Population genetic study of the STR loci (HUMCSF1PO,HUMTPOX, HUMTHO1, HUMLPL,HUMF13A01, HUMF13B,HSFESFPS and HUMVWA) in North Indians

Background: Highly polymorphic genetic markers like short tandem repeats (STRs) have been used successfully in disease analysis and studies of human evolution and population genetic diversity. However, DNA-based population genetic studies of Indian populations are limited. Subjects and Methods: To enlarge our understanding of genetic variation in Indian populations, a population genetic study was carried out on Jat Sikh (Punjab, North India) individuals ( n = 150) using a battery of the STR loci. The STR loci analysed by means of PCR amplification followed by electrophoresis and silver staining included HUMCSF1PO, HUMTPOX, HUMTHO1, HUMLPL, HUMF13A01, HUMF13B, HUMFESFPS and HUMVWA loci. Results: The overall pattern of allele frequencies was similar to many Caucasian and Indian populations and heterozygosity varied from 65% (HUMLPL) to 85% (HUMVWA). For all eight loci, no deviations from the Hardy-Weinberg equilibrium hypothesis were detected. Significant differences were observed between Jat Sikhs and African, Chinese and Indian tribes. The mean exclusion probability ranged from 35% to 70%, and the power of discrimination from 81% to 93%, indicating the potential of these loci for forensic and paternity investigations. Conclusion: The allele frequency spectrum, heterozygosity, probability of exclusion, match probability and discrimination probability estimates show interesting variation and suggest the usefulness of these loci for anthropogenetic, paternity and forensic investigations in Indian populations.     

HUMTH01, HUMVWA31A, HUMCSF1PO and HUMTPOX polymorphisms in Amerindian populations living in the Beni department of Bolivia

This report presents allele frequency and absolute genotype data of the short tandem repeat (STR) loci HUMTH01, HUMVWA31A, HUMCSF1PO and HUMTPOX for three autochthonous Amerindian populations living in the Beni Department of Bolivia. These related groups are the Quechua, Aymara and Beni populations all living in specific although sometimes overlapping areas that extend from the Andean habitat to the lowland Llanos de Moxos savannah passing through the Piedmont hills. The usefulness of these loci for paternity and identification testing was also examined. The present work completes previous genetic studies performed by the authors in these populations including mtDNA haplogroups (Bert et al., Hum Biol, 73:1-16, 2001) and HVRI data (Bert et al., Ann Hum Biol 31:9-28, 2004; Corella et al., Ann Hum Biol 34:34-35, 2007).     

HUMTH01, HUMVWA31A,HUMCSF1PO and HUMTPOX polymorphisms in Amerindian populations living in the Beni Department of Bolivia

This report presents allele frequency and absolute genotype data of the short tandem repeat (STR) loci HUMTH01, HUMVWA31A, HUMCSF1PO and HUMTPOX for three autochthonous Amerindian populations living in the Beni Department of Bolivia. These related groups are the Quechua, Aymara and Beni populations all living in specific although sometimes overlapping areas that extend from the Andean habitat to the lowland Llanos de Moxos savannah passing through the Piedmont hills. The usefulness of these loci for paternity and identification testing was also examined. The present work completes previous genetic studies performed by the authors in these populations including mtDNA haplogroups (Bert et al., Hum Biol, 73:1–16, 2001) and HVRI data (Bert et al., Ann Hum Biol 31:9–28, 2004; Corella et al., Ann Hum Biol 34:34–35, 2007).     

中国新疆锡伯族人群CSF1PO、TH01和TPOX三个短串联重复序列位点的遗传多态性

目的：获得CSF1PO、TPOX和TH01 3个短串联重复序列（short tandem repeats,STR)在新疆锡伯族人群中的等位基因频率、基因型频率及相关法医学数据。方法：应用聚合酶链反应、4％变性聚丙烯酰胺凝胶电泳及银染技术对上述3个STR位点分型。结果：新疆锡伯族人群CSF1PO位点有9个等位片段，TPOX位点有8个等位片段，TH01位点有8个等位片段；3个位点的基因型分布均符合HardyWeinberg平衡；各位点杂合度分别为0．9426、0．8361、0．8853，多态信息量分别为0．8298、0．7213、0．7626。结论：上述3个位点的基因频率数据可为新疆锡伯族人群遗传学研究和法医学应用提供依据。     

中国广州汉族人群六个STR位点的调查

目的 了解广州汉族人在ｖＷＡ３１Ａ等６个短串联重复序列（ｓｈｏｒｔ ｔａｎｄｅｍ ｒｅｐｅａｔ,ＳＴＲ）位点法医学的有关数据。方法 运用ＳＴＲ－ＰＣＲ、４％变性聚丙烯酰胺凝胶电池,结合荧光ＤＮＡ自动测技术,对汉族人群６个ＳＴＲ位点的等位基因频率和基因型频率进行了调查,并与其他种族或人群的等位基因频率进行了比较。结果 ６个ＷＴＲ位点是ｖＷＡ３１Ａ、ＴＨ０１、Ｆ１２Ａ０１、Ｆ１３Ａ０１、ＦＥＳ、ＴＰＯ     

中国汉族人群11号和19号染色体上13个STR位点的遗传多态性分析

目的 分析中国汉族人群中11号染色体上8个短串联重复序列（short tanden repeat,STR)位点和19号染色体上5个STR位点的遗传多态性。方法 采用PCR扩增技术和聚丙烯酰胺凝胶电泳方法。对11号染色体上D11S1984、D11S1999、D11S1999、D11S1392、D11S1985、D11S2002、D11S1986、D11S4464、D11S2359位点和19号染色体上D19S247、D19S71D19S433、D19S246、D19S254位点在100名中国汉族人中的遗传多态性进行分析。结果 在中国汉族人群中,11号染色体的D11S1984、D11S1999、D11S1392、D11S1985、D11S202、D11S1986、D11S4464、D11S2359,位点分别检出8、9、6、12、6、12、8和7个等位基因26、115、16、40、19、48、20和13个基因型,杂合度分别为87%、68%、73%、92%、71%、86%、75%和71%;在19号染色体上的D19S247、D19S714、D19S433、D19S246和D19S254位点分别检出10、10、10、11和8个等位基因,19、26、24、29和13个基因型,杂合度分别为87%、68%、73%、92%、71%、86%、75%和71%;在19号染色体上的D19S247、D19S714、D19S714、D19S433、D19S246和D19S254位点分别检出10、10、10、11和8个等位基因,19、26、24、29和18个基因型,杂合度分别为63%、82%、72%、81%和74%。结论 11号染色体的8个STR位点和19号染色体的5个STR位点在中国汉族人群中有较好的多态性,其基因频率分布符合Hardy-Weinberg平衡。     

温州汉族人群TH01和TPOX基因座的遗传多态性研究

目的研究STR位点TH01和TPOX在温州汉族人群的遗传多态性,获得相应的群体遗传学数据。方法EDTA抗凝血样采自温州197名无血缘关系汉族个体,用chelex-100法提取DNA,PCR扩增,聚丙烯酰胺凝胶电泳,银染显色分析。结果TH01观察到6个等位基因及16种基因型;TPOX观察到5个等位基因及12种基因型。各基因座的杂合度（H）分别为0.659和0.619;非父排除率（PE）分别为0.367和0.315;个人识别能力（Dp）分别为0.839和0.766。结论TH01和TPOX基因座在温州地区汉族群体中具有较高杂合度,等位基因分布符合Hardy-Weinberg平衡,在法医学应用和群体遗传学研究中有较高的价值。     

Linked loci in chromosome 1 (FXIIIB,HF, PEPC) and their variability in Brazilian Indians

A total of 352 individuals living in seven localities of two Brazilian Indian groups (Macushi and Içana River Indians) were variously studied for coagulation factor XIIIB, human factor H, and a new polymorphism of peptidase C. No significant inter- or intra-tribal differences were found for the FXIIIB alleles, the frequencies varying around 95% for F13B*3 and 5% for F13B*1. Results for HF were heterogeneous, HF*A presenting a much higher frequency among the Macushi (32%) than among the Içana River Indians (9%). Intratribal differences were also found among both groups. Linkage disequilibrium exists between alleles of these two systems (0.03 ± 0.01). These are the first results for human factor H obtained among Amerindians. The data for PEPC were limited to the Içana River Indians. There is heterogeneity among the three localities sampled and evidence of moderate linkage disequilibrium between markers in this locus and in F13B (0.02 ± 0.01). © 1992 Wiley-Liss, Inc.     

Silver STR(R) Ⅲ系统基因座中等位基因在葡萄胎基因组中的分布及其意义

目的研究Silver STR(R) Ⅲ系统3个基因座中各等位基因在葡萄胎基因组中的分布及潜在意义.方法对应用多重PCR和变性聚丙烯酰胺凝胶电泳技术鉴别出的39例遗传物质完全来自父方的完全性葡萄胎进行分析,统计Silver STR(R) Ⅲ系统3个基因座中各等位基因的出现率.结果在39例葡萄胎中,Silver STR(R) Ⅲ系统的D16S539座位出现6个等位基因,D7S820座位出现5个等位基因,D13S317座位出现7个等位基因;D16S539座位中等位基因14出现率显著高于人群(P＜0.05),D7S820座位中等位基因9出现率显著低于人群(P＜0.01),其余各等位基因出现率与人群基因频率无显著差异;D16S539、D7S820和D13S317基因座位杂合度分别为0.1795,0.1282和0.1538;其中可追踪的23例良性葡萄胎中,D16S539出现6个等位基因,D7S820出现4个等位基因,D13S317出现7个等位基因;可追踪的7例侵袭性葡萄胎中,D7S820出现5个等位基因,D16S539与D13S317均出现4个等位基因,其中D16S539和D13S317座位的等位基因9出现率高于良性葡萄胎(P＜0.01和P＜0.05).结论葡萄胎D16S539、D7S820和D13S317基因座位等位基因杂合度远低于人群杂合度;葡萄胎具有侵袭性与D16S539和D13S317座位的等位基因9出现率具有相关性.     

温州汉族人群D20S85和D2S441基因座的遗传多态性调查

目的 研究D20S85和D2S441位点的遗传多态性及其法医学应用价值.方法 应用聚合酶链式反应、聚丙烯酰胺凝胶电泳及银染显带技术对温州地区212名汉族无关个体的D20S85和D2S441位点进行分型,并检验其基因型频率分布是否符合Hardy-Weinberg平衡定律.结果 D20S85观察到9个等位基因及32种基因型,D2S441观察到10个等位基因及36种基因型.多态性分布符合Hardy-Weinberg平衡.两基因座的杂合度(H)分别为0.750、0.731,多态性信息量(PIC)为0.75、0.79.结论 该研究所得到的等位基因频率数据可为温州汉族人群法医个体识别、亲子鉴定及遗传学研究提供更多依据.     

贵州汉族群体F13A01、FESFPS、vWA基因座遗传多态性研究

目的 了解贵州汉族人群F13A01、FESFPS、vWA的遗传多态性分布，获得这3个多态位点的群体遗传学数据。方法 应用聚合酶链反应复合扩增技术，对160名无血缘关系的汉族个体的F13A01、FESFPS、vWA3个短串联重复序列(short tandem repeats，STlR)基因座等位基因频率进行了分析。结果 3个STR基因座基因频率的分布均符合Hardy—Weinberg平衡，3个STR基因座总个体识别率为0．9984，累积多态信息含量为0．97。结论 所得到的等位基因频率数据可为贵州汉族人群法医个体识别、亲子鉴定及遗传学研究提供更多依据。     

温州地区汉族群体D13S317基因座的遗传多态性研究

目的研究STR位点D13S317在温州地区的遗传多态性,获得相应的群体遗传学数据。方法在温州地区随机抽取128名无血缘关系汉族个体的静脉血,EDTA抗凝,用chelex-100法提取DNA。用Beckm an CEQ 8800毛细管测序仪测定序列,应用PCR技术和聚丙烯酰胺凝胶垂直板电泳分型。结果温州地区汉族群体D13S317基因座发现7个等位基因及19种基因型,其基因型分布符合Hardy-W e iberg平衡(P>0.05)。其个人识别能力(Dp)、其杂合度(H)、非父排除率(PE)和多态性信息含量(PIC)分别为0.921、0.875、0.745和0.77。其重复序列为[TATC]n。结论D13S317在法医学应用和群体遗传学研究中有较高的价值。     

Study of HLA alloantigens of the Navajo Indians of North America: II. HLA–A, B, C, DR and other genetic markers

This report presents the antigen frequencies for HLA-A, B, C, DR, immunoglobulin, and red blood cell systems for the Navajo Indians of North America. HLA-A-B, B-C, and B-DR haplotype frequencies and significant delta values are given. These data are compared with similar data for other American Indians and major non-Indian ethnic groups. Very restricted HLA polymorphism is unique for the Navajo as well as American Indians in general and this feature has important implications with regard to disease association and transplantation.     

Molecular variation at the HLA-A, B, C, DRB1, DQA1, and DQB1 loci in full heritage American Indians in Arizona: private haplotypes and their evolution

A sample of 492 full heritage, unrelated residents of the Gila River Indian Community (GRIC) of Arizona were characterized for their high-resolution DNA alleles at the HLA-A, B, C, DRB1, DQA1, and DQB1 loci. Only five allelic categories are found at HLA-A, 10 at HLA-B, 8 at HLA-C and HLA-DR, and 4 at DQA1 and DQB1. There is little evidence for population structure at the 6 loci. Two 'private' alleles, B*5102 and B*4005, which are found nearly exclusively in American Indian populations in the desert southwest and northern Mexico, are likely new mutations after the first inhabitation of the area, the evolution of which are reflected in the contemporary distribution of their respective haplotypes. DRB1*1402 has the highest reported frequency of any specificity at the DRB1 locus, 0.7461, and serves as a sensitive probe for locating related east Asian populations. The haplotypes in this population also exhibit a highly restricted distribution and strong genetic disequilibria, which has important implications for matching solid organ and bone marrow allografts. It is shown that, when one considers HLA-A-B-DRB1 homozygotes as allograft donors for all full heritage members of the GRIC, 50% of the community would find a non-mismatched organ within the homozygotes for the six most common haplotypes. This raises questions about transplantation policy and whether, in the presence of high-frequency private alleles and a restricted number of haplotypes, the full heritage American Indian community of the desert southwest should act as its own pool of donors for its affected members.     

广西金秀瑶族CSFlPO、TPOX和TH01的多态性

目的了解广西金秀瑶族CSF1PO、TPOX、TH01的群体遗传多态性,探讨该民族的变迁及为法医学鉴定提供数据。方法广西金秀瑶族无相关个体血样175例,用Chelex-100方法提取DNA,应用AmpFISTRIdentifilerTMkit荧光标记复合PCR扩增技术对175例血样提取样本DNA3个STR基因座进行扩增,用ABIPrism3100型遗传分析仪对扩增产物进行电泳,然后用GeneScanAnalysis3.7和Genetyper3.7软件对基因进行分析。结果在3个位点中共检测出19种等位基因,基因频率分布在0.0029～0.5514之间;44种基因型,其频率分布在0.0054～0.3657之间。经检验该3个位点的基因型分布均符合Hardy-Weinberg平衡定律。广西金秀瑶族3个STR基因座的杂合度分布在0.5657～0.7257之间,个体识别力分布在0.7241～0.8567之间,累积个体识别力为0.9942,非父排除率在0.3658～0.5644之间,累积非父排除率0.8743,多态信息量分布在0.3042～0.7178;该群体与广西侗族、水族、苗族、毛南族等相邻的少数民族有较近的血缘关系,与广西壮族和汉族的关系相对较远。结论广西金秀瑶族该3个STR基因座分布有较高的多态性,可用于民族遗传学的研究和法医学鉴定。     

COL1A2 (type I collagen) polymorphisms in the Colorado Indians of Ecuador

BACKGROUND: EcoRI, MspI and RsaI restriction fragment length polymorphisms (RFLPs) of the COL1A2 (type I collagen) gene are proving to be extremely informative markers for describing human populations; therefore they hold considerable potential for anthropogenetic research. AIM: The objective of this study was to characterize at the DNA level the Colorado Indians from Ecuador, for whom only blood group frequency information is available, and to investigate their relationships with the Cayapa-another Ecuadoran Native American group belonging to the same linguistic affiliation-and other world populations. SUBJECTS AND METHODS: Colorado Indians (n = 80) were analysed for the three anthropologically informative RFLPs of the COL1A2 gene. To better define the genetic relationship between this group and other populations, principal component analysis (PCA) was performed and genetic distances were estimated. Population genetic structure was tested through analysis of molecular variance (AMOVA) by comparing haplotype frequencies. RESULTS: COL1A2 allele and haplotype frequencies showed a certain degree of heterogeneity between the two Chibchan populations of Ecuador. The AMOVA test detected a significant level of differentiation (Fst = 0.034, p = 0.0049) between Colorado and Cayapa Indians. PC and genetic distance analyses showed a clear-cut separation between African and non-African populations; within the latter, the two Native American groups were differentiated from each other. CONCLUSIONS: The present findings suggest the presence of a low level of genetic relatedness between the Colorado and the Cayapa, despite their supposed common ethnogenesis. This confirms what has been inferred from other genetic data about the high degree of heterogeneity among Native Americans, even within the same linguistic branch, thus supporting the existence of genetic sub-structure within the central and southern American populations.     

温州汉族群体D1S518、D3S1358、D6S1043基因座遗传学多态性调查

目的研究D1S518、D3S1358、D6S1043基因座在温州汉族人群中的遗传学多态性。方法应用聚合酶链反应（PCR）、聚丙烯酰胺凝胶电泳（PAGE）及银染显带技术对温州地区汉族180例无关个体的D1S518、D3S1358、D6S1043基因座进行分型。结果D1S518观察到10个等位基因,36种基因型;D3S1358观察到9个等位基因,18种基因型;D6S1043观察到12个等位基因,52种基因型。各基因座的杂合度（H）分别为：0.6609、0.7024、0.6545;个人识别能力（DP）：0.9421、0.8654、0.9772;多态信息含量（PIC）：0.7923、0.6604、0.8784。结论三个基因座具有较高多态性,等位基因分布符合Hardy-Weinberg平衡,在法医学应用和群体遗传学研究中有较高的实用价值。