Construction and evaluation of in-house methylation-sensitive SNaPshot system and three classification prediction models for identifying the tissue origin of body fluid / 浙江大学学报（英文版）（B辑：生物医学和生物技术）

The identification of tissue origin of body fluid can provide clues and evidence for criminal case investigations. To establish an efficient method for identifying body fluid in forensic cases, eight novel body fluid-specific DNA methylation markers were selected in this study, and a multiplex singlebase extension reaction (SNaPshot) system for these markers was constructed for the identification of five common body fluids (venous blood, saliva, menstrual blood, vaginal fluid, and semen). The results indicated that the in-house system showed good species specificity, sensitivity, and ability to identify mixed biological samples. At the same time, an artificial body fluid prediction model and two machine learning prediction models based on the support vector machine (SVM) and random forest (RF) algorithms were constructed using previous research data, and these models were validated using the detection data obtained in this study (n=95). The accuracy of the prediction model based on experience was 95.79%; the prediction accuracy of the SVM prediction model was 100.00% for four kinds of body fluids except saliva (96.84%); and the prediction accuracy of the RF prediction model was 100.00% for all five kinds of body fluids. In conclusion, the in-house SNaPshot system and RF prediction model could achieve accurate tissue origin identification of body fluids.

Genetic polymorphism of rsl051169 G/C and rs9984765 T/C in S100B gene in Chinese Guangxi population / 解剖学报

Objective: To explore the distribution characteristics of S100B gene rsl051169 G/C and rs9984765 T/C polymorphisms in Guangxi population, and to compare the distribution differences among different races and districts population. Methods: Polymerase chain reaction-single base extension (SBE-PCR) and DNA sequencing were used to detect the genotype of rslOSl 169 G/C and rs9984765 T/C among 398 individuals in Guangxi. The results were compared with the allele and genotype of other four populations (HapMap-CEU, HapMap-YRI, HapMap-JPT, HapMap-HCB) from Haplotype Map(Hap Map). Results: There were GG, CG and CC genotypes at the rs 1051169 G/C of S100B gene in Guangxi population, with frequencies of 41.2%, 44.7% and 14. 1%, respectively, and G and C allele frequencies were 63.6% and 36.4%, respectively. TT, CT and CC genotypes were found at rs9984765 T/C, with frequencies of 47. 7%, 44.5% and 7. 8%.respectively, and allele frequencies of T and C were 70.0% and 30. 0%, respectively. There were no significant differences in genotype and allele frequencies of rsl051169 G/C and rs9984765 T/C among male and female in Guangxi population (P>0. 05). The genotype and allele frequency of rs 1051169 G/C in Guangxi population showed significant difference as compared with HapMap-CEU, HapMap-YRI and HapMap-JPT (P0. 05). The genotype and allele frequency of rs9984765 T/C in Guangxi population showed significant difference as compared with HapMap-YRI, HapMap- JPT and HapMap-HBC (1 0. 05). Conclusion: The polymorphisms of rs 1051169 G/C and rs9984765 T/C in S100B gene in Guangxi populations, and their polymorphisms are different from different races and district populations.

Rapid and Simple Screening of Mitochondrial DNA in Koreans by the Analysis of Highly Variable Control Region SNPs / 대한법의학회지

Human mitochondrial DNA (mtDNA) is generally used to identify highly degraded forensic samples, particularly when the extracted DNA is not sufficient for nuclear DNA analysis. However, direct sequencing, the most widely used mtDNA analysis method, is laborious and time-consuming, and precludes the simultaneous analysis of many samples. Here, we describe a rapid and simple screening method for mtDNA analysis in Koreans using single base extension (SBE) methods. Sixteen highly polymorphic mtDNA SNPs from the control region were selected, and a multiplex SBE system was constructed to analyze them. Because the developed system consists of two duplex PCRs, which produce small amplicons with fewer than 270 bp, it works well with highly degraded samples such as old skeletal remains. Using this multiplex SBE system, 145 different haplotypes were expected to be observed from 593 unrelated Koreans. Seventy-three haplotypes were expected to be observed only once, and the most frequent haplotype was expected to occur 80 times. Since the mean number of pairwise differences was estimated to be 4.55, the developed system could be useful to exclude samples that do not match evidence and reference samples. Therefore, the multiplex SBE system used in this study will be a useful tool to analyze many samples simultaneously and to efficiently screen out non-matching mtDNA sequences in forensic casework.

A multiplex single-base extension protocol for genotyping Cdx2, FokI, BsmI, ApaI, and TaqI polymorphisms of the vitamin D receptor gene

The well-described role of the vitamin D endocrine system in bone metabolism makes its receptor a widely investigated candidate gene in association studies looking for the genetic basis of complex bone-related phenotypes. Most association studies genotype five polymorphic sites along the gene using PCR-RFLP and allele-specific amplification methods, which may not be the better choice in large case/control or cross-sectional studies. In this case, genotyping SNPs in parallel and using automated allele-calling methods are important to decrease genotyping errors due to manual data handling and save sample in cases where the amount of DNA is limited. The aim of this study was to present a straightforward method based on multiplex PCR amplification followed by multiplex single-base extension as a simple way to genotype five vitamin D receptor gene polymorphisms in parallel, which may be implemented in medium- to large-scale case/control or cross-sectional studies. The results regarding method feasibility and optimization are presented by genotyping eight paternity trios and seven samples of Brazilian postmenopausal women who took part in an ongoing association study carried out by members of our group.