Y-chromosome STR haplotype diversity in Brazilian populations

A sample of 198 unrelated males distributed among the five geopolitical regions in Brazil were typed for the minimal Y-STR haplotype composed of microsatellite loci DYS19, DYS385I/II, DYS389I, DYS389II, DYS390, DYS391, DYS392 and DYS393. Gene frequency data, gene diversity, haplotype diversity and power of discrimination were estimated. An AMOVA indicated that 99.97% of the haplotypic variation is found within regions and only a small 0.03% and non significant variation is found among the five regions (Fst=0.00031, P-value=0.43). This result suggests that a single national database of Y-STR haplotypes can be used in the quantitative assessment of matches in forensic casework in the Brazilian population. A significant haplotype diversity of 99.8% was found and 172 different haplotypes were observed in 198 chromosomes. Haplotype (14-11, 14-13-29-24-11-13-13) with five occurrences in 198 chromosomes was the most frequent in Brazil.     

云南白族群体Y-STR及Y-SNP关联性探讨

目的探讨Y-STR与Y-SNP单倍群间的关联性及其法医学应用价值。方法用Y-filer的17个Y-STR基因座及6个Y-SNPs（M122、M95、M9、M130、M119和M45）对云南白族146名无关男性个体样本进行检测。结果①17个Y-STR基因座构成的单倍型在146名男性个体中共检出114种单倍型,其中93种仅出现于一名个体中。②6个Y-SNPs在白族中的频率为4.1%～47.3%,其中O3-M122频率最高,占47.3%。③综合两类遗传标记结果,出现于2名或2名以上个体的21种Y-STR单倍型中,有5种其Y-SNP不同;分别只有一个Y-STR基因座分型不同的29对单倍型中,有8对其Y-SNP分别不同。Y-SNP单倍群间部分Y-STR基因座等位基因频率分布存在一定差异。结论 Y-STR单倍型相同或相近的个体间其Y-SNP分型可不相同,结合两者进行检测分析对于男性嫌疑人家系排查具有重要意义。     

Examination of Y-STR mutations in sex chromosomal abnormality in forensic cases

The Y-STR typing was carried out on eight DNA samples (three from criminal cases) demonstrating Klinefelter's syndrome. STR types in the X chromosome were randomly distributed. However, some Y-STR markers were distributed within the normal range but restricted to only one or two specific alleles, that is, some specific haplotypes were found in Klinefelter's syndrome. In addition, a single nucleotide polymorphism in DYS390 (transversion of G to A at the 28th position downstream of tandem repeats) was detected in Klinefelter samples. This Y-STR polymorphism and restricted Y-STR alleles in Klinefelter's syndrome is not known, but it might be related to the genesis of Klinefelter's syndrome. We also found that extended standard haplotypes of these samples are extremely rare in the normal population, according to the Y-STR haplotype reference database (YHRD). The extended standard haplotype database in a Japanese population is also reported. In 100 unrelated Japanese, 89 haplotypes were observed, and the haplotype diversity was calculated to be 0.9866.     

Online Y-chromosomal short tandem repeat haplotype reference database (YHRD) for U.S. populations

We describe here an online Y-chromosomal short tandem repeat haplotype reference database (YHRD) for U.S. populations, which represents 9-locus Y-STR haplotypes for 1705 African-Americans, European-Americans and Hispanics as of October 2001. This database is available online (http://www.ystr. org/usa/), free to access and was generated in order to supply the U.S. forensic DNA community with a valuable resource for frequencies of complete or incomplete 9-locus Y-STR haplotypes, as well as information about typing protocols and population genetic analyses. Pairwise R(ST)-statistics derived from the Y-STR haplotypes indicate no significant substructure among African-American populations from different regions of the U.S., nor (usually) among European-American and Hispanic populations. Thus, pooling of Y-STR haplotype data from regional populations within these three major groups is appropriate in order to obtain larger sample sizes. However, pooling of different major populations is generally not recommended due to statistically significant differences between African-American populations and all European-American/Hispanic populations, as well as between some European-American and Hispanic populations.     

Analysis of 16 Y-chromosomal STRs in an African descent sample population of Chocó (Colombia)

We studied and established a database and some parameters of forensic importance were calculated of 16 Y-STR (DYS19, DYS385, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS460, DYS461, GATA-A10, GATA-H4 and DYS635) in a population of 298 unrelated males of African descent of Chocó (Colombia) and a total of 257 haplotypes were identified using the present set of Y-STR markers, of which 224 were represented only once in the database. Twenty-six haplotypes were presents two times, six haplotypes were presents in three individuals and one haplotype in four men. The haplotype diversity was 0.9987 ± 0.0004. By combining the allelic states of the 16 Y-chromosomal STRs we could construct highly informative haplotypes that allowed the discrimination of 86.2% of the samples tested. With this work we established a database of Y-STR and some parameters of forensic importance. This approach represents a very powerful tool for individual identification and paternity testing in forensic genetic.     

北京汉族人群三个Y染色体STR基因座的遗传多态性研究

目的　获得DYS4 37,A7 1,H4三个Y染色体STR基因座及其单倍型在北京汉族人群中的遗传多态性分布 ,并探讨其法医学应用价值。方法　应用自行建立的Y STR 15 plex复合扩增体系 ,对用酚 /氯仿法提取的 132份北京地区汉族无关男性个体血样DNA样品进行复合扩增 ,用ABI310型遗传分析仪对扩增产物进行检测 ,统计分析 3个Y STR基因座的群体遗传学参数。结果　DYS4 37,A7 1,H4三个Y STR基因座在该群体中分别检出 4 ,5 ,4个等位基因 ,GD值分别为 0 4 977,0 6 731,0 5 42 0 ;观察到 32种单倍型 ,其中 17种单倍型出现 1次 ,最多 1种单倍型出现 2 0次 ,单倍型累积GD值为 0 9118。结论　 3个Y STR基因座具有较强的个体识别能力 ,在法医学个体识别和亲权鉴定中具有很高的应用价值     

Y染色体STR的银染复合扩增

目的建立一套Y染色体STR的复合扩增体系,检测中国藏族人群的单倍型分布。方法利用复合扩增的方法扩增DYS434、DYS443和DYS456三个基因座,利用聚丙烯酰胺凝胶电泳银染进行分型,检测西藏藏族101名无关男性个体单倍型分布。结果三个基因座在藏族样本中分别检测出4、4、6个等位基因,共检测出31种单倍型,其单倍型的变异度是0.9481,标准误为0.0049。结论Y-STR的复合扩增在法医学的亲权鉴定和个人识别中有重要的作用。     

Online reference database of European Y-chromosomal short tandem repeat (STR) haplotypes

The reference database of highly informative Y-chromosomal short tandem repeat (STR) haplotypes (YHRD), available online at http://ystr.charite.de, represents the largest collection of male-specific genetic profiles currently available for European populations. By September 2000, YHRD contained 4688 9-locus (so-called "minimal") haplotypes, 40% of which have been extended further to include two additional loci. Establishment of YHRD has been facilitated by the joint efforts of 31 forensic and anthropological institutions. All contributing laboratories have agreed to standardize their Y-STR haplotyping protocols and to participate in a quality assurance exercise prior to the inclusion of any data. In view of its collaborative character, and in order to put YHRD to its intended use, viz. the support of forensic caseworkers in their routine decision-making process, the database has been made publicly available via the Internet in February 2000. Online searches for complete or partial Y-STR haplotypes from evidentiary or non-probative material can be performed on a non-commercial basis, and yield observed haplotype counts as well as extrapolated population frequency estimates. In addition, the YHRD website provides information about the quality control test, genotyping protocols, haplotype formats and informativity, population genetic analysis, literature references, and a list of contact addresses of the contributing laboratories.     

Grouping of Y-STR haplotypes discloses European geographic clines

Y-STR haplotypes are widely studied in Europe and an extensive databasing effort has been conducted (http://www.ystr.org). The distribution of these haplotypes has been considered to present no evidence for substructure at central and southern European level. This picture contrasts with the one that results from Y haplogroups defined by binary markers. This paradox has been solved by admitting that the high STR mutation rate and corresponding recurrence has erased geographic structuration. This explanation prompted us to reanalyse Y-STR haplotypes distribution bearing in mind the commonly admitted model for the generation of diversity in these markers, namely the stepwise mutation model (SMM) and, thus, taking the molecular distance between haplotypes into consideration. Accordingly, we have studied the European distribution of the two most frequent haplotypes in the Iberian Peninsula and their one step neighbours using the European samples deposited in the Y STR database (http://www.ystr.org). For the first group we found a clear-cut decreasing W-E gradient, while for the second the highest frequencies were found in the Iberian Peninsula (3.98% in Portugal and 3.85% in Spain), dropping to 2.88% in France and showing a less well defined SW-NW gradient. Furthermore, we have tested the agreement between haplotype groups and binary markers haplogroups in a random sample of 292 individuals from Northern Portugal. Our results demonstrate that (a) Y-STR haplotype data can be used for wide-scale anthropological approaches disclosing information that has been considered only available through binary markers and (b) forensic use of continental databases needs careful refinement, due to the macro-geographic pattern now evidenced.     

Utility of the Y-STR typing systems Y-PLEX 6 and Y-PLEX 5 in forensic casework and 11 Y-STR haplotype database for three major population groups in the United States

The Y-PLEX 6 and Y-PLEX 5 systems enable analysis for 11 Y-STR loci. We present here the utility of these systems in forensic casework. A total of 188 samples, including 127 evidence samples, were analyzed using either or both of the systems. The evidence sample types included fingernail scrapings, sperm or seminal fluid, epithelial cells, blood and other tissues. The Y-STR typing systems provided useful probative results in difficult cases. A reference database for Caucasian (n = 517), African American (n = 535), and Hispanic (n = 245) population groups within the United States was generated for estimating the haplotype frequency in forensic casework. Among the individuals profiled, 311 Caucasians, 412 African Americans, and 194 Hispanics provided unique profiles in their respective population datasets. This is the first report describing the haplotype database for the set of 11 Y-STR loci recommended by the Scientific Working Group on DNA Analysis Methods (SWGDAM). Linkage analysis reveals that the frequencies from forensically important autosomal loci can be multiplied with the Y-STR haplotype frequency. The results from Y-PLEX systems have been accepted in courts in the United States.     

3个Y-STR的复合扩增及其单倍型

目的 建立复合扩增Y-STR基因座的体系,获得广东汉族人的单倍型频率。方法 复合扩增DYS439、DYS437和DYS434三个基因座,用聚丙烯酰胺凝胶电泳银染法进行基因分型,检测广东汉族327名无关男性个体的单倍型。结果 3个基因座分别检出6个、4个和4个等位基因,共38种单倍型,其单倍型的个体识别率为0.8796。结论 Y-STR基因座复合扩增体系和建立的Y染色体STR数据库,在法医学鉴定中有应用意义。     

珠海地区汉族人群10个Y-STR基因座的多态性

目的 调查珠海地区汉族人群10个Y-STR基因座及其单倍型的遗传多态性，探讨其法医学应用价值。方法 应用Y-PLEX荧光标记复合扩增系统，对珠海地区汉族200名无关男性个体进行10个Y-STR基因座的复合扩增，用ABI310型基因分析仪对扩增产物进行检测，统计10个Y-STR基因座的群体遗传学参数。结果 9个Y-STR基因座分别检出5、6、6、5、4、5、5、5、7个等位基因，DYS385基因座检出44种单倍型；GD值最低为0.3904(DYS391)，最高为0.9497(DYS385)；10个Y-STR基因座共同构成的单倍型161种，其中134种单倍型只出现1次，20种单倍型出现2次，3种单倍型出现3次，3种单倍型出现4次，1种单倍型出现5次，累计GD值为0.9948。结论 10个Y-STR基因座具有较高的个体识别能力，可应用于法庭科学中的个体识别与亲权鉴定。     

Mismatch distribution analysis of Y-STR haplotypes as a tool for the evaluation of identity-by-state proportions and significance of matches—the European picture

We suggest the use of the mismatch distribution methodology as an easy way to estimate the distance between all pairs of haplotypes present in a sample. This approach allows the evaluation of the proportion of pairs of Y-STR haplotypes that are prone to become identical by state (IBS), in one generation, by recurrent mutation, a statistic of major importance in the forensic field. The mismatch approach presents some advantages alternatively to the empirical one, since it is not necessary to have simultaneous information on STRs and SNPs, and it allows the evaluation of IBS also within-haplogroups. The estimation of IBS at an European scale showed that there is a high population substructuring for this parameter, increasing from southern-central European countries towards west and north, in accordance to what was found for Y-biallelic markers. This result seems to imply a more careful use of large databases for matching evaluation, even in the absence of population structure for general Y-STR diversity. Furthermore, mismatch distribution can be used to measure the distance between a particular haplotype and all the haplotypes in a sample. When applied to the most frequent haplotypes in Europe it revealed that the opportunity for IBS is not directly related to the frequency of a haplotype, but highly dependent on the proportion of neighbouring haplotypes—so, that reporting on the haplotype frequency for evaluating the significance of a match can be misleading.     

Mismatch distribution analysis of Y-STR haplotypes as a tool for the evaluation of identity-by-state proportions and significance of matches--the European picture

We suggest the use of the mismatch distribution methodology as an easy way to estimate the distance between all pairs of haplotypes present in a sample. This approach allows the evaluation of the proportion of pairs of Y-STR haplotypes that are prone to become identical by state (IBS), in one generation, by recurrent mutation, a statistic of major importance in the forensic field. The mismatch approach presents some advantages alternatively to the empirical one, since it is not necessary to have simultaneous information on STRs and SNPs, and it allows the evaluation of IBS also within-haplogroups. The estimation of IBS at an European scale showed that there is a high population substructuring for this parameter, increasing from southern-central European countries towards west and north, in accordance to what was found for Y-biallelic markers. This result seems to imply a more careful use of large databases for matching evaluation, even in the absence of population structure for general Y-STR diversity. Furthermore, mismatch distribution can be used to measure the distance between a particular haplotype and all the haplotypes in a sample. When applied to the most frequent haplotypes in Europe it revealed that the opportunity for IBS is not directly related to the frequency of a haplotype, but highly dependent on the proportion of neighbouring haplotypes--so, that reporting on the haplotype frequency for evaluating the significance of a match can be misleading.     

复合扩增20个Y-STR基因座及其法医学的应用

目的建立20个Y-STR基因座的复合扩增体系,进行遗传多态性调查,并评价其法医学应用价值。方法采用五色荧光素标记技术,对20个Y-STR基因座(DYS391、DYS389Ⅰ、DYS390、DYS389Ⅱ、DYS438、DYS460、Y GATA H4、DYS456、DYS439、DYS635、DYS448、DYS393、DYS388、DYS437、DYS19、DYS392、DYS458、DYS447、DYS385 a/b)进行复合扩增和毛细管电泳检测;调查辽宁汉族376名无关男性个体20个Y-STR基因座的遗传多态性数据;并对系统性能进行检测。结果本文方法同时检测20个Y-STR基因座,在376名个体中共检出376种单倍型,基因多样性在0.371 1～0.969 8之间;方法特异性好,分型结果准确稳定,灵敏度达0.062 5ng,实际案例常见生物检材的检验结果良好。结论20个Y-STR基因座复合扩增检测法可以用于实际案例检验,调查所获数据对建立Y-STR数据库和相关研究和应用具有重要意义。     

Population genetics of Y-chromosomal microsatellites in Baltic males

Y-chromosomal microsatellites (STRs) are potentially useful in forensic practice but, in contrast to autosomal systems, large and diverse population databases are required in order to facilitate the statistical evaluation of donor-stain matches. Since appropriate data from the Baltic region have so far been lacking, blood samples were obtained from 430 males originating from one of the three Baltic states and these samples were genotyped using a previously described "extended core set" of nine Y-STR marker systems. Allele frequency distributions and discrimination indices were calculated, and the three populations were tested for genetic differences by means of analysis of molecular variance (AMOVA). A larger genetic difference became apparent between Estonian and both Lithuanian and Latvian males than between the latter two, non-Finno-Ugric speaking populations. The haplotype data reported here have been included into the Y-STR database maintained at the Institute of Legal Medicine, Humboldt University, Berlin.     

Searching for the origin of Romanies: Slovakian Romani, Jats of Haryana and Jat Sikhs Y-STR data in comparison with different Romani populations

Haplotype frequencies for 11 Y-STR markers (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385, DYS437, DYS438 and DYS439) in a Romani population (n=63) from Slovakia, Jats of Haryana (n=84) and Jat Sikhs (n=80) from India were determined. The Slovakian Romani, the Haryana and Sikh populations were endogamous based on their unique haplotype ratio and haplotype diversity values, although the Sikh population appeared to be more diverse. AMOVA revealed non-significant differences between the Romanies and significant differences with non-Romani populations. The Macedonian Romani population differed from all Romani populations examined. Frequent haplotypes observed in Romani populations were sporadic in northwest Indian populations. Thirteen out of 316 populations worldwide were found to share the six most frequent haplotypes of the Slovakian Romanies when the screening conditions were narrowed based on the population size to be over 40, the occurrence of the haplotypes was more than one and the sum frequencies of the most frequent haplotypes was at least 0.02. The most common haplotypes were also observed in other Romani groups. When searching with two Indian (Malbar and Malaysian Indian) most frequent haplotypes under the same conditions matches could be detected in all Romani populations except for the Macedonian Romanies. The search with the Jat Sikhs and Jats of Haryana most frequent haplotypes resulted no matches in Romani populations.     

Y-chromosomal STR haplotypes in a population from the Amazon region, Brazil

Haplotype and allele frequencies of the nine Y-STR (DYS19, DYS389 I, DYS389 II, DYS390, DYS391, DYS392, DYS393, DYS385 I/II) were determined in a population sample of 200 unrelated males from Belém, Brazil. The most common haplotypes are shared by 1.5% of the sample, while 186 haplotypes are unique. The haplotype diversity is 0.9995+/-0.0006. The data obtained were compared to those of other Brazilian populations. AMOVA indicates that 99.91% of all the haplotypical variation is found within geopolitical regions and only 0.09% is found among regions.     

26个Y-STR基因座遗传多态性及突变调查

目的 调查26个Y-STR基因座的突变率和遗传多态性,研究其法医学应用效能.方法 本文以575对蒙古族父子对为模板,统计26个Y-STR基因座的突变率,并且研究26个Y-STR基因座在黑龙江省蒙古族、江西省汉族及福州市汉族等3个地区777个无关男性个体中的遗传多态性,评估该试剂盒的法医学应用价值.结果 26个Y-STR...     

荧光复合扩增检测3个Y—STR基因座单倍型

目的建立检测3个Y-STR基因座Y-GATA-A7.1、DYS456和DYS443的荧光复合扩增体系,并获取中国汉族人群单倍型频率分布。方法用荧光标记引物对郑州地区203名汉族男性无关个体进行3个基因座复合扩增,ABI3100型遗传分析仪检测、分型。结果Y-GATA-A7.1、DYS456和DYS443基因座分别检出5、6和6个等位基因,其基因多样性(GD值)分别为0.6692、0.5839和0.7053。三个基因座构成的单倍型共有44种,单倍型多样性(HD值)为0.9523。结论建立的3个Y-STR基因座荧光标记复合扩增系统具有很高的识别能力,可应用于法医学实践。