Y chromosome STRs in Croatians

Eight Y chromosome short tandem repeat (STR) polymorphisms (DYS19, DYS388, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393) were analyzed in the sample of 457 unrelated Croatian men. A general STR allelic frequency pattern in Croatians corresponds to other European populations with the exception of the loci DYS19 and DYS389II. The most frequent DYS19 allele was 16, while at the DYS389II the most frequent were alleles 30 and 31. The most frequent Y chromosome haplotype (16-13-13-31-24-11-11-13) was found in 33 individuals (7.22%). One hundred and seventy-four haplotypes (38.07%) were observed in single copies.     

Y chromosome STR polymorphisms in a Serbian population sample

Eight Y chromosome short tandem repeat (STR) polymorphisms (DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393) were analyzed in the sample of 114 unrelated males living in Serbia. A general STR allelic frequency pattern in Serbians corresponds to other European populations with the exception of loci DYS19, DYS389II and DYS385. Out of ninety identified haplotypes, 74 (64.91%) appeared in single copies. The most frequent haplotypes (DYS19-DYS385-DYS389I-DYS389II-DYS390-DYS391-DYS392-DYS393) 16-14/15-13-31-24-11-11-13 and 15-15/19-12-28-23-10-12-12 were found in four copies (3.51%). Total haplotype diversity was 0.9947+/-0.0021.     

Allelic and haplotypic frequencies at 11 Y-STR loci in Buryats from South-East Siberia

We have obtained Y-STR haplotypes in 12 loci (DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438 and DYS439) from 215 Buryat males. We have found that one haplotype (15-11,18-13-28-23-10-11-14-14-10-12) comprises more than 30% of Y chromosomes in this population while another haplotype (14-11,13-14-30-23-10-14-14-14-10-10) comprises additional 14% of chromosomes. The population under study seems to be very homogenous as far as Y chromosome is regarded and the most frequent haplotype seems to be the modal haplotype for Buryats.     

Y-chromosomal STR haplotypes in a population sample from continental Greece, and the islands of Crete and Chios

Eight Y chromosome short tandem repeat (STR) polymorphisms (DYS19, DYS385, DYS389I, DYS389II, DYS390, DYS391, DYS392, and DYS393) were analyzed in the sample of 117 unrelated Albanian males living in Kosovo. A general STR allelic frequency pattern in the Albanian population from Kosovo corresponds to other European populations. Fourty six haplotypes were observed in single copy. The most frequent haplotypes were (DYS19-DYS385-DYS389I-DYS389II-DYS390-DYS391-DYS392-DYS393) 14-11/11-13-29-24-11-13-13 (10.26%), 14-14/17-12-28-24-10-11-12 (9.40%), 13-16/18-13-30-24-10-11-13 (9.40%), and 14-17/17-13-31-24-10-11-13 (9.40%).     

26-Locus Y-STR typing in a Bhutanese population sample

26 Y chromosome short tandem repeat (STR) loci were amplified in a sample of 856 unrelated males from Bhutan, using two multiplex polymerase chain reaction (PCR) assays. The first multiplex is the Y-STR 20plex described by Butler et al. [J.M. Butler, R. Schoske, P.M. Vallone, M.C. Kline, A.J. Redd, M.F. Hammer, A novel multiplex for simultaneous amplification of 20 Y chromosome STR markers, Forensic Sci. Int. 129 (2002) 10-24], and the second is a novel (but overlapping) 14plex that targets six additional Y-STRs (DYS425, DYS434, DYS435, DYS436, DYS461, DYS462) and also amplifies the amelogenin locus. The 26-loci give a discriminating power of 0.9957, though even at this resolution one haplotype occurs 24 times. We identify novel alleles at five loci and microvariants at a further three, which were characterised by sequencing. Extended (11-locus) haplotypes for these samples have been submitted to the Y-STR Haplotype Reference Database (YHRD).     

Distribution of Y chromosome lineages in Jerba island population

We have analysed Y chromosome polymorphism on six STR markers (DYS19, DYS389I, DYS390, DYS391, DYS392, and DYS393) and eight classical UEP markers (SRY10831a, YAP, SRY4064, M2, 92R7, M9, SRY2627 and 12f2) in three distinct ethnical, linguistic and cultural groups of Jerba island (Berbers, Arabs and a Jerban group of Sub-Saharan origin). Fst genetic distance and principal co-ordinate analysis based on STR haplotype frequencies, showed a genetic differentiation between the three Jerban groups and a genetic relationship between Jerban Berbers and Mozabites (a well defined Berber group in Algeria). Compound use of UEP and STR markers have increased discriminatory capacity. The detection of the most common haplotype (H9) in both Berbers and Mozabites may be useful in forensic special cases.     

湖北地区汉族人群24个 Y-STR基因座遗传多态性研究

目的 对湖北汉族人群24个Y-STR基因座多态性进行调查,并获得相关的基础遗传学数据.方法 应用AGCU Y24 STR荧光标记复合直接扩增系统及3130XL型DNA测序仪,对湖北地区320对已确定父子关系的640个男性个体血样进行24个Y-STR检测分型.结果 在320名父亲男性个体中,在DYS391、DYS389工、DYS439、DYS389Ⅱ、DYS438、DYS449、DYS456、DYS458、DYS437、DYS635、DYS448、Y-GATA-H4、DYS447、DYS19、DYS392、DYS522、DYS393、DYS388、DYS390、DYS444基因座在湖北地区汉族人群分别检出4～17个等位基因,DYS527a/b检出45个等位基因组,DYS385a/b检出57个等位基因组,各基因座基因多样性最低为0.3838,最高为0.9650;并检出320种单倍型.比对320对父子Y-STR分型,在7680次基因遗传传递中,在DYS449、DYS527、DYS444、DYS389Ⅱ、DYS447、DYS522、DYS385、Y-GATA-H4等10个基因座中检出16个突变,突变率为1.5625‰～1.5653％,平均突变率为2.0833‰;等位基因增加突变与等位基因减少突变比为1∶1.结论 24个基因座单倍型在湖北地区汉族人群中具有丰富的遗传多态性,其数据对法医学应用、Y-STR数据库建设和群体遗传学等研究应用具有重要意义.     

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。     

The X-linked STRs DXS7130 and DXS6803

This paper presents sequence and population genetic data of two new X-linked microsatellite markers, suitable for forensic purposes. Data were obtained from a sample of unrelated German individuals (male and female). Two highly informative markers could be added to the panel of ChrX STRs [J. Edelmann, S. Hering, M. Michael, R. Lessig, D. Deichsel, G. Meier-Sundhausen, L. Roewer, I. Plate, R. Szibor, 16 X-chromosome STR loci frequency data from a German population, For. Sci. Int. 124 (2001) 215-218; J. Edelmann, D. Deichsel, S. Hering, I. Plate, R. Szibor, Sequence variation and allele nomenclature for the X-linked STRs DXS9895, DXS8378, DXS7132, DXS6800, DXS7133, GATA172D05, DXS7423 and DXS8377, For. Sci. Int. 129 (2002) 99-103].     

Population data for Y-chromosome haplotypes defined by 17 STRs (AmpFlSTR YFiler) in Portugal

The 17 Y-chromosomal short tandem repeats (STRs) included in the AmpFlSTR YFiler Amplification Kit (AB Applied Biosystems) (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635 and GATA H4.1) were typed in 250 samples from Portugal. A total of 231 different haplotypes were found, where 17 haplotypes were shared by two individuals and one haplotype by three. The overall haplotype diversity (HD) was 0.9994. DYS458 non-consensus alleles found in 5 samples (out of 85) are all associated with paragroup J*(xJ1,2). Population comparisons with available Yfiler loci data in European samples were undertaken, namely with Northern Portuguese data (N=174) where no significant differences were observed with our sample (Rst=0.0000; P=0.8649+/-0.0310). Since both Portuguese databases can be joined (N=424; HD=0.9997; 394 distinct haplotypes), a study on the best loci for HD increment in this sample was also undertaken: by fixing the haplotypes generated from the minimal haplotype and SWGDAM core set (www.yhrd.org) and adding the other Yfiler loci one by one, the order in which the loci contribute more is DYS458, DYS456, GATA H4.1, DYS437 or DYS635, and finally DYS448. Therefore, at least in this population sample, all Yfiler loci are contributing for haplotype discrimination.     

Chelating resin-based extraction of DNA from dental pulp and sex determination from incinerated teeth with Y-chromosomal alphoid repeat and short tandem repeats

A procedure utilizing Chelex 100, chelating resin, was adapted to extract DNA from dental pulp. The procedure was simple and rapid, involved no organic solvents, and did not require multiple tube transfers. The extraction of DNA from dental pulp using this method was as efficient, or more so, than using proteinase K and phenol-chloroform extraction. In this study, the Chelex method was used with amplification and typing at Y-chromosomal loci to determine the effects of temperature on the sex determination of the teeth. The extracted teeth were incinerated in a dental furnace for 2 minutes at 100 degrees C, 200 degrees C, 300 degrees C, 400 degrees C, and 500 degrees C. After the isolation of DNA from the dental pulp by the Chelex method, alphoid repeats, and short tandem repeats, the human Y chromosome (DYZ3), DYS19, SYS389, DYS390, and DYS393 could be amplified and typed in all samples incinerated at up to 300 degrees C for 2 minutes. The DYS389 locus in some samples could not be amplified at 300 degrees C for 2 minutes. An autopsy case is described in which genotypings of DYS19, DYS390, and DYS393 from dental pulp obtained from a burned body were needed. The data presented in this report suggest that Chelex 100-based DNA extraction, amplification, and typing are possible in burned teeth in forensic autopsy cases.     

Population genetic study in two Transylvanian populations using forensically informative autosomal and Y-chromosomal STR markers

Our study provides population genetic data on two population samples collected in a Hungarian speaking region of Transylvania, Romania. Allele frequency and profile databases were generated on 17 autosomal STR loci (D2S1338, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D19S433, D21S11, VWA, FGA, TH01, TPOX, CSF1PO, Penta E and Penta D) as well as at the 12 European Y-STR extended haplotype loci (DYS19, DYS389-I/II, DYS390, DYS391, DYS392, DYS393, DYS385 loci, DYS437, DYS438 and DYS439). Data were compared to a Central Hungarian (Budapest region) population sample [B. Egyed, S. Füredi, M. Angyal, L. Boutrand, A. Vandenberghe, J. Woller, Z. Padar, Analysis of eight STR loci in two Hungarian populations, Forensic Sci. Int. 113 (2000) 25-27] that was used as a reference group of the Hungarian population. Calculating the F(ST) indices and with the pairwise comparisons of interpopulation molecular variance (AMOVA) the two populations from Transylvania could be fit into the Hungarian population data showing less substructuring effects as compared to the previous findings in Hungary [B. Egyed, S. Füredi, M. Angyal, L. Boutrand, A. Vandenberghe, J. Woller, Z. Padar, Analysis of eight STR loci in two Hungarian populations, Forensic Sci. Int. 113 (2000) 25-27; B. Egyed, S. Füredi, M. Angyal, I. Balogh, L. Kalmar, Z. Padar, Analysis of the population heterogeneity in Hungary using fifteen forensically informative STR markers, Forensic Sci. Int. 158 (2005) 244-249].     

Y-chromosome STR haplotypes in Sweden

A total of 708 men, with Swedish names, from different parts of Sweden have been typed for the Y-chromosome minimal haplotype STR markers DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393 and DYS385. Of these, 403 men were of geographically undefined Swedish origin and the rest, 305, from seven defined geographical regions. PCR-products were detected by ABI377 using sequenced allelic ladders. An evaluation of the 708 chromosomes revealed 423 different haplotypes. Only 100 of the haplotypes were found more than once. The over all haplotype diversity was 0.994. The haplotype 14, 12, 28, 23, 10, 11, 13, 14-14 has the highest frequency of 5.79% and is significantly Swedish, when compared to other European populations.     

Allele frequencies and population data for 17 Y-STR loci (AmpFlSTR Y-filer) in a Northern Portuguese population sample

Allele frequencies and population data for 17 Y-STR loci included in a new commercial kit that has recently been available, the AmpFlSTR Y-filer PCR amplification kit (Applied Biosystems), that permits the simultaneous amplification of all the markers included in the actually used European "extended haplotype", DYS19, DYS189I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385I/II, DYS438, DYS439 and also DYS437, DYS448, DYS456, DYS458, DYS635 and Y GATA H4, were obtained from a sample of 175 healthy unrelated males and 45 father-son pairs from the North of Portugal. A total of 171 haplotypes were identified, of which 167 were unique and 4 were found in 2 individuals. The haplotype diversity (99.97%) and discrimination capacity (95.43%) were calculated. We report some non-standard situations, such as allele duplications and mutations. We also report a case of disputed paternity in which duplicated alleles plus an inconsistency of the transmitted alleles appeared.     

Twelve short tandem repeat loci Y chromosome haplotypes: genetic analysis on populations residing in North America

A total of 2443 male individuals, previously typed for the 13 CODIS STR loci, distributed across the five North American population groups African American, Asian, Caucasian, Hispanic, and Native American were typed for the Y-STR loci DYS19, DYS385a/b, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438 and DYS439 using the PowerPlex Y System. All population samples were highly polymorphic for the 12 Y-STR loci with the marker DYS385a/b being the most polymorphic across all sample populations. The Native American population groups demonstrated the lowest genetic diversity, most notably at the DYS393 and DYS437 loci. Almost all of the 12-locus haplotypes observed in the sample populations were represented only once in the database. Haplotype diversities were greater than 99.6% for the African Americans, Caucasians, Hispanics, and Asians. The Native Americans had the lowest haplotype diversities (Apaches, 97.0%; Navajo, 98.1%). Population substructure effects were greater for Y-haplotypes, compared with that for the autosomal loci. For the apportionment of variance for the 12 Y-STRs, the within sample population variation was the largest component (>98% for each major population group and approximately 97% in Native Americans), and the variance component contributed by the major population groups was less than the individual component, but much greater than among sample populations within a major group (11.79% versus 1.02% for African Americans/Caucasians/Hispanics and 15.35% versus 1.25% for all five major populations). When each major population is analyzed individually, the R(ST) values were low but showed significant among group heterogeneity. In 692 confirmed father-son pairs, 14 mutation events were observed with the average rate of 1.57x10(-3)/locus/generation (a 95% confidence bound of 0.83x10(-3) to 2.69x10(-3)). Since the Y-STR loci reside on the non-recombining region of the Y chromosome, the counting method is one approach suggested for conveying an estimate of the rarity of the Y-haplotype. Because the Y-STR loci are not all in disequilibrium to the same extent, the counting method is a very conservative approach. The data also support that autosomal STR frequencies can be multiplied by the upper bound frequency estimate of a Y-haplotype in the individual population group or those pooled into major population groups (i.e., Caucasian, African American, Hispanic, and Asian). These analyses support use of the haplotype population data for estimating Y-STR profile frequencies for populations residing in North America.     

24个Y-STR基因座在云南苗族人群中的序列多态性

目的研究法医学常用Y-STR基因座在中国云南苗族男性个体中的序列多态性。方法采用M48磁珠提取纯化试剂盒提取样本DNA,使用ForenSeqTM DNA Signature Prep试剂盒制备文库,Miseq FGx平台进行测序,ForenSeq Universal Analysis v1.2.1软件进行数据分析,用Arlequin v3.5软件计算各Y-STR基因座相关的统计学参数,将Y-STR基因座长度多态性与序列多态性进行比较。结果108名云南苗族个体中共检出106种单倍型,总体单倍型多样性(HD)和Y-STR分型系统的分辨能力(DC)分别为0.9993和0.9815。24个Y-STR基因座共检出204个基因,基因多样性(gene diversity,GD)值为0.2177~0.9481,15个Y-STR基因座的GD值大于0.6。DYF387S1、DYS390、DYS389II、DYS437、DYS438、DYS448、DYS612基因座存在长度相同的基因核心序列不同的情况。结论该24个Y-STR基因座在云南苗族男性人群中具有丰富的遗传多态性。研究结果可为Y-STR数据库的建立、群体遗传学和法医学实践提供参考。     

REVIEWS

Book reviewed in this article: English Justice between the Norman Conquest and the Great Charter 1066–1215. By Doris M. Stenton . International Law , Chiefly as Interpreted and Applied in Canada . By J. G. Castel . Space Law . By C. Wilfred Jenks . The International Position of Communist China . Edited by Lyman M. Tondel , Jr . Dobbs Ferry, N.Y. Deb räumliche Anwendungsbereich der Verwaltungsrechtsnorm . By Klaus Vogel . Die Anerkennung Ausländischer Verwaltungsakte . By Klaus König . Abortion and the Law . By Bernard M. Dickens , LL.M. (Lond.), of the Inner Temple, Barrister-at-Law. How to Get Industrial Injuries Benefits . By J. Bell . A Modern View of the Law of Torts . By J. S. Colyer , M.A., Barrister-at-Law.     

A distinct Y-STR haplotype for Amelogenin negative males characterized by a large Y(p)11.2 (DYS458-MSY1-AMEL-Y) deletion

The use of STR multiplexes with the incorporated gender marker Amelogenin is common practice in forensic DNA analysis. However, when a known male sample shows a dropout of the Amelogenin Y-allele, the STR system falsely genotypes it as a female. To date, our laboratory has observed 18 such cases: 12 from our Y-STR database and six from casework. A study on 980 male individuals in the Malaysian population using the AmpFlSTR Y-filer has revealed a distinct Y-chromosome haplotype associated with the Amelogenin nulls. Our results showed that whilst the Amelogenin nulls were noticeably absent among the Chinese, both the Indians and Malays exhibited such mutations at 3.2 and 0.6%, respectively. It was also found that the Amelogenin negative individuals predominantly belonged to the J2e lineage, suggesting the possibility of a common ancestor for at least some of these chromosomes. The null frequencies showed concordance with the data published in Chang et al. [Higher failures of Amelogenin sex test in an Indian population group, J. Forensic Sci. 48 (2003) 1309-1313] on a smaller Malaysian population of 338 males which used a Y-STR triplex. In the current study, apart from the absence of the Amelogenin Y-locus, a complete absence of the DYS458 locus in all the nulls was also observed. This study together with the 2003 study has indicated a similar deletion region exists on the Y(p)11.2 band in all the 18 Y-chromosomes. Using bioinformatics, this deletion has been mapped to a region of at least 1.13 Mb on the Y(p)11.2 encompassing the Amelogenin, MSY1 minisatellite and DYS458 locus. Further, the Y-filer haplotypes revealed an additional null at Y-GATA H4 in two of the Indian males presented here.     

Development of a harmonised method for the profiling of amphetamines V: Determination of the variability of the optimised method

This paper is the fifth in a series of six in relation to the development of a harmonised method for the profiling of amphetamine [L. Aalberg, K. Andersson, C. Bertler, H. Borén, M.D. Cole, J. Dahlén, Y. Finnon, H. Huizer, K. Jalava, E. Kaa, E. Lock, A. Lopes, A. Poortman-van der Meer, E. Sippola, Development of a harmonised method for the profiling of amphetamines I. Synthesis of standards and compilation of analytical data, Forensic Sci. Int. 149 (2005) 219-229; L. Aalberg, K. Andersson, C. Bertler, M.D. Cole, Y. Finnon, H. Huizer, K. Jalava, E. Kaa, E. Lock, A. Lopes, A. Poortman-van der Meer, E. Sippola, J. Dahlén, Development of a harmonised method for the profiling of amphetamines II. Stability of impurities in organic solvents, Forensic Sci. Int. 149 (2005) 231-241]. The third paper [K. Andersson, K. Jalava, E. Lock, L. Aalberg, Y. Finnon, H. Huizer, E. Kaa, A. Lopes, A. Poortman-van der Meer, M.D. Cole, J. Dahlén, E. Sippola, Development of a harmonised method for the profiling of amphetamines III. Development of the gas chromatographic method, Forensic Sci. Int., in press] dealt with the optimisation of the gas chromatographic and detection methods whereas the fourth paper [K. Andersson, K. Jalava, E. Lock, Y. Finnon, S. Stevenson, L. Aalberg, H. Huizer, E. Kaa, A. Lopes, A. Poortman-van der Meer, M.D. Cole, J. Dahlén, E. Sippola, Development of a harmonised method for the profiling of amphetamines IV. Optimisation of sample preparation, Forensic Sci. Int., in press] concerned the optimisation of the extraction method prior to GC analysis. This paper is a study of the optimised method in order to determine its stability. Investigations of within and between day variations were carried out in four laboratories. Moreover, variations between laboratories were also determined. Both flame ionisation detector (FID) and MS detection were used. One laboratory studied nitrogen-phosphorous detector (NPD) detection as well. For this task, 12 batches of amphetamine were prepared. Six of them were synthesised via the Leuckart route, three via the nitrostyrene route and three via the reductive amination route [A.M.A. Verweij, Impurities in illicit drug preparations: amphetamine and methamphetamine, Forensic Sci. Rev. 1 (1989) 2-11]. Taking into account all studied target compounds and the average results from four laboratories, the within day variation was around 6% for FID and 5% for MS, the between days variation was around 10% for FID and 8% for MS. For NPD detection, within day variation was 5% and between days variation 9% (only one laboratory). Finally, the inter-laboratory variation was about 12% for FID (four laboratories) and 10% for MS (three laboratories).     

Y chromosome SNP analysis in a Portuguese population sample using a multiplex PCR and minisequencing strategy

The study of single nucleotide polymorphisms (SNPs) located on the Y chromosome specific region Y-SNPs (92R7, M70, M22, Tat, P25, SRY10831, M173, M213 and M9) was used to characterize a population sample from Central Portugal, in order to investigate the frequency distribution of the male lineages and to compare the observed results with those obtained in other Portuguese regions.The genotyping strategy was according to the described by Brion et al. [M. Brion, et al., Int. J. Legal Med. 119 (2004) 10-15].In this population sample from Central Portugal a typical Western European haplogroup composition was found. The majority of samples (almost 70%) were assigned inside haplogroup R. As for other Iberian populations, the most frequent haplogroup was R1b-P25 (52.2%), followed by F(xK)-M213 (15.2%), E-B-SRY10831.1, R1(xR1a,b)-M173 and R1a-SRY10831.2 (each of them with a 8.7% frequency), K2-M70 (4.3%) and L-M22 (2.2%). When comparing our sample with other samples from Portugal, no significant differences were found.