Population genetics for Y-chromosomal STRs haplotypes of Chinese Tibetan ethnic minority group in Tibet

Y-chromosomal STRs loci were analyzed from a sample of 119 healthy unrelated autochthonous male individuals of Chinese Tibetan ethnic minority group using a multiplex PCR system. Allele and haplotype frequencies for DYS19, DYS389 I, DYS389 II, DYS390, DYS391, DYS392, DYS393, DYS385a,b, DYS438, and DYS439 were determined by the Y-PLEXtrade mark 12 kit. The gene diversity values for the Y-STRs loci ranged from 0.3347 (DYS438) to 0.9547 (DYS385a,b). A total of 110 haplotypes were identified in the Y-STR loci, among which 104 were unique, while six occurred more than once. The overall haplotype diversity for the Y-STRs loci was 0.9981, and the discrimination capacity was 0.9897. The results in the present study can be used for routine forensic application in the region, and enrich Chinese ethnical genetic informational resources.     

Population genetics for Y-chromosomal STRs haplotypes of Chinese Korean ethnic group in northeastern China

Y-chromosomal STRs loci were analyzed from a sample of 201 healthy unrelated male individuals of Chinese Korean ethnic group. Allele and haplotype frequencies for DYS19, DYS385a/b, DYS388, DYS389 I, DYS389 II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438 and DYS439 were determined by the general PCR and silver staining methods. The gene diversity values for the Y-STRs loci ranged from 0.4146 (DYS437) to 0.9631 (DYS385a/b). A total of 194 haplotypes were identified in the Y-STR loci, among which 188 were unique, while 6 occurred more than once. And the combined haploytpes diversity was 0.9996. The results in the present study can be used for routine forensic application in the region, and enrich Chinese ethnical genetic informational resources.     

Haplotypes for 12 Y-chromosomal STR loci in a Korean population (the central region)

Haplotypes and allele frequencies of 12 STR loci included in the PowerPlex Y system (DYS391, DYS389I, DYS439, DYS389II, DYS438, DYS437, DYS19, DYS392, DYS393, DYS390, and DYS385a/b) were obtained from a sample of 569 unrelated individuals living in the central region of Korea. A total of 473 haplotypes were observed in the 569 individuals studied, of which 426 (90.06%) were unique. The overall haplotype diversity for the 12 Y-STR loci was 0.9985, and the discrimination capacity was 0.8313. In DYS439, we found a new intermediate-sized allele that added an A at base 3 upstream from the repeat region's first GATA motif. The allele was named 11 (U3Ains) according to its sequence structure.     

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。     

Population genetics of 17 Y-chromosomal STR loci in Japanese

Haplotypes and allele frequencies of 17 Y-chromosomal short tandem repeat (Y-STR) markers were examined using the AmpFlSTR Yfiler PCR Amplification Kit (Applied Biosystems) in a population sample of 1166 Japanese male volunteers in 6 prefectures: Miyagi, Yamagata, Osaka, Tottori, Fukuoka, and Okinawa. A total of 1058 haplotypes were observed from 1166 males, and the most common haplotype detected in 12 males had a frequency of 1.03% and the discrimination capacity was 0.907. The R_ST analysis showed statistically significant differences between Okinawa and the other subpopulations.     

Genetic analysis of 17 Y-chromosomal STRs haplotypes of Chinese Tibetan ethnic group residing in Qinghai province of China

We have co-amplified and analyzed 17 Y-chromosomal STRs loci including European 'extended haplotypes' (DYS19, DYS389 I, DYS389 II, DYS390, DYS391, DYS392, DYS393, DYS385a,b, DYS438, and DYS439) and also six additional loci DYS437, DYS448, DYS456, DYS458, DYS635 and YGATA H4 in a population sample of 167 healthy unrelated autochthonous male individuals of Chinese Tibetan ethnic minority group residing in Qinghai province of China using a multiplex PCR system. The gene diversity values for the Y-STRs loci ranged from a minimum 0.3581 for DYS391 locus to a maximum of 0.8702 for DYS385a,b loci in Tibetan population. A total of 163 haplotypes were identified in the set of Y-STR loci, of which 159 were unique and 4 found in two individuals. The overall haplotype diversity for the set of Y-STRs loci was 0.9998, and the discrimination capacity was 0.9938. Research results will be valuable for human identification and paternity tests in the region and for Chinese population genetic study in the future.     

4个STR基因座在广东汉族人群的单倍型分布

调查DYS19、DYS390和DYS389Ⅰ/Ⅱ基因座在广东汉族群体的单倍型分布。PCR扩增后,用不连续PAGE电泳系统分型。在130名无关男性个体中,共检出81种不同的单倍型,其中52种只出现过1次。4个基因座单倍型的遗传多样性、个体识别率和非父排除率分别为0.9989,0.9824,0.9824,结果表明,4个STR基因座的单倍型检测在法医学个体识别和亲权鉴定方面有较高的应用价值。     

Genetic polymorphism for the PowerPlex 16 system from the Chinese Tujia Ethnic Minority Group

POPULATIONS: The population studied was the Tujia population, living in the Hunan Province, China. Their ancestors had lived in the region for at least three generations. As a Chinese minority group, the Tujia ethnic group, with a population of 8,028,133 (year of 2000), is mainly distributed in the Wuling mountain area in the three provinces of Hunan, Hubei, and Sichuan. The Tujia population have their own language, which belongs to the Tibetan-Myanmese Language Group of the Chinese-Tibetan Language Family, but the large majority have come to speak the Han and Miao languages, now that the Tujias have been largely assimilated.     

Direct amplification of STRs from blood or buccal cell samples

Forensic databasing laboratories routinely analyze blood or buccal cell samples deposited on FTA^® paper. Prior to PCR amplification of the STRs, the FTA^® samples must undergo multi-step sample purification protocols to remove the PCR inhibitors present within the sample and from the FTA^® paper. The multi-step sample purification protocols are laborious, time-consuming and increase the potential for sample cross-contamination.To eliminate the need for DNA purification, we conducted studies to optimize the PCR buffer and thermal cycling parameters to allow for direct amplification of STRs from blood or buccal samples on FTA^® paper. We evaluated the effect of various factors on the DNA profile including: FTA^® disc size, blood sample load variation, and buffer formulation. The new STR assay enables the direct amplification of DNA from single source samples on FTA^® discs without sample purification. The new STR assay improves the workflow by eliminating tedious steps and minimizing sample handling. Furthermore, the new STR assay reduces cost by eliminating the need for purification reagents and expensive robots.     

Haplotype diversity of 16 Y-chromosomal STRs in three main ethnic populations (Malays, Chinese and Indians) in Malaysia

We have analyzed 16 Y-STR loci (DYS456, DYS389I, DYS390, DYS389II, DYS458, DYS19, DYS385a/b, DYS393, DYS391, DYS439, DYS635 or Y-GATA C4, DYS392, Y-GATA H4, DYS437, DYS438 and DYS448) from the non-recombining region of the human Y-chromosome in 980 male individuals from three main ethnic populations in Malaysia (Malay, Chinese, Indian) using the AmpFlSTR((R)) Y-filertrade mark (Applied Biosystems, Foster City, CA). The observed 17-loci haplotypes and the individual allele frequencies for each locus were estimated, whilst the locus diversity, haplotype diversity and discrimination capacity were calculated in the three ethnic populations. Analysis of molecular variance indicated that 88.7% of the haplotypic variation is found within population and 11.3% is between populations (fixation index F(ST)=0.113, p=0.000). This study has revealed Y-chromosomes with null alleles at several Y-loci, namely DYS458, DYS392, DYS389I, DYS389II, DYS439, DYS448 and Y-GATA H4; and several occurrences of duplications at the highly polymorphic DYS385 loci. Some of these deleted loci were in regions of the Y(q) arm that have been implicated in the occurrence of male infertility.     

Post-injection hybridization of complementary DNA strands on capillary electrophoresis platforms: A novel solution for dsDNA artifacts

Several laboratories have reported the occurrence of a split or n − 1 peak at the vWA locus in PowerPlex^® 16 and PowerPlex^® ES amplification products separated on 4- and 16-capillary electrophoresis instruments. The root cause of this artifact is post-PCR reannealing of the unlabeled, unincorporated vWA primer to the 3′-end of the tetramethylrhodamine (TMR)-labeled strand of the vWA amplicon. This reannealing occurs in the capillary post-electrokinetic injection. The split peak is eliminated by incorporation into the loading cocktail of a sacrificial hybridization sequence (SHS) oligonucleotide that is complementary to the vWA primer. The SHS preferentially anneals to the primer instead of the TMR-labeled strand of the vWA amplicon. In addition, the n − 10/n − 18 artifact that may be seen at the vWA locus was determined to be due to double-stranded amplicon formed post-electrokinetic injection into the capillary. This was also eliminated by adding in two Complementary Oligo Targets (COT1 and COT2) in addition to the SHS oligonucleotide into the loading cocktail. These three oligonucleotides are complementary to the 33 bases at the 5′-end of the unlabeled vWA amplicon strand and the 60 bases at its 3′-end and therefore compete for hybridization to the TMR-labeled amplicon strand. Incorporation of these three oligonucleotides in the Internal Lane Standard 600 (ILS600) eliminate both the split peak and n − 10/n − 18 artifact in PowerPlex^® 16 and PowerPlex^® ES amplification products without affecting sizing of alleles at the vWA locus or any locus in the PowerPlex^® 16, PowerPlex^® Y, PowerPlex^® ES, AmpFlSTR^® Profiler Plus^® ID, AmpFlSTR^® Cofiler^®, and AmpFlSTR^® SGM Plus^® kits.     

多重PCR检测FFv三个基因座在景颇族人群中的遗传多态性

短串联重复序列（STR）是由几个碱基对作为核心单位串联重复形成的一类DNA序列,作者将3个STR基因座在同一反应体系中进行互不干扰的复合扩增,采用高分辨率的聚丙烯酰胺凝胶电泳分离、银染法显影技术,对云南省景颇族的F13A01,FESFPS和vWA等3个基因座等位基因的基因频率进行了调查,获得了满意的结果,显示了广阔的应用前景。F13A01基因座观察到8个等位基因、13个基因型;FESFPS基因应观察到7个等位基因、18个基因型;vWA基因应观察到7个等位基因、21个基因型。     

中国朝鲜族线粒体DNA编码区序列多态性

目的调查中国朝鲜族群体线粒体DNA（mtDNA）编码区内5个部位 3954～4506nt、5218～5974nt、7942～871Int、10296～10653nt 及14496～14867nt的序列多态性。方法采用PCR产物直接测序方法,对212名中国朝鲜族（吉林省延边地区）无关个体进行序列多态性变化和单倍型分布调查。结果在212名无关个体中,共分出148种单倍型。遗传变异度为0．9931,耦合概率为0．0116。测序结果与Anderson标准序列比较,共检测出109个变异位点,其中79个已收录于MITOMAP。结论mtDNA编码区多态性联合应用可以提高mtDNA的个体识别能力。町为相关遗传学研究提供基础数据资料。     

An analysis of single and multi-copy methods for DNA quantitation by real-time polymerase chain reaction

The goal of this paper was to examine and compare two different commercially available approaches to the determination of the relative quantities of autosomal and Y chromosomal DNA using real-time PCR. One, Quantifiler^® Duo, utilizes a TaqMan^® assay with single copy probes for both autosomal human and Y quantification. The other method, Plexor HY^® utilizes a primer quenching assay with multi-copy probes for its quantification of autosomal human and Y chromosomal DNA. To test these approaches we have utilized the NIST Human DNA Quantitation Standard Reference Material 2372, a set of three different NIST human DNA quantification standards, to examine the precision, accuracy and sensitivity of the real-time PCR assays. We also examined data from both systems utilizing casework samples. The results show that both systems produced linear estimates for DNA quantity over a broad range of input DNA. However we did observe some apparent copy number effects when comparing the three different NIST standards which we attributed to issues with sequence variations in the different standards. Overall, the single copy approach provided better accuracy while the multi-copy approach produced better sensitivity. Thus the choice of which system to use should depend upon the goals of the user.