Haplotype data for 23 Y-chromosome markers in four U.S. population groups

The PowerPlex Y23 kit contains 23 Y-chromosomal loci including all 17 of the markers in the Yfiler Y-STR kit plus six additional markers: DYS481, DYS533, DYS549, DYS570, DYS576, and DYS643. We have typed 1032 unrelated population samples from four self-declared US groups: African Americans, Asians, Hispanics, and Western European Caucasians. An analysis of the population genetic parameters and the improvement of adding additional Y-STR markers to the dataset are described.     

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.     

Bimodal allele frequency distribution at Y-STR loci DYS392 and DYS438: no evidence for a deviation from the stepwise mutation model

A deviation from the stepwise mutation model (SMM) has been suggested for the trinucleotide Y-STR locus DYS392, based upon its bimodal allele frequency distribution in various populations. The same type of distribution is also observed for the pentanucleotide Y-STR DYS438. In order to verify whether a departure from an SMM is likely for these two loci, we studied a large number of Portuguese male DNA samples typed for the two loci and in addition, for the Y-STR loci DYS19, DYS389I/II, DYS390, DYS391 and DYS393. The compatibility of the observed allele frequency spectrum with an SMM was assessed by an apportionment of the molecular variance among, and consideration of the molecular distances between, haplotype groups defined according to their allelic state at each of the two markers of interest. For haplotypes carrying either modal alleles 11 or 13 of DYS392, 18.6% of the molecular variance of the remaining Y-STR background could be attributed to variation between the two groups. When all pairwise _st values between haplotype groups were compared, group 12 was found to be closer to 11 than to 13, and group 14 was much closer to 13 than to 12 and 11. It may therefore be concluded that DYS392 allele 13 represents an evolutionary lineage with little or no relationship to 11 and 12. Furthermore, allele 14 is a one-step neighbour of 13 and is therefore likely to represent an offshoot from group 13. For haplotypes carrying either modal allele 10 or modal allele 12 of DYS438, 27.7% of the molecular variance of the Y-STR background was found to be due to variation between the two groups. Comparison of the other pairwise _st values indicated that group 10 was closer to 9 and 11 than to 12, and that group 12 was closer to 11 and 13 than to 10. The lineages defined by the two modal alleles of DYS438 therefore also seem to be phylogenetically distant. When the two loci were analysed in combination, using the standardised linkage disequilibrium measure (D'), a strong association was noted between alleles DYS392*11 and DYS438*10 (D'=0.70) and between DYS392*13 and DYS438*12 (D'=0.72). Taken together, these results show that the bimodal allele frequency distributions of DYS392 and DYS438 are explicable in terms of (probably the same) historical and demographic causes, rather than a mutational mechanism other than SMM. The loci do therefore not appear to warrant any special attention when applied in population genetic or forensic studies.     

Genetic diversity and haplotype structure of 27 Y-STR loci in a Yanbian Korean population from Jilin Province,Northeast China

In this study, 27 Y-STRs were analyzed in 347 male individuals from the Yanbian Korean population. Haplotype diversity (HD) and discrimination capacity (DC) values were calculated. Pairwise R_st values were evaluated in AMOVA analysis and visualized through multidimensional scaling (MDS). Yflier Plus system indicated higher Discrimination Power (DP), HD and DC which is 0.9969, 0.9998 and 0.9769. There is no significant genetic distance between Yanbian Koreans and South Koreans, however, there is a great distance from Chinese Han population. The present results may provide useful information for paternal lineages in forensic cases and increase our understanding of the genetic relationships between Yanbian Korean and other groups.     

Is MPS always the answer? Use of two PCR-based methods for Y-chromosomal haplotyping in highly and moderately degraded bone material

Forensic and population genetics often rely on Y-chromosomal studies. Whether it is a human identification case, trace evidence examination or phylogenetic analysis, a Y-STR haplotype is an important tool in the hands of law enforcement agencies. A common obstacle in achieving satisfactory results in all of the above mentioned circumstances, is low DNA quantity and quality within samples obtained.In this study we have examined Y-STR haplotypes in 75 bone material samples, coming from different time periods. For this purpose we have chosen YFiler Plus PCR Amplification Kit (ThermoFisher Scientific) and ForenSeq Signature DNA Prep Kit (Verogen Inc.), which use two different allele calling technologies – capillary electrophoresis and Massively Parallel Sequencing respectively. Full profiles were obtained from DNA extracts with as little as 0.1896 ng (Degradation Index 1.3) (ForenSeq) and 0.0591 ng (Degradation Index 26.8) (YFiler Plus) DNA input. The results that we present in this paper show differences in amplification rates between common markers in both kits. The differences strictly reflect mean amplicon length of markers. This, however, does not seem to influence Y-haplogroup estimation results noticeably. In one sample a discordance occurred between haplotypes obtained with both methods, where a 24 allele was called in DYS390 marker by capillary electrophoresis, while for the same sample in this locus a 23 allele was shown with MPS. A reason for this is yet to be investigated. The sequence analysis revealed a significant variation between isometric alleles, especially within repetitive regions of studied Y-STR markers.     

利用重新设计的引物对三个Y-STR基因座进行复合扩增

目的改良一种同步检测Y—STR基因座的方法。方法采用重新设计的Y—STR基因座引物，用优化的复合扩增技术同时扩增3个Y—STR基因座(DYS390、DYS391、DYS393)。结果成功地同步扩增出3个Y—STR基因座，将其中DYS391基因座的片段大小由279～287bp缩短至142～150bp，同时还提高了DYS393基因座的男性特异性。结论利用重新设计的Y—STR基因座引物进行复合扩增，为快速检测多个基因座提供了有效的途径，是法科学领域中一种值得推荐的方法。     

Y-STR多态性与人类学

人类Y染色体短串联重复序列(Y-STR)具有父系遗传、缺乏重组、分型简单、信息量大、多态性高等特点,是研究人类的起源进化、民族差异、种族差异、群体及地区分布等的有力工具。本文就Y-STR多态性与其在人类学方面的应用作一综述。     

负荷试验CT灌注成像结合HIF1α、MMP2及VEGF评价大鼠C6胶质瘤侵袭力

 目的 探寻负荷试验CT灌注成像中可以无创评估神经胶质瘤侵袭性的影像学生物标志物。方法 取20只雄性大鼠随机分为4组,其中3组分别在原位种植C6胶质瘤10、14、18天后行CT灌注成像,1组注射生理盐水作为对照。在乙酰唑胺负荷前后进行CT灌注,收集并分析各项灌注生物标志物。再取各组鼠脑开展病理学检验,进行缺氧诱导因子1α（hypoxia-inducible factor-1 α,HIF1α）、基质金属蛋白酶2（matrix metalloproteinase 2,MMP2）及血管内皮生长因子（vascular endothelial growth factor,VEGF）免疫组织化学染色。结果 乙酰唑胺负荷后脑血流量（cerebral blood flow,CBF）、脑血容量（cerebral blood volume,CBV）和表面通透性（surface-permeability,PS）明显高于负荷前;随肿瘤种植天数的增加,CBF、CBV和PS百分比变化率随之降低,尤其是18天组与对照组之间比较：对照组分别为119.5%±21.2%、125.6%±9.0%、816.2%±116.4%,而18天组分别为54.6%±2.0%、24.5%±4.3%、4.5%±0.8%;HIF1α、MMP2及VEGF阳性率和CBF、CBV、PS百分比变化率之间呈显著负相关（P均 < 0.01）。结论 负荷试验CT灌注成像的影像学生物标志物CBF、CBV和PS百分变化率可以无创评价大鼠C6胶质瘤的侵袭性。     

Haplotype frequencies of nine Y-chromosome STR loci in the Taiwanese Han population

Haplotype frequencies of nine Y-chromosome STR loci (DYS19, DYS385, DYS388, DYS389I, DYS389II, DYS390, DYS391, DYS392 and DYS393) in the Taiwanese Han population were established. A total of 183 unrelated individuals produced 162 haplotypes, of which 146 were unique, 1 was found in 5 individuals, 2 were found in 3 individuals and 13 were found in 2 individuals. The haplotype diversity (99.99%) and discrimination capacity (88.5%) were calculated. A family study of 109 father/son pairs in 100 families showed 2 mutational events in the DYS389II locus and 1 in the DYS392 locus. Received: 20 February 2001 / Accepted: 15 May 2001     

Appel Botha Cornelitz: The abc of a three hundred year old divorce case

In 1683 Maria Kickers and Jan Cornelitz got married in Cape Town. Today, 330 years later, the living patrilineal descendants of Maria's four sons, number in excess of 76,000 people. Curiously, none of them carry the surname Cornelitz – in fact, they are all called Botha and include former President P.W. Botha, general Louis Botha and Minister Pik Botha. The reason for this anomaly is also the reason why Jan got divorced from Maria in 1700. According to Maria's testimonies she did indeed have a long term relationship with Frederik Botha, but in her defence she claimed that her husband was impotent and that he actually encouraged her. Other witnesses, presumably prompted by Jan, gave testimonies that implied that Maria was in fact licentious. We combined haplotyping with the AmpFℓSTR^® Yfiler™ kit with deep-rooting genealogies to show that Maria's first son was actually fathered by Ferdinandus Appel and that roughly half the living Bothas (38,000 people) actually descend from Ferdinandus Appel while the remaining three sons all stem from the same father, presumably Frederik Botha, and this implies that Maria's husband did not father any of her sons.