Libing Yun

Characteristics of eight X-STR loci for forensic purposes in the Chinese population

X-chromosomal short tandem repeats (ChrX STRs) loci are used for forensic practice in recent years. Considering the unique heredity characteristics of ChrX, recombination and linkage disequilibrium (LD) among ChrX STR loci vary between male and female and different populations as well. However, there is a lack of data for analysis of recombination and linkage disequilibrium on ChrX STR loci in the Chinese population. In this work, a total of 303 unrelated individuals (203 males and 100 females) in the Chinese Han population were analyzed with Mentype Argus X-8 PCR amplification kit (DXS10135-DXS8378, DXS7132-DXS10074, HPRTB-DXS10101, and DXS10134-DXS7423). The recombination and linkage disequilibrium of the eight ChrX STR loci were investigated with HapMap LD plots and software ARLEQUIN 3.1. Allele frequencies of the eight loci and further population forensic genetic parameters were obtained. Our results revealed hotspots for recombination, and there was no obvious evidence for LD among the eight loci in the Chinese population. Our work implied that single locus frequencies rather than haplotype frequencies should be applied for forensic practice in the Chinese population.

Revisiting the male genetic landscape of China: a multi-center study of almost 38,000 Y-STR haplotypes

China has repeatedly been the subject of genetic studies to elucidate its prehistoric and historic demography. While some studies reported a genetic distinction between Northern and Southern Han Chinese, others showed a more clinal picture of small differences within China. Here, we investigated the distribution of Y chromosome variation along administrative as well as ethnic divisions in the mainland territory of the People’s Republic of China, including 28 administrative regions and 19 recognized Chinese nationalities, to assess the impact of recent demographic processes. To this end, we analyzed 37,994 Y chromosomal 17-marker haplotype profiles from the YHRD database with respect to forensic diversity measures and genetic distance between groups defined by administrative boundaries and ethnic origin. We observed high diversity throughout all Chinese provinces and ethnicities. Some ethnicities, including most prominently Kazakhs and Tibetans, showed significant genetic differentiation from the Han and other groups. However, differences between provinces were, except for those located on the Tibetan plateau, less pronounced. This discrepancy is explicable by the sizeable presence of Han speakers, who showed high genetic homogeneity all across China, in nearly all studied provinces. Furthermore, we observed a continuous genetic North–South gradient in the Han, confirming previous reports of a clinal distribution of Y chromosome variation and being in notable concordance with the previously observed spatial distribution of autosomal variation. Our findings shed light on the demographic changes in China accrued by a fast-growing and increasingly mobile population.

Exploring of tri-allelic SNPs using pyrosequencing and the SNaPshot methods for forensic application.

Tri‐allelic single nucleotide polymorphisms (SNPs) are potential forensic markers for DNA analysis. Currently, only a limited number of tri‐allelic SNP loci have been proved to be fit for forensic application. In this study, we aimed to develop an effective method to select and genotype tri‐allelic SNPs based on both Pyrosequencing (PSQ) and the SNaPshot methods. 50 candidate SNPs were chosen from NCBIs dbSNP database and were analyzed by PSQ. The results revealed that 20 SNPs were tri‐allelic and were located on 16 autosomal chromosomes. Then 20 SNP loci were combined in one multiplex polymerase chain reaction to develop a single base extension (SBE)‐based SNP‐typing assay. A total of 100 unrelated Chinese individuals were genotyped by this assay and allele frequencies were estimated. The total discrimination power was 0.999999999975 and the cumulative probability of exclusion was 0.9937. These data demonstrated that the strategy is a rapid and effective method for seeking and typing tri‐allelic SNPs. In addition, the 20 tri‐allelic SNP multiplex typing assay may be used to supplement paternity testing and human identification.

Population genetics of 23 Y-STR loci in the Mongolian minority population in Inner Mongolia of China

In this study, 23 Y chromosomal STRs (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385a, DYS385b, DYS438, DYS439, DYS437, DYS448, DYS456, DYS458, DYS635, YGATAH4, DYS576, DYS481, DYS549, DYS533, DYS570, and DYS643) were investigated in 258 unrelated individuals of Mongolian descent living in the Inner Mongolia Autonomous Region. A total of 233 different haplotypes were found, and 209 of them were unique. Haplotype diversity was 0.9992 and gene diversity ranged from 0.4840 (DYS391) to 0.9679 (DYS385ab). Both Rst pairwise analysis and multidimensional scaling plot showed that the genetic structure of the Mongolian population was significantly different from some Chinese ethnic groups and neighboring populations. It is notable that there were null features existing at DYS448 as observed by the PowerPlex® Y23 System, which could be also obtained by sequencing in the Tibetan population.

Phylogenetic analysis and forensic characteristics of 12 populations using 23 Y-STR loci

Genetic analysis of Y-STRs has the potential to be used to explore the complexity in population substructures and to perform forensic ancestry inference. In this study, 334 individuals from 12 populations were typed using the PowerPlex(®) Y23 System (Promega, USA) to investigate their relationship. Population comparisons with other East Asian populations collated from YHRD (Y-STR Haplotype Reference Database) were also performed. Variant alleles, including seven intermediate alleles in 15 samples were observed, while the novel allele 11.3 at the DYS549 locus was confirmed by sequencing. Our results showed that the fraction of unique haplotypes differed among the 12 populations studied here. A close relationship was found between Chinese and other East Asian populations. The present study contributed to the enrichment of the forensic Y-chromosome databases with a high resolution 23 Y-STR marker set, which is informative in forensic casework, such as familial searching and estimating the geographical origin of the offender.

Development of a candidate method for forensic microbial genotyping using multiplex pyrosequencing combined with a universal biotinylated primer

Bacterial genotyping can be used for crime scene investigations and contribute to the attribution of biological attacks for microbial forensics. PyroMark ID Pyrosequencer as an accurate detection platform for single nucleotide polymorphisms (SNPs) has been applied to identify and resolve microorganisms involved in closely Escherichia coli O157:H7 (E. coli O157:H7). To explore more applications and improve the efficiency for pyrosequencing in this field, we developed a method integrated multiplex pyrosequencing with a universal primer. Two multiplex pyrosequencing assays with a universal biotinylated primer were designed to analyze five SNPs located in four gene of E. coli O157:H7 strain. The accuracy of the established assays was validated by genotyping reference strain E. coli O157:H7 EDL933 and E. coli K-12. We also demonstrated that two multiplex pyrosequencing assays were specific and sensitive for genotyping closely related E. coli O157 strains. Reproducibility of results and multiplexing capability were evaluated by a comparison of this method with the monoplex pyrosequencing. Furthermore, these two multiplex pyrosequencing assays have been successfully applied to detect 11 E. coli O157 strains isolated from 1504 Chinese livestock samples. This method reduces costs and time consumption in the process of pyrosequencing analysis, and potentially serves as a rapid tool and reliable candidate strategy for the microbial identification and other genotyping application.

No association between schizophrenia and rs27388 of the MEGF10 gene in Chinese case-control sample.

In the last several years, a neurodevelopmental hypothesis of schizophrenia has been proposed and some corresponding structural abnormalities have been reported (Caruncho et al., 2004). According to the study of Hamon et al. (2006), the MEGF10 gene, a human ortholog gene of ced-1of C. elegans, participates in engulfing and clearing apoptotic cells. Furthermore, ced-1 orthologs were also reported to cause abnormal axon branching and navigation patterns in Drosophila and mouse, which in turn may play an essential role in axon pruning during brain development (Awasaki et al., 2006). Given the fact that this pathway is highly conserved in evolution, MEGF10 might participate in similar functions in humans (i.e., axon navigation, and pruning process). Because neuron apoptosis, axon navigation, and pruning are critical in shaping the developing brain, the dysfunction of these processes may cause inappropriate neuron connection and circuitry. Therefore, the variants of the MEGF10 gene could be related to the pathophysiology of schizophrenia. Chen et al. (2008) reported an association between rs27388 in the MEGF10 gene and schizophrenia in an Irish population. Given the above results, a reasonable approach to follow-up with MEGF10 would be to seek independent evidence from other samples. We undertook a case–control design to investigate the relationship between rs27388 in the MEGF10 gene and schizophrenia in Chinese Han population. There were 650 in-patients (aged 29.85± 12.26 years, 372 males) and 650 healthy blood donors (aged 27.07± 10.43 years, 340 males) included in our study. Clinical diagnosis was made by at least two psychiatrists for all cases and controls according to DSM-IV criteria. All patients in the case group were diagnosed with schizophrenia, poor-outcome schizoaffective disorder, and simple schizophrenia according to the narrow definition of schizophrenia mentioned in Chens study (Chen et al., 2008). DNA for control subjects was obtained fromblood donation centers, and recruitmentwas limited to only those without lifetime history of schizophrenia. Written informed consent was obtained and the study was approved by the Ethics Committee for the Protection of Human Subjects of Sichuan University. Genotyping of rs27388was conducted by PCR-based RFLP analysis. The primers used for PCR are 5′-AATTGCCATGAGAATTACTTTAAAC and 5′-TTGTGATGTTTGGATTTCAATT. The predicted power was calculated by the Power Calculation Tool (http://pngu.mgh.harvard.

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.

Genetic variation for five short tandem repeat loci in a central China population sample

POPULATION: Chinese.

Polymorphism of three STR loci in 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/D12S1064.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). Data of population genetics and