Genetic profile of nine autosomal STR loci among Halakki and Kunabhi populations of Karnataka, India

POPULATION: Blood samples were collected from a total of 84 healthy and unrelated Halakki (44) and Kunabhi (40) populations, with their informed written consent. The geographic location of the sampled area is shown in Fig. 1. Both the populations are endogamous, and they belong to Dravidian linguistic family. Halakki is a tribal group having a population size of approximately 3383. They claim that they originally belong to Gujarat and Rajasthan, and migrated through Andhra Pradesh to Karnataka. Kunabhi is also a tribal population, who are approximately 35,214 in number. The male Kunabhi can be identified by their tattoo marks. A necklace is the symbol of married women. They were hunters and gatherers, but at present they practice agriculture.     

Allele frequencies of 20 Y-chromosomal short tandem repeat loci in a tribal population of Deccan Plateau, India

Population: Eighty male individuals from a nomadic tribal population belonging to Dravidian and Indo-Caucasian ethnicities from Deccan Plateau, Andhra Pradesh, India, were analyzed in the present study.     

Genetic structure among 38 populations from the United States based on 11 U.S. core Y chromosome STRs

A DNA database consisting of the 11 Y chromosome short-tandem-repeat (Y-STR) recommended by the Scientific Working Group on DNA Analysis Methods is constructed for 2517 individuals from 38 populations in the United States. The population samples derive from five ethnic groups currently living in 10 states. A multidimensional scaling (MDS) plot places the populations into four discrete clusters (African Americans (AA), European Americans (EA), Hispanic Americans (HA), and Asian Americans (SA)) and one dispersed cluster of Native Americans. An analysis of molecular variance (AMOVA) indicates that a large proportion of the total genetic variance is partitioned among ethnic groups (24.8%), whereas only a small amount (1.5%) is found among-populations within ethnic groups. Separate AMOVA analyses within each ethnic group show that only the NA sample contains statistically significant among-population variation. Pair wise population differentiation tests do uncover heterogeneity among EA and among HA populations; however, this is due to only a single sample within each group. The analyses support the creation of AA, EA, HA, and Asian American databases in which samples from different geographic regions within the United States are pooled. We recommend that separate databases be constructed for different NA groups.     

Genotype profile for fifteen tetranucleotide repeat loci in two Tibeto-Burman speaking tribal populations of Arunachal Pradesh, India

POPULATION: Two Tibeto-Burman-speaking Adi tribal populations of Arunachal Pradesh, India, Adi Pasi ( n =121) from Upper Siang district, and Adi Minyong ( n =33) from East Siang district were analyzed for polymorphisms at 15 microsatellite loci. The populations belong to Mongoloid ethnicity and are of special significance in genetic studies due to their small population size, relative isolation in remote hilly areas, and traditional subsistence patterns.     

Haplotype frequencies of eight Y-chromosome short tandem repeats loci in four Amerindian populations (state of Hidalgo, Mexico)

Population: Amerindian populations: Huastecos (n=97), Otomies de la Sierra (n=41), Otomies del Valle (n=40), and Tepehuas (n=13).     

Genetic analysis for Y chromosome short tandem repeat haplotypes of Chinese Han population residing in the Ningxia province of China

POPULATION: One hundred and one unrelated, autochthonous healthy males of the Chinese Han population living in Yongning county of the Ningxia Hui Autonomous Region of China.     

Analysis of mutations in father–son pairs with 17 Y-STR loci

We have examined 389 father/son sample pairs from U.S. Caucasians, African Americans, Hispanics and Asians using the 17 Y-STR loci in the Yfiler™ kit and observed a total of 24 differences between father and son. Thirteen mutations resulted in the gain of a repeat in the son and 11 resulted in a loss of a repeat. All samples resulted in single repeat mutations except one sample which contained a two repeat loss at Y-GATA-H4. Furthermore, two different sample pairs were found to have two mutations. An African American sample pair had a mutation at DYS458 and a second at DYS635 and an Asian sample pair had mutations at DYS439 and Y-GATA-H4.     

Internal Validation of the AmpFlSTR Yfiler™ Amplification Kit for Use in Forensic Casework

Abstract:  Y-chromosomal short-tandem repeat (Y-STR) amplification has been used in forensic casework at the Bureau of Criminal Apprehension (BCA) Forensic Science Laboratory since 2003. At that time, two separate amplifications were required to type the SWGDAM recommended loci (DYS19, DYS385a/b, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS438, and DYS439). The Yfiler™ kit coamplifies these loci as well as DYS437, DYS448, DYS456, DYS458, DYS635, and Y GATA H4. The Yfiler™ kit was validated following the internal validations outlined in the SWGDAM revised validation guidelines. Our studies show that 0.125 ng of male DNA will generate a complete 17 locus profile and that as little as 0.06 ng of male DNA yields an average of nine loci. In the male–male mixtures, a complete profile from the minor component was detected up to 1:5 ratio; most of the alleles of the minor component were detected at a 1:10 ratio and more than half the alleles of the minor component were detected at a 1:20 ratio. Complete YSTR profiles were obtained when 500 pg male DNA was mixed with female DNA at ratios up to 1:1000. At ratios of 1:5000 and 1:10,000 (male DNA to female DNA) inhibition of the YSTR amplification was evident. The YSTR results obtained for the adjudicated case samples gave significantly more probative information than the autosomal results. Our studies demonstrate that the Yfiler™ kit is extremely sensitive, does not exhibit cross-reactivity with female DNA, successfully types male DNA in the presence of overwhelming amounts of female DNA and is successful in typing actual forensic samples from adjudicated cases.     

Population data of 10 Y-chromosomal STR Loci in Cebu province, Central Visayas (Philippines)

Population: 103 unrelated male individuals from Cebu province, Central Visayas region of the Philippines.     

Y-chromosome and autosomal STR diversity in four proximate settlements in Central Anatolia

Due to the longstanding human presence in the region and the influence of social traditions, the genetic make-up of populations currently inhabiting Turkey (Anatolia) is quite complex. To characterize the patterns of genetic diversity in rural Central Anatolian villages, we analyzed samples collected at four local settlements for variation at 17 Y-chromosome STR and 15 autosomal STR loci. The resulting data reveal considerable diversity within these settlements, as well as some structure in the paternal genetic variation, with a limited number of haplotypes being shared between the communities. These findings have important implications for forensic studies of Turkish populations.     

Analysis of Y-STR loci in a population sample from northeast China

POPULATION: A total of 141 unrelated Chinese Han male individuals living in Liaoning in northeast China.     

Twelve-locus Y-STR haplotypes in the Flemish population

POPULATION: One hundred and thirteen unrelated Flemish men from Belgium.     

Polymorphism analysis of Y-chromosomal haplotypes in the Chinese Han population living in the Shaanxi province of China

Population: Chinese Han population living in the Shaanxi Province of China.     

中国北方汉族人DYS19基因座多态性及应用

调查了DYS19基因在中国北方汉人群体中的基因频率分布(0.013～0.516),观察到6个等位基因,各等位基因分布存在明显的地域性差异,并对陈旧、微量、降解的生物检材具有良好的适用性.     

Development and validation of the AmpFlSTR Yfiler PCR amplification kit: a male specific, single amplification 17 Y-STR multiplex system

In the past 5 years, there has been a substantial increase in the use of Y-short tandem repeat loci (Y-STRs) in forensic laboratories, especially in cases where typing autosomal STRs has met with limited success. The AmpFlSTR Yfiler PCR amplification kit simultaneously amplifies 17 Y-STR loci including the loci in the "European minimal haplotype" (DYS19, DYS385a/b, DYS389I, DYS389II, DYS390, DYS391, DYS392, and DYS393), the Scientific Working Group on DNA Analysis Methods (SWGDAM) recommended Y-STR loci (DYS438 and DYS439), and the highly polymorphic loci DYS437, DYS448, DYS456, DYS458, Y GATA H4, and DYS635 (formerly known as Y GATA C4). The Yfiler kit was validated according to the FBI/National Standards and SWGDAM guidelines. Our results showed that full profiles are attainable with low levels of male DNA (below 125 pg) and that under optimized conditions, no detectable cross-reactive products were obtained on human female DNA, bacteria, and commonly encountered animal species. Additionally, we demonstrated the ability to detect male specific profiles in admixed male and female blood samples at a ratio of 1:1000.     

Forensic value of 14 novel STRs on the human Y chromosome

We identified and characterized 14 novel short-tandem-repeats (STRs) on the Y chromosome and typed them in two samples, a globally diverse panel of 73 cell lines, and 148 individuals from a European–American population. These Y-STRs include eight tetranucleotide repeats (DYS449, DYS453, DYS454, DYS455, DYS456, DYS458, DYS459, and DYS464), five pentanucleotide repeats (DYS446, DYS447, DYS450, DYS452, and DYS463), and one hexanucleotide repeat (DYS448). Sequence data were obtained to designate a repeat number nomenclature. The gene diversities of an additional 22 Y-STRs, including the most commonly used in forensic databases, were directly compared in the cell line DNAs. Six of the 10 most polymorphic markers include the newly identified Y-STRs. Furthermore, these novel Y-STRs greatly improved the resolution of paternal lineages, above the level obtained with commonly used Y-STRs, in the European–American population.     

Genetic variation at 15 autosomal microsatellite loci in the three highly endogamous tribal populations of Orissa, India

Although microsatellite diversity in autosomal chromosomes has been extensively described for many of the Indian populations, there is still a lacuna left on information about the genetic diversity of tribal populations. This paper reports the genetic data on the three tribal populations belonging to the Austroloid ethnic group from Orissa (Juang, Paroja and Saora). The 15 STR (D3S1358, THO1, D21S11, D18S51, PentaE, D5S818, D13S317, D7S820, D16S539, CSF1PO, PentaD, vWA, D8S1179, TPOX, FGA) polymorphism would help to accentuate the STR database for better understanding of population genetics and forensic applications. The microsatellites included in the system are found to be highly polymorphic, with the combined power of exclusion being greater than 0.999, in all the three investigated populations.     

Genetic variation at 15 autosomal microsatellite loci in the three highly endogamous tribal populations of Orissa,India

Although microsatellite diversity in autosomal chromosomes has been extensively described for many of the Indian populations, there is still a lacuna left on information about the genetic diversity of tribal populations. This paper reports the genetic data on the three tribal populations belonging to the Austroloid ethnic group from Orissa (Juang, Paroja and Saora). The 15 STR (D3S1358, THO1, D21S11, D18S51, PentaE, D5S818, D13S317, D7S820, D16S539, CSF1PO, PentaD, vWA, D8S1179, TPOX, FGA) polymorphism would help to accentuate the STR database for better understanding of population genetics and forensic applications. The microsatellites included in the system are found to be highly polymorphic, with the combined power of exclusion being greater than 0.999, in all the three investigated populations.     

Evaluation of 15 biparental STR loci in human identification and genetic study of the Kannada-speaking groups of India

Thirteen tetranucleotide and 2 pentanucleotide repeat units were analyzed in 167 unrelated Kannada-speaking individuals belonging to 3 important communities, namely, Kuruva, Bhovi, and Christians, residing in different districts of Karnataka, India. Allele frequency data obtained from the analysis of 15 short tandem report (STR) markers of the subpopulation groups included in the study were observed to be similar, indicating a common ancestry or gene flow among these communities. Departures from Hardy-Weinberg equilibrium were observed in Kuruva population at locus D5S818 and D18S51 and at locus CSF1PO in the Christian community. The data of these communities were analyzed with allele frequency data of 4 other populations from Karnataka, India-Iyengar Brahmin, Gowda, Lingayat, and Muslim-to compute the combined power of discrimination, ranged from 0.962 to 0.974, with negligible difference between populations. The combined power of exclusion, however, remained constant at 0.999 for all populations evaluated in the study. Thus, the 15 markers selected for this study were found to be highly suitable in human identification and for providing information on genetic polymorphism.     

中国成都汉族群体三个Y-STR基因座复合扩增及其单倍型的研究

目的建立一种同步检测Y-STR基因座的方法。方法采用复合扩增的方法同时对三个基因座(DYS390、DYS391及DYS393)进行扩增。结果成功地对这三个Y-STR基因座进行了同步扩增,并用其对中国成都汉族群体进行群体遗传学研究。结论三个Y-STR基因座在中国成都汉族群体个人识别几率为0.8965±0.0081,证明这个体系可用于个人识别和群体遗传学研究。