Y. P. Hou

Allele sequences of six new Y-STR loci and haplotypes in the Chinese Han population.

Human chromosome Y-specific short tandem repeat (Y-specific STR) markers have useful properties for forensic applications. However, there is a need to develop more Y-specific STR markers, because the discriminating power of each STR locus is limited. In the present study, we describe our results on six new Y-specific STR markers that were initially located using sequence database information by Ayub et al. and were named DYS434, DYS435, DYS436, DYS437, DYS438 and DYS439. Our studies focused on the analysis of the DNA sequence for each allele at all six Y-specific STR loci in order to understand their structures in the human genome and to construct human allelic ladders, which are necessary for forensic DNA typing. In addition, the haplotype distribution for all six analyzed loci was studied in a Chinese Han population sample. The results indicate that DYS434, DYS435, DYS436, DYS437, DYS438 and DYS439 are useful Y-specific STR markers for forensic sciences.

Characterization of eight Y-STR loci and haplotypes in a Chinese Han population

In this study we analyzed the eight Y-STR loci, DYS443, DYS444, DYS448, DYS453, DYS455, DYS456, DYS457 (DYS437) and DYS458, investigated haplotype distributions of these Y-STR loci in a Chinese Han population, and sequenced alleles of the eight loci for clarifying the structure. Extracted DNA was amplified by PCR and the PCR products were analyzed by non-denaturing horizontal polyacrylamide gel electrophoresis with a discontinuous buffer system. Alleles were sequenced on an ABI 3700 using a Dye Terminator Cycle sequencing kit. DYS443, DYS453, DYS455 and DYS456 were found to be simple repeat systems, while DYS444, DYS448, DYS457 (DYS437) and DYS458 were complex repeat systems. The gene diversities of DYS443, DYS444, DYS448, DYS453, DYS455, DYS456, DYS457 (DYS437) and DYS458 were 0.7742, 0.7671, 0.7453, 0.3545, 0.0549, 0.6988, 0.6148 and 0.8213, respectively. The haplotype diversity for 8 Y-STR loci was 0.9996, and the discrimination capacity was 0.9815. The results indicate that these eight loci are useful Y-linked markers for forensic applications.

Use of multi-InDels as novel markers to analyze 13 X-chromosome haplotype loci for forensic purposes.

Many studies have been proposed to identify insertion/deletion (InDel) polymorphisms in humans for forensic genetic studies. However, the discriminatory power of InDels is limited by the poor polymorphisms of diallelic markers. To improve their discriminatory power, we developed multi‐InDel, a novel autosomal marker comprising more than two InDel loci that are tightly linked by their physical position and combined into a specific marker by a pair of PCR primers. This strategy gives at least three haplotypes for each multi‐InDel marker. Such markers can be potentially very useful in forensic applications. In this study, we focused on multi‐InDel markers located on X chromosome (ChrX). A multiplex system with 13 multi‐InDel markers, including 28 InDel loci in ChrX, was developed. To validate the multi‐InDel panel, the haplotype distribution in a population sample and in a set of pedigrees was investigated. This study demonstrates usefulness of these markers for individual identification and relationship studies. We highlight the fact that the multi‐InDel markers located on ChrX can provide new supporting information for complex kinship testing.

Further characterization and population data for the pentanucleotide STR polymorphism D10S2325.

Pentanucleotide tandem repeat markers are interesting for forensic sciences, because they may present less stutter on the electrophoretic pattern. We focused on the analysis of the DNA sequence for each allele at the pentanucleotide STR locus D10S2325 in order to understand their structures in the human genome and to construct human allelic ladder, which is necessary for forensic DNA typing. In order to evaluate the forensic applicability of D10S2325 and to construct a preliminary database, the genotype distributions and allele frequencies in three major ethnic groups were investigated. The population samples included Caucasians (Germans), Africans (African Americans), and Asians (Chinese). A total of 520 samples from unrelated individuals was analyzed by Amp-FLP. An example of each allele and new alleles were sequenced. Allele determination was carried out by comparison with a sequenced human allelic ladder made in-house. This pentanucleotide STR provided easily interpretable results. A total of 15 alleles was found in our population samples. Three new alleles were observed and named as alleles 19 and 21 based on the number of repeat motifs, while allele 19 can be divided further into two alleles, 19a and 19 according to analysis of the sequence. No evidence of deviation from Hardy-Weinberg equilibrium was observed. In 64 confirmed father/mother/child triplets no mutation event was observed. Using a maximum likelihood method, the mutation rate was indirectly estimated as 2.5 x 10(-5). These results suggest that D10S2325 is a useful marker for forensic casework and paternity analysis.

STR data for the AmpFlSTR profiler plus from western China.

Blood samples were collected from unrelated individuals ofChinese Han ethnic group in Chengdu of China. DNA was ex-tracted using Chelex method (1). 0.5–2ng target DNA followedthe protocols described in the AmpFlSTR Cofiler user’s manual(PE Applied Biosystems), the exception was that the PCR vol-umewas25µL.ThesampleswereamplifiedusingGeneAmpPCRSystem 9700 (Applied Biosystems, Foster City, CA). DNA typ-ing was carried out on the ABI 3100 Genetic Analyzer (AppliedBiosystems). The amplified products were detected with the ABIPRISM 3100 Genetic Analyzer using the separation medium Per-formance Optimized Polymer (POP) 4

Detecting a hierarchical genetic population structure via Multi-InDel markers on the X chromosome

Detecting population structure and estimating individual biogeographical ancestry are very important in population genetics studies, biomedical research and forensics. Single-nucleotide polymorphism (SNP) has long been considered to be a primary ancestry-informative marker (AIM), but it is constrained by complex and time-consuming genotyping protocols. Following up on our previous study, we propose that a multi-insertion-deletion polymorphism (Multi-InDel) with multiple haplotypes can be useful in ancestry inference and hierarchical genetic population structures. A validation study for the X chromosome Multi-InDel marker (X-Multi-InDel) as a novel AIM was conducted. Genetic polymorphisms and genetic distances among three Chinese populations and 14 worldwide populations obtained from the 1000 Genomes database were analyzed. A Bayesian clustering method (STRUCTURE) was used to discern the continental origins of Europe, East Asia, and Africa. A minimal panel of ten X-Multi-InDels was verified to be sufficient to distinguish human ancestries from three major continental regions with nearly the same efficiency of the earlier panel with 21 insertion-deletion AIMs. Along with the development of more X-Multi-InDels, an approach using this novel marker has the potential for broad applicability as a cost-effective tool toward more accurate determinations of individual biogeographical ancestry and population stratification.

Polymorphism data of two STR loci DYS632 and DYS634 in a Chinese Han population.

Blood samples were collected from 100 unrelated healthy males of the Chinese Han ethnic group in Chengdu of China. DNA was extracted using the Chelex method (1). The allelic variation at the two Y-STR loci named as DYS632 and DYS634 were analyzed by PCR amplification system. PCR amplification conditions can be accessed at: http://www.legalmed.org/dna/DYS632.htm. The volume of PCR reaction for each locus was 37.5 μL. The PCR products were analyzed by horizontal non-denaturing polyacrylamide gel electrophoresis with discontinuous buffer system and visualized by silver staining (2). Alleles were designated according to the recommendation of the International Society of Forensic Genetics (3). The gene diversity, the haplotype diversity, and the standard errors of diversity were calculated in accordance with Hou’s method (4). The complete data can be accessed at: http://www.legalmed. org/dna/DYS632.htm.

Allele Frequencies of 18 STR Loci in Chinese Population

Specimens of 100 unrelated individuals were collected from Han ethnic group in Sichuan Province of China. DNA was extracted from blood specimens using Chelex 100 method (1).

Population genetics of two STR loci D4S2366 and D6S1281 in a Chinese population.

Blood samples were collected from unrelated individuals of Chinese Han ethnic group in Chengdu of China. DNA was extracted using Chelex method (1). PCR amplification conditions can be accessed at http://www.legalmed.org/dna/d2s1396.htm. The PCR reaction volume for each locus was 25 μL. The PCR products were analyzed by horizontal non-denaturing polyacrylamide gel electrophoresis with discontinuous buffer system and visualized by silver staining (2). Data of population genetics and forensic science were analyzed using POWERSTATS program (3). The genotype distribution was analyzed for Hardy-Weinberg equilibrium according to Hou’s method (4). No deviation from Hardy-Weinberg equilibrium was observed.

Distributions of Allelic Frequencies and Haplotypes of Two New STR Loci in a Chinese Han Population

Blood samples were collected from unrelated individuals of Chinese Han ethnic group in Chengdu of China. DNA was extracted using Chelex method (1). PCR amplification conditions can be accessed at http://www.legalmed.org/dna/d3s4014.htm. The PCR reaction volume for each locus was 37.5μL. The PCR products were analyzed by horizontal non-denaturing polyacrylamide gel electrophoresis with discontinuous buffer system and visualized by silver staining (2). Data of population genetics and forensic science were analyzed using POWERSTATS program (3). The genotype distribution was analyzed for Hardy-Weinberg equilibrium