A method for genotyping Y chromosome-linked DYS385a and DYS385b loci

We developed a method for genotyping Y chromosome-linked homologous DYS385 loci individually, combining locus-specific polymerase chain reaction (PCR) amplification and previously reported procedures. Duplicated DYS385a (5'-end) and DYS385b (3'-end) loci were located about 41 kb apart and inverted to each other in the Y chromosome, which data was obtained from the human genome sequence in National Center for Biotechnology Information (NCBI), and sequence differences were found at 424 bp down- and upstream of each locus. The locus-specific amplifications were performed using primers designed for this intergenic region, and fragments about 900 bp in length were produced. Polymorphic tetranucleotide arrays in the PCR products were typed according to procedures reported previously. Twenty male subjects were genotyped using this method. Alleles (GAAA)13-(GAAA)21 were observed at the DYS385a locus, and those at DYS385b included alleles (GAAA)9-(GAAA)15. DYS385a alleles, excluding those of identical arrays, were always larger than DYS385b alleles in the same subjects. These data suggest that the DYS385a and DYS385b loci can be amplified completely for discrimination, and the genotypes of the alleles provide information useful for forensic case work and population genetics.     

中国22个人群3个Y-STR基因座的群体遗传学研究

目的：用Y-STR基因座的基因频率探讨中国22个人群的群体遗传关系。方法：收集中国22个人群DYS390、DYS391和DYS393基因座的基因频率资料,采用Phylip3．66统计软件包计算出Nei’s遗传距离,再用MEGA3．1输出系统发生树。结果：天津、安徽、浙江、福建、北京、云南、潮汕、湖南、成都汉族聚为Ⅰ簇;辽宁满族、新疆维吾尔族、陕西汉族、云南藏族、云南蒙古族、新疆柯尔克孜族和甘肃回族为Ⅱ簇;海南黎族和广西壮族、贵州水族和广州汉族为Ⅲ簇;云南普米族和纳西族为Ⅳ簇。结论：汉族人群间群体遗传关系较近,而少数民族群体间遗传关系较远。同时提示Y-STR基因座的基因频率分布与民族起源和地域有相关性。     

Molecular diversity of 23 Y-chromosome short tandem repeat loci in the population of Tuzla Canton,Bosnia and Herzegovina

Abstract

Background: Tuzla Canton is the most populated region in the ethnically mixed territory of Bosnia and Herzegovina, whose genetic analysis could provide an insight into past demographic events.

Aim: Analysis of 23 Y-chromosome STR markers in the population of Tuzla Canton and investigation of the genetic relationship of the male population of the Tuzla Canton and that of the larger Bosnian and Herzegovinian population as well as neighbouring and other European populations.

Subjects and methods: The study was conducted among 100 unrelated healthy adult males from Tuzla Canton that have been genotyped using 23 Y-STR loci included in the PowerPlex Y23 kit. Statistical parameters such as haplotype diversity and allele frequencies were calculated, as well as the R_st-based genetic distances between the new dataset and those from Bosnia and Herzegovina and elsewhere, which were then visualised through multi-dimensional scaling plot and neighbour-joining phylogenetic tree analyses.

Results: The PowerPlex Y23 kit has shown high discrimination capacity, as all 100 individuals have unique haplotypes. The newly incorporated loci seem to be highly informative. Population comparison reveals no statistically significant differences between the study population and the general Bosnian-Herzegovinian population, and between the study population and neighbouring populations.

Conclusion: These results could be used as an additional investigation of the genetic relationship between the regional populations in Bosnia and Herzegovina and neighbouring human populations, as well as for further human population and forensic genetics studies.     

Autosomal and Y-STR analysis of degraded DNA from the 120-year-old skeletal remains of Ezekiel Harper

The 120-year-old skeletal remains of Confederate Civil War soldier Captain Ezekiel “Zeke” Harper were exhumed by court order in January 2011 for DNA analysis. The goal of the DNA testing was to support or refute whether Captain Harper had fathered a son (Earl J. Maxwell) with his Native American maid prior to his murder in 1892. Bones with adequate structural integrity (left tibia, right tibia, right femur, mandible, four teeth) were retrieved from the burial site and sent to the Institute of Applied Genetics in Fort Worth, Texas for analysis. Given the age and condition of the remains, three different extraction methods were used to maximize the probability of DNA recovery. The majority of the DNA isolates from over fifty separate bone sections yielded partial autosomal STR genotypes and partial Y-STR haplotypes. After comparing the partial results for concordance, consensus profiles were generated for comparison to reference samples from alleged family members. Considering the genetic recombination that occurs in autosomal DNA over the generations within a family, Y-STR analysis was determined to be the most appropriate and informative approach for determining potential kinship. Two of Earl J. Maxwell's grandsons submitted buccal samples for comparison. The Y-STR haplotypes obtained from both of these reference samples were identical to each other and to the alleles in Ezekiel Harper's consensus profile at all 17 loci examined. This Y-STR haplotype was not found in either of two major Y-STR population databases (U.S. Y-STR database and YHRD). The fact that the Y-STR haplotype obtained from Ezekiel's skeletal remains and Earl's grandsons is not found in either population database demonstrates its rarity and further supports a paternal lineage relationship among them. Results of the genetic analyses are consistent with the hypothesis that Earl J. Maxwell is the son of Ezekiel Harper.     

A Perspective on the History of the Iberian Gypsies Provided by Phylogeographic Analysis of Y-Chromosome Lineages

The European Gypsies, commonly referred to as Roma, are represented by a vast number of groups spread across many countries. Although sharing a common origin, the Gypsy groups are highly heterogeneous as a consequence of genetic drift and different levels of admixture with surrounding populations. With this study we aimed at contributing to the knowledge of the Roma history by studying 17 Y-STR and 34 Y-SNP loci in a sample of 126 Portuguese Gypsies. Distinct genetic hallmarks of their past and migration route were detected, namely: an ancestral component, shared by all Roma groups, that reflects their origin in India (H1a-M82; ∼17%); an influence from their long permanence in the Balkans/Middle-East region (J2a1b-M67, J2a1b1-M92, I-M170, Q-M242; ∼31%); traces of contacts with European populations preceding the entrance in the Iberian Peninsula (R1b1c-M269, J2b1a-M241; ∼10%); and a high proportion of admixture with the non-Gypsy population from Iberia (R1b1c-M269, R1-M173/del.M269, J2a-M410, I1b1b-M26, E3b1b-M81; ∼37%). Among the Portuguese Gypsies the proportion of introgression from host populations is higher than observed in other groups, a fact which is somewhat unexpected since the arrival of the Roma to Portugal is documented to be more recent than in Central or East Europe.     

Y-STR haplotyping in two Hungarian populations

A set of seven Y-chromosomal STR loci (DYS19, DYS389-I, DYS389-II, DYS390, DYS391, DYS392, DYS393) with the addition of the bilocal marker DYS385 was used to generate male-specific haplotype databases for two Hungarian population samples, Caucasians from the Budapest area and Romanies from Baranya county. At the locus DYS385 three types of intermediate sized alleles were detected in six males. The presence of a (GA) dinucleotide, probably due to an (AA) deletion in the second (GAAA) repeat of the polymorphic repeat region leads to an intermediate allelle 17.2. The intermediate alleles 17.-1 and 18.-1 with the consensus repeat structure of (GAAA)₁₇ and (GAAA)₁₈, respectively, were found to lack a T in the same (T)₇ stretch located within the 3′ flanking region of each allele. The forensic efficiency values for the Romany population were significantly lower than those found in the Central Hungarian and other non-isolated Causasian populations, which may imply a possible common paternal ancestry of some haplotypes in the Romany sample. With pairwise comparisons of inter-population molecular variance, the two populations analyzed here and an Italian population sample, could be clearly distinguished using the seven monolocal Y-STRs. A sizing precision of ≤ 0.14 nucleotide standard deviation was obtained with capillary electrophoresis carried out on an ABI Prism 310 Genetic Analyzer. Objective and accurate genotyping is thus possible using an internal size standard with a high density of fragments. Received: 14 July 1998 / Received in revised form: 8 March 1999     

Investigation of extended Y chromosome STR haplotypes in Sardinia

Y-chromosomal variation of selected single nucleotide polymorphisms (SNPs) and 32 short tandem repeat (STR) loci was evaluated in Sardinia in three open population groups (Northern Sardinia, n = 40; Central Sardinia, n = 56; Southern Sardinia, n = 91) and three isolates (Desulo, n = 34; Benetutti, n = 45, Carloforte, n = 42). The tested Y-STRs consisted of Yfiler^® Plus markers and the seven rapidly mutating (RM) loci not included in the YFiler^® Plus kit (DYF399S1, DYF403S1ab, DYF404S1, DYS526ab, DYS547, DYS612, and DYS626).As expected, inclusion of additional Y-STR loci increased haplotype diversity (h), though complete differentiation of male lineages was impossible even by means of RM Y-STRs (h = 0.99997).Analysis of molecular variance indicated that the three open populations were fairly homogeneous, whereas signs of genetic heterogeneity could be detected when the three isolates were also included in the analysis.Multidimensional scaling analysis showed that, even for extended haplotypes including RM Y-STR markers, Sardinians were clearly differentiated from populations of the Italian peninsula and Sicily. The only exception was represented by the Carloforte sample that, in accordance with its peculiar population history, clustered with Northern/Central Italian populations.The introduction of extended forensic Y-STR panels, including highly variable RM Y-STR markers, is expected to reduce the impact of population structure on haplotype frequency estimations. However, our results show that the availability of geographically detailed reference databases is still important for the assessment of the evidential value of a Y-haplotype match.     

27个Y-STR基因座在中国3个民族的遗传多态性及与其他13个群体的聚类分析

目的研究河南回族、贵州仡佬族和贵州苗族人群的27个Y-STR基因座的遗传多态性及与其他13个群体间的遗传关系,探讨其在法医学和群体遗传学研究中的应用价值。方法采用STRtyper-27Y复合扩增体系分别对河南回族(1080例)、贵州仡佬族(297例)、贵州苗族(221例)无血缘关系的男性个体的27个Y-STR基因座进行扩增,应用3500XL遗传分析仪进行基因分型,采用Mega6.0软件进行群体间的AMOVA分析、聚类分析。结果河南回族、贵州仡佬族和贵州苗族人群的Y-STR基因座单倍型多样性分别为0.9999725、0.9997271和0.9998355,系统鉴别能力分别为0.9851852、0.9629630和0.9819004。AMOVA分析显示,16个人群间的遗传距离在-0.0001~0.2120,相同民族间遗传距离较低,而不同民族群体间遗传距离普遍较大。结论27个Y-STR基因座在河南回族、贵州仡佬族和贵州苗族人群中具有丰富的遗传多态性,研究数据对建立Y染色体数据库、群体遗传学研究和法医学应用中具有重要的参考价值。     

Population genetic data of 4 multicopy Y-STR markers in Chinese

Novel Y chromosomal STR (Y-STR) markers have been continuously discovered during the past decades, promoting the widely application of Y-STRs in the area of forensic science. Here, four multicopy Y-STR markers were focused, including DYF383S1, DYF409S1, DYF411S1 and DYF371, which are rarely reported in China and differ in the number of copies on Y chromosome. Characterization of the markers was performed in population of Hunan province, China, based on sequence analysis. Allele nomenclature and allelic ladder were then developed to avoid the disunity of typing standard. To evaluate their forensic performance, gene diversity of the four loci was investigated in 548 unrelated male individuals from Hunan population. The number of haplotype was analyzed by both conservative (C-type) and expanded approach (E-type) for markers containing more than 2 copies. As detected, there were 7, 9, 13 alleles and 15, 22, 23 haplotypes for DYF383S1, DYF409S1 and DYF411S1, respectively. Thirty-two C-types and 56 E-types were found in DYF371, indicating the highest haplotype diversity (HD) among all tested loci (0.871 and 0.888 for C-type and E-type, respectively). Two other Y-STRs (DYF409S1, DYF411S1) also showed high haplotype diversity (>0.8) in the population. Combining the four loci, discrimination capacity reached 0.505 (C-type) or 0.533 (E-type), and the total HD values exceeded 0.991. The results inferred great potential of the multicopy markers to improve the resolution of paternal identification in China population.     

Genetic polymorphism of 17 Y-STR loci in Han Chinese living in Lanzhou

The genetic polymorphism across 17 Y-STR loci in a population of Hart Chinese in Lanzhou was investigated. Haplotypes and allele frequencies for the 17 Y-chromosomal STRs loci DYS456, DYS389I, DYS390, DYS389 II, DYS458, DYS19, DYS385a/b, DYS393, DYS391, DYS439, DYS635, DYS392, Y GATA H4, DYS437, DYS438 and DYS448 were determined in 500 healthy unrelated autochthonous males from Lanzhou. The results showed that no shared haplotypes were observed. Gene diversity values ranged from 0.3987 （DYS391） to 0.9740 （DYS385a,b）. It was concluded that these loci will be very useful for human identification in forensic cases and paternity tests within the Han Chinese population inhabiting Lanzhou.