshot minisequencing is a rapid and robust methodology based on a single base extension with a labeled ddNTP. The present study detected 15 selected SNPs in the mitochondrial DNA (mtDNA) control and coding regions by minisequencing methodology using SNaPshot for forensic purpose. The samples were collected from 99 unrelated individuals of the Yi ethnic minority group in Yunnan Province. We have predominantly found high-frequency transitions (91.7%) and a significantly lower frequency of transversions (8.3%). The nt152, 489, 8701, 10,398, 16,183, and 16,362 loci were highly polymorphic, while the nt231, 473 and 581 loci were not polymorphic in the studied population. Based on these 15 SNPs, a total of 28 mtDNA haplotypes were defined in 99 individuals with the haplotype diversity of 0.9136. Also, we compared the mtDNA sequences of Yi group and other 9 populations worldwide and drew a Neighbor-Joining tree based on the shared 12 mtDNA SNP loci, which demonstrated a close relationship between Yi and Bai groups. In conclusion, the analysis of the 15 selected SNPs increases considerably the discrimination power of mtDNA. Moreover, the SNaPshot minisequencing method could quickly detect mtDNA SNPs, and is economical and sensitive. The set of selected 15 SNPs is highly informative and is capable for anthropology genetic analysis.

Forensic evaluation and population genetic study of 30 insertion/deletion polymorphisms in a Chinese Yi group.

Insertion/deletion polymorphisms have become a research hot spot in forensic science due to their tremendous potential in recent years. In the present study, we investigated 30 indel loci in a Chinese Yi ethnic group. The allele frequencies of the short allele of the 30 indel loci were in the range of 0.1025-0.9221. The power of discrimination values were observed ranging from to 0.2630 (HLD111 locus) to 0.6607 (HLD70 locus) and probability of exclusion values ranged from 0.0189 (HLD111 locus) to 0.2343 (HLD56 locus). The combined power of discrimination and power of exclusion for 30 loci in the studied Yi group were 0.99999999995713 and 0.97746, respectively, which showed tremendous potential for forensic personal identification in the Yi group. Moreover, the DA distances, phylogenetic tree, principal component analysis, and cluster analysis showed the Yi group had close genetic relationships with the Tibetan, South Korean, Chinese Han, and She groups.

Genetic variability and phylogenetic analysis of Han population from Guanzhong region of China based on 21 non-CODIS STR loci.

In the present study, we presented the population genetic data and their forensic parameters of 21 non-CODIS autosomal STR loci in Chinese Guanzhong Han population. A total of 166 alleles were observed with corresponding allelic frequencies ranging from 0.0018 to 0.5564. No STR locus was observed to deviate from the Hardy-Weinberg equilibrium and linkage disequilibriums after applying Bonferroni correction. The cumulative power of discrimination and probability of exclusion of all the 21 STR loci were 0.99999999999999999993814 and 0.999998184, respectively. The results of genetic distances, phylogenetic trees and principal component analysis revealed that the Guanzhong Han population had a closer relationship with Ningxia Han, Tujia and Bai groups than other populations tested. In summary, these 21 STR loci showed a high level of genetic polymorphisms for the Guanzhong Han population and could be used for forensic applications and the studies of population genetics.

Genetic polymorphism analyses of 30 InDels in Chinese Xibe ethnic group and its population genetic differentiations with other groups.

In the present study, we obtained population genetic data and forensic parameters of 30 InDel loci in Chinese Xibe ethnic group from northwestern China and studied the genetic relationships between the studied Xibe group and other reference groups. The observed heterozygosities ranged from 0.1704 at HLD118 locus to 0.5247 at HLD92 locus while the expected heterozygosities ranged from 0.1559 at HLD118 locus to 0.4997 at HLD101 locus. The cumulative power of exclusion and total probability of discrimination power in the studied group were 0.9867 and 0.9999999999902 for the 30 loci, respectively. Analyses of structure, PCA, interpopulation differentiations and phylogenetic tree revealed that the Xibe group had close genetic relationships with South Korean, Beijing Han and Guangdong Han groups. The results indicated that these 30 loci should only be used as a complement for autosomal STRs in paternity cases but could provide an acceptable level of discrimination in forensic identification cases in the studied Xibe group. Further studies should be conducted for better understanding of the Xibe genetic background.

Developmental validation of the AGCU 21+1 STR kit: a novel multiplex assay for forensic application.

In this study, we describe the developmental validation assay performed on a novel designed STR multiplex system, AGCU 21+1 STR kit. This kit contains a sex-determining locus amelogenin and 21 noncombined DNA index system STR loci, that are, D6S474, D12ATA63, D22S1045, D10S1248, D1S1677, D11S4463, D1S1627, D3S4529, D2S441, D6S1017, D4S2408, D19S433, D17S1301, D1GATA113, D18S853, D20S482, D14S1434, D9S1122, D2S1776, D10S1435, and D5S2500. The 21+1 kit was validated by a series of tests including optimized PCR conditions, sensitivity, precision and accuracy, stutter ratio, DNA mixture, inhibitors, and species specificity according to the revised validation guidelines issued by the Scientific Working Group on DNA Analysis Methods (SWGDAM). Our results in this study show that the kit is a useful tool for forensic application.

Single nucleotide polymorphisms of mitochondrial DNA HVS-I and HVS-II in Chinese Bai ethnic group.

For forensic and population genetic purposes, a total of 125 unrelated volunteers' blood samples were collected from Chinese Bai ethnic minority group to analyze sequence variation of two hypervariable segments (HVS-I and HVS-II) in the mitochondrial DNA control region. Comparing the HVS-I and HVS-II sequences of the 125 Chinese Bais to the Anderson reference sequence, we found 86 polymorphic loci in HVS-I and 40 in HVS-II in mitochondrial DNA sequences of the Chinese Bai ethnic minority group, which defined 93 and 53 different haplotypes, respectively. Haplotype diversity and the mean pairwise differences were 0.992 ± 0.003 and 6.553 in HVS-I, and 0.877 ± 0.027 and 2.407 in HVS-II, respectively. We defined four macrohaplogroups R, M, N and D with the proportions ranging from 9.6% to 40.0%. With the analysis of the hypervariable domain from nucleotide 16 180-16 193 in HVS-I, our study revealed new haplotypes of sequence variations. In addition, the Fst metric, phylogenetic tree, and principal component analysis demonstrated a close genetic relationship between the Bai group and Chinese Han populations from South China, Changsha, and Guangdong. The results support that the Bai group is a multiorigin ethnic minority that has merged with the Chinese Han population.

Structural polymorphism analysis of Chinese Mongolian ethnic group revealed by a new STR panel: genetic relationship to other groups.

Mongolian is the eighth largest ethnic minority on Chinese population data according to the 2010 census. In the present study, we presented the first report about the allelic frequencies and forensic statistical parameters at the 21 new STRs and analyzed linkage disequilibrium of pairwise loci in the Mongolian ethnic minority, China. Hardy-Weinberg equilibrium tests demonstrated no significant deviations except for the D1S1627 locus. The cumulative power of discrimination and power of exclusion of all the loci are 0.9999999999999999992576 and 0.9999997528, respectively. The results of analysis of molecular variance showed that significant differences between the Mongolian and the other eight populations were found at 1-9 STR loci. In population genetics, the results of principal component analysis, structure analysis, and phylogenetic reconstruction analysis indicated shorter genetic distance between the Mongolian group and the Ningxia Han. All the results suggest that the 21 new STR loci will contribute to Chinese population genetics and forensic caseworks in the Mongolian group.

Polymorphic distribution and forensic effectiveness study of eight miniSTR in Chinese Uyghur ethnic group.

We obtained the allelic frequencies and forensic efficiency data for eight mini short tandem repeat loci including Penta E, D12S391, D6S1043, D2S1338, D19S433, CSF1PO, Penta D and D19S253 loci from a sample of 128 unrelated Uyghur individuals from China. The amplification products of the eight STR loci are <240 bp in size. A total of 94 alleles were observed and the corresponding allelic frequencies ranged from 0.0039 to 0.3438 in the present study. Observed genotype distributions for each locus do not show deviations from Hardy-Weinberg equilibrium expectations. The combined power of discrimination, combined power of exclusion and combined matching probability of the eight STR loci equaled to 0.999999999963373, 0.9997770 and 3.6627 × 10(-11), respectively. Because of the small fragment length of PCR products and the high degree of polymorphisms, the eight STR loci are highly beneficial for the forensic analysis of degraded DNA samples which are commonly observed in forensic cases. The STR data of the Uyghur group were compared with the previously published population STR data of other groups from different ethnic or areas, and significant differences were observed among these groups at some loci.

Genetic profile characterization and population study of 21 autosomal STR in Chinese Kazak ethnic minority group.

Short tandem repeat loci have been recognized as useful tools in the routine forensic application and in recent decades, more and more new short tandem repeat (STR) loci have been constantly discovered, studied, and applied in forensic caseworks. In this study, we investigated the genetic polymorphisms of 21 STR loci in the Kazak ethnic minority as well as the genetic relationships between the Kazak ethnic minority and other populations. Allelic frequencies of 21 STR loci were obtained from 114 unrelated healthy Kazak individuals in the Ili Kazak Autonomous Prefecture, Xinjiang Uigur Autonomous Region of China. We observed a total of 159 alleles in the group with the allelic diversity values ranging from 0.0044 to 0.5088. The highest polymorphism was found at D19S433 locus and the lowest was found at D1S1627. Statistical analysis of the generated data indicated no deviation from Hardy-Weinberg equilibriums at all 21 STR loci. In order to estimate the population differentiation, allelic frequencies of all STR loci of the Kazak were compared with those of other neighboring populations using analysis of molecular variance method. Statistically significant differences were found between the studied population and other populations at 2-7 STR loci. A neighbor-joining tree was constructed based on allelic frequencies of the 21 STR loci and phylogenetic analysis indicates that the Kazak has a close genetic relationship with the Uigur ethnic group. The present results may provide useful information for forensic sciences and population genetics studies, and can also increase our understanding of the genetic background of this group. The present findings showed that all the 21 STR loci are highly genetically polymorphic in the Kazak group, which provided valuable population genetic data for the genetic information study, forensic human individual identification, and paternity tests.

Population genetics and forensic efficiency of twenty-one novel microsatellite loci of Chinese Yi ethnic group.

In this study, we investigated polymorphic distributions of allelic frequencies and forensic genetic parameters of 21 novel autosomal microsatellite loci from 110 unrelated healthy individuals of Chinese Yi ethnic group. Expected heterozygosity, power of discrimination, and polymorphic information content ranged from 0.617 to 0.812, 0.777 to 0.936 and 0.560 to 0.790. The microsatellite loci showed high forensic efficiency. The total discrimination power and cumulate probability of exclusion were 0.99999999999999999986902 and 0.999998818, respectively. Locus-by-locus allelic frequencies were compared using analysis of molecular variance (AMOVA) method, and the statistically significant differences were observed between Yi group and Russian, Tujia, Kazak, Bai, Ningxia Han, Salar, Tibetan, and Uigur groups at 5, 6, 7, 7, 7, 8, 12, and 13 loci, respectively. The results of genetic distance comparisons, genetic structure analyses, and principal component analysis all indicated that the Yi group showed relatively short genetic relationships with Russian, Salar, and Bai group. The experimental results showed that the 21 loci in the multiplex system provided highly polymorphic information and forensic efficiency for forensic individual identification and paternity testing, also basic population data for population genetics and anthropological research.

Allelic frequency distributions of 21 non-combined DNA index system STR loci in a Russian ethnic minority group from Inner Mongolia, China.

We studied the allelic frequency distributions and statistical forensic parameters of 21 new short tandem repeat (STR) loci and the amelogenin locus, which are not included in the combined DNA index system (CODIS), in a Russian ethnic minority group from the Inner Mongolia Autonomous Region, China. A total of 114 bloodstain samples from unrelated individuals were extracted and co-amplified with four fluorescence-labeled primers in a multiplex polymerase chain reaction (PCR) system. Using capillary electrophoresis, the PCR products of the 21 STR loci were separated and genotyped. A total of 161 alleles were observed in the Russian ethnic minority group, and corresponding allelic frequencies ranged from 0.0044 to 0.5965. The 21 non-CODIS STR loci of the Russian ethnic minority group were characterized by high genetic diversity and therefore may be useful for elucidating the population's genetic background, for individual identification, and for paternity testing in forensic practice.