温州汉族群体4个Y-STR复合扩增及其单倍型多态性研究

目的建立DYS426、DYS393、DYS390、DYS438基因座的复合扩增体系，研究四基因座单倍型频率。方法建立复合扩增体系，利用聚合酶链式反应（PCR）、聚丙烯酰胺凝胶电泳（page）及银染分型技术，对温州地区汉族155名无关个体的DYS426、DYS393、DYS390、DYS438位点进行分型，检验其单倍型多态性。结果复合扩增DYS426、DYS393、DYS390、DYS438位点分别检出4、8、5和4个等位基因，共52种单倍型，其平均基因差异度为0．9608。结论该研究Y-STR基因座复合扩增体系和所获单倍型频率数据在法医学个人识别和亲子鉴定中有较高实用价值，适用于温州汉族群体。     

Polymorphism analysis and evaluation of nine non-CODIS STR loci in the Han population of Southern China

Background: Knowledge of allele and genotype frequencies is an essential prerequisite to the use of any human polymorphism in forensic work.

Aim: To study the genetic polymorphism and evaluate the application value of nine STR loci.

Subjects and methods: Genotyping of nine STR loci, including D11S2368, D12S391, D13S325, D18S1364, D22-GATA198B05, D6S1043, D2S1772, D7S3048 and D8S1132, of 1050 unrelated individuals was performed with the STR_Typer_10_v1 kit and Genetic Analyzer 3100 and analyzed with PowerState V12.xls and Arlequin ver 3.11 analyzing software.

Results: Allele frequency distribution was statistically analyzed and Hardy–Weinberg equilibrium determined. Several common parameters used in forensic sciences were found: the heterozygosity (H) ranged from 0.827 to 0.892; the matching probability (MP) ranged from 0.029 to 0.074; the power of discrimination (PD) ranged from 0.926 to 0.971; the power of exclusion (PE) ranged from 0.649 to 0.779; the polymorphic information content (PIC) ranged from 0.77 to 0.86; and the typical paternity index (TPI) ranged from 2.88 to 4.62.

Conclusion: The results indicate that nine STR loci are high polymorphic among the Han population in Southern China. This set of polymorphic STR loci is a useful tool in forensic paternity testing and anthropological study.     

人类Y染色体STR位点在群体遗传学中的应用

Y染色体STR位点在群体遗传学研究中是线粒体DNA的有益补充,是研究男性进化历史的绝好工具.本文介绍了Y-STR位点的遗传学特点以及多态性研究进展;总结了应用Y-STR位点进行群体遗传学研究的常用方法:直接比较法、分子变异分析构建系统树、分层聚类分析、主成分分析等;同时指出了应用Y-STR位点用于群体遗传学研究存在的问题和今后的发展方向.     

Structure and genetic relationship of five populations from central India based on 15 autosomal STR loci

Aim: To estimate population parameters based on allele frequencies obtained for 15 polymorphic autosomal STR loci investigated in caste and tribal populations of central India (n?=?419).

Methods: Multiplexed PCR amplifications of the 15 Autosomal STR Loci were performed and amplified products were genotyped using multi-capillary electrophoresis on an ABI 3100 genetic analyser. Parameters of population genetics and forensic interest based on the allele frequencies were calculated. Genetic affinity of the studied populations among themselves and with previously reported populations of India was also analysed using distance-based NJ tree and using PCA plot.

Results: All the 15 STR loci were highly informative and discriminating, with CPD of 0.999 99. Except for Brahmins and Rajput, all other studied populations were in Hardy–Weinberg equilibrium (HWE). The only tribe (Gond) population studied showed significant variation with the other four caste populations (Brahmin, Yadav, Rajput and Muslim) studied and formed a cluster with other previously reported tribal populations of India. Nei’s genetic distance based clustering pattern of the NJ tree and the PCA plot showed the same pattern of genetic relationship, i.e. caste and tribal populations formed a distinct cluster.

Conclusions: With respect to the distribution of alleles at each STR locus, the studied loci were found to be substantially polymorphic in all the studied populations, indicating good informativeness of all 15 STR markers. The population data generated in this study are useful for forensic, anthropological and demographic studies.     

Genetic diversity of 23 STR loci in Guangxi Zhuang population and its phylogenetic relationship with 25 other populations

Abstract

Aim: To estimate genetic diversity of 23 STR loci included in the DNA Typer^TM 25 Kit, and evaluate its effectiveness in forensic application.

Subjects and methods: A total of 450 (251 males and 179 females) unrelated healthy individuals from Guangxi Zhuang population were amplified with DNA Typer^TM 25 Kit, isolated by the 3730 Series Genetic Analyzer^TM, and genotyped using the GeneMapper ID-X. Genetic parameters and population relationships were analysed.

Results: Allele frequencies ranged from 0.001 to 0.5889. The combined power of discrimination (CPD) and the combined power of exclusion (CPE) of the 23 STR loci were 0.999999999999999999 and 0.999996765, respectively. No deviations from Hardy–Weinberg equilibrium and linkage disequilibrium were observed. Inter-population comparison based on Fst, PCA, genetic distance, phylogenetic trees, and MDS showed that Zhuang population clustered with the populations holding a close geographic distance with Zhuang (Guangdong Han and Hainan Li populations).

Conclusions: Our study indicated that the 23 autosomal STR loci included in DNA Typer^TM 25 Kit can be used as forensic tools for individual identification and parentage testing. Moreover, the result of our mass investigation will enrich the forensic database of Chinese populations and serve for further study of the origin of anthropology.     

Genetic polymorphisms of 20 autosomal STR loci in the Han population of Putian City,Southeastern China

Abstract

Background: Short tandem repeats (STRs) are genetic markers that are more informative than single nucleotide polymorphisms and they are widely used in forensic DNA analysis.

Aim: To carry out the genetic analysis of 20 autosomal STR loci in Han individuals of Putian City, Southeast China, to expand the available population information for human genetic databases and forensic analysis.

Subjects and methods: Saliva swabs from 1417 unrelated Chinese Han individuals from Putian City of Southeast China were collected and then genotyped using the SureID^® 21G Human STR Identification Kit. Moreover, phylogenetic analysis based on the Nei’s standard genetic distance was performed between the Han population and other relevant populations based on the shared autosomal STR genotyping.

Results: We found 272 alleles among 1417 unrelated individuals and the corresponding allelic frequencies ranged from 0.5409 to 0.0004. The combined power of exclusion (CPE) was 0.999999995514, and the combined power of discrimination (CPD) was 0.9999999999999999999999994061. Population comparison revealed that the Putian Han population makes a cluster with other Han populations from China while showing significant differences when compared with other worldwide populations.

Conclusions: Our results found that the SureID^® 21G Human STR Identification Kit panel was appropriate for forensic identity testing and paternity testing. Putian Han population had a closer genetic relationship with Han populations from other regions in China, while other minorities like Uighurs and Kazakhs from China showed significant differences.     

Evaluation of genetic parameters of 23 autosomal STR loci in a Southern Chinese Han population

Aim: To evaluate the 23 autosomal short tandem repeat (STR) loci included in GoldenEye? 25?A kit using forensic human identification and paternity testing.

Subjects and methods: In total, 3751 unrelated individuals from the Southern Chinese Han population were genotyped with the 5-dye GoldenEye? 25?A multiplex amplification system. PCR products were separated using arrayed capillary electrophoresis. Allele frequencies and forensic parameters for the 23 autosomal STR loci were statistically analysed.

Results: A total of 344 alleles were observed, with corresponding allelic frequencies ranging from 0.0001–0.5519 for the 23 STR loci. No significant deviation from the Hardy-Weinberg equilibrium and linkage disequilibrium was observed. The combined power of discrimination (CPD) was 1–1.6290?×?10^?28 and the combined power of exclusion (CPE) was 0.999 999 999 89 and 0.999 999 286 93 for trio and duo cases, respectively. From 3865 meioses, 87 mutation events were discovered. The mutation rate varied from 0–0.00285 for each locus. One-step mutation accounted for 94.25% of total mutations. The ratio of paternal vs maternal mutation was 3.76:1.13 kinds of n/(n?+?1) heterozygote genotypes were observed.

Conclusions: The results show that 23 STR loci of GoldenEye? 25?A kit are highly polymorphic in the Southern Chinese Han population, indicating the kit is suitable for forensic application.     

Identification of the sequence variations of 15 autosomal STR loci in a Chinese population

Background: DNA sequence variation including base(s) changes and insertion or deletion in the primer binding region may cause a null allele and, if this changes the length of the amplified fragment out of the allelic ladder, off-ladder (OL) alleles may be detected.

Aim: In order to provide accurate and reliable DNA evidence for forensic DNA analysis, it is essential to clarify sequence variations in prevalently used STR loci.

Subjects and methods: Suspected null alleles and OL alleles of PlowerPlex16® System from 21?934 unrelated Chinese individuals were verified by alternative systems and sequenced.

Results: A total of 17 cases with null alleles were identified, including 12 kinds of point mutations in 16 cases and a 19-base deletion in one case. The total frequency of null alleles was 7.751?×?10^?4. Eight hundred and forty-four OL alleles classified as being of 97 different kinds were observed at 15 STR loci of the PowerPlex®16 system except vWA. All the frequencies of OL alleles were under 0.01.

Conclusion: Null alleles should be confirmed by alternative primers and OL alleles should be named appropriately. Particular attention should be paid to sequence variation, since incorrect designation could lead to false conclusions.     

Genetic polymorphisms,forensic efficiency and phylogenetic analysis of 15 autosomal STR loci in the Kazak population of Ili Kazak Autonomous Prefecture,northwestern China

Aim: We investigated the frequencies of 15 autosomal STR loci in the Kazak population of the Ili Kazak Autonomous Prefecture with the aim of expanding the available population information in human genetic databases and for forensic DNA analysis.

Subjects and methods: Genetic polymorphisms of 15 autosomal short tandem repeat (STR) loci were analysed in 456 individuals of the Kazak population from Ili Kazakh Autonomous Prefecture, northwestern China.

Results: A total of 173 alleles at 15 autosomal STR loci were found; the allele frequencies ranged from 0.5022–0.0011. The combined power of discrimination and exclusion statistics for the 15 STR loci were 0.999 999 999 85 and 0.999 998 800 65, respectively. In addition, phylogenetic analysis involving the Ili Uygur population and other relevant populations was carried out. A neighbour-joining tree and multidimensional scaling plot were generated based on Nei’s standard genetic distance.

Conclusions: Results of the population comparison indicated that the Ili Uygur population was most closely related genetically to the Uygur populations from other regions in China. These findings are consistent with the historical and geographic backgrounds of these populations.     

四川汉族人群Y染色体单倍组及其特点的研究

目的建立四川汉族人群Y染色体单倍组的分布资料。方法应用PCR-限制性片段长度多态性、变性高效液相色谱技术、DNA测序方法对341份四川汉族男性标本Y染色体18个二态位点进行基因分型。结果共观察到14个Y染色体单倍组,其中H2、H4单倍组在四川汉族中被首次证实,N＊、H14单倍组为中国人群首次报道。四川汉族人群Y染色体单倍组分布频率与已报道的中国南方汉族人群相比差异具有统计学意义。结论该研究获得了更为准确的四川汉族人群的Y染色体单倍组分布频率,为生精障碍、前列腺癌和睾丸癌等男性特异性疾病的Y连锁遗传因素研究奠定了基础。     

Genetic polymorphisms,forensic efficiency,and phylogenetic analysis of 15 autosomal STR loci in the Uygur population of Ili Kazakh Autonomous Prefecture,Northwestern China

The genetic polymorphisms of 15 autosomal short tandem repeat (STR) loci were analyzed in 449 individuals of the Uygur population from Ili Kazakh Autonomous Prefecture, Northwestern China. Phylogenetic analysis was performed among the Ili Uygur population and other relevant populations. The neighbor‐joining tree and multidimensional scaling plot were generated based on the Nei's standard genetic distance. We found a total of 173 alleles with corresponding frequencies ranging from 0.5022 to 0.0011. The combined powers of discrimination and exclusion for the 15 autosomal STR loci were 0.99999999985 and 0.99999880065, respectively. Population comparisons indicated that the Ili Uygur population had a relatively close genetic relationship with the Uygur populations from other regions of China. The pairwise genetic distance and P‐values between Ili Uygur and 10 published populations showed that no statistically significant differences existed between the Ili Uygur population and the Kashi, Kashgar, and Kotan Uygur. Therefore, the Ili Uygur population has its own unique Uygur genetic characteristics that were different from the other ethnic populations of China.     

上海地区汉族人群杀伤细胞免疫球蛋白样受体基因多样性及单倍型组合研究

目的 分析上海地区汉族人群杀伤细胞免疫球蛋白样受体(killer Ig-like receptors，KIR)基因多态性及单倍型，为进一步研究不同人群KIRs与某些疾病的相关性提供线索。方法 采用序列特异性引物PCR法对87名无关汉族健康志愿者进行KIR基因低分辨率检测和单倍型分析。结果 (1)共检出Xv、KIRlD在内的18个KIRs基因。3DL3、2DL4、3DL2和3DLl存在于所有个体；较常见为2DL3、Z、2DLl、X；其次为2DS4、1D、2DL5、2DSl、3DSl、2DS5；2DS2、2DL2、2DS3、Xv频率较低。(2)共检出13种单倍型，最常见的是单倍型2。(3)共检出18种基因型．以AJ(2．2)、AF(1．2)型最常见，其次为AH(5，2)、AI(1，5)和AG(1，1)。另外有5种基因型FZl(2，9或6，16)、FZ2(1，16或2，15)、FZ3(6，17)、FZ4(4，13)和FZ5(2，6)，目前在白人中尚未发现。结论 上海地区汉族人群有其独特的KIRs基因频率、单倍型频率和基因型频率分布。     

CD31/PECAM-1 genotyping and haplotype analyses show population diversity

Using direct sequencing of complementary DNA products, the sequences of human CD31 from exon 1 through exon 16 of 179 individuals (139 unrelated) were systematically examined. Of the 14 biallelic single nucleotide polymorphic sites detected, 7 polymorphic sites involved amino acid substitution. These 14 polymorphic sites yielded 18 observed CD31 alleles and 9 predicted CD31 polypeptide sequences. Based on molecular haplotyping and family pedigree analysis, linkage disequilibrium among some single nucleotide polymorphic sites was observed. Single nucleotide polymorphism frequencies between populations were also measured using dot-blot hybridization with DNA or peptide nucleic acid probes.     

The declines in dizygotic twinning rates and in birth rates

It is suggested that, contrary to Elwood (1973), the current secular decline in age-specific dizygotic twinning rates is not due to the current decline in birth rates except to a minor extent.     

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.     

African-American HLA class II allele and haplotype diversity

Molecular genetic techniques were used to type nine loci in the HLA class II region in 241 unrelated African-Americans from New York City (NYC). Several effects attributable to recent genetic admixture were evident: the number of distinct class II alleles and haplotypes was larger in the African-Americans than in people of African or European origin, the allele frequencies were more consistently even, and linkage disequilibrium was present across the entire class II region. The African-American DRB1 allele frequencies almost always fell between frequencies among samples from northern Europe and the Gambia, two possible founding populations. The exceptions are attributed to the contribution of other genetically dissimilar African groups to the African-American gene pool. DRB1 allele frequencies (specifically DRB1*1501) and some haplotypes of DRB1-DPB1 were different in our NYC and the 11th International Histocompatibility Workshop (IHW) samples of African-Americans. The high level of allele and haplotype diversity found in African-Americans has important implications for the construction of pools of unrelated potential donors for tissue transplantation.     

STR genetic diversity in a Mediterranean population from the south of the Iberian Peninsula

Abstract

Sixteen Y-chromosomal short tandem repeats (STRs) (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635 and GATA H4.1) were typed in DNA samples from 52 unrelated men and 15 autosomal STRs (CSF1PO, D2S1338, D3S1358, D5S818, D7S820, D8S1179, D13S317, D16S539, D18S51, D19S433, D21S11, FGA, TH01, TPOX, vWA) were also studied for a group of 90 individuals (men and women) from the same population (Andalusians from La Alpujarra, South of Spain). The Alpujarrenian population represents an example of an isolated population with remarkable geographical, cultural and historical characteristics. High haplotype diversities were observed for the studied polymorphisms, 0.98 and 1 for YSTRs and autosomal STRs, respectively. Population comparisons for the autosomal STR allele distributions revealed remarkable levels of global homogeneity among samples geographically related.     

Mutation rates at Y chromosome specific microsatellites

A collaborative work was carried out by the Spanish and Portuguese ISFG Working Group (GEP-ISFG) to estimate Y-STR mutation rates. Seventeen Y chromosome STR loci (DYS19, DYS385, DYS389I and II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS460, DYS461, DYS635 [GATA C4], GATA H4, and GATA A10) were analyzed in a sample of 3,026 father/son pairs. Among 27,029 allele transfers, 54 mutations were observed, with an overall mutation rate across the 17 loci of 1.998 x 10(-3) (95% CI, 1.501 x 10(-3) to 2.606 x 10(-3)). With just one exception, all of the mutations were single-step, and they were observed only once per gametogenesis. Repeat gains were more frequent than losses, longer alleles were found to be more mutable, and the mutation rate seemed to increase with the father's age. Hum Mutat 26(6), 520-528, 2005. (c) 2005 Wiley-Liss, Inc.