Population data and forensic efficiency of 21 autosomal STR loci included in AGCU EX22 amplification system in the Wanzhou Han population

Improving DNA mixtures analysis using compound markers composed of InDels and SNPs screened from the whole genome with next-generation sequencing

Next-generation sequencing (NGS) allows for better identification of insertion and deletion polymorphisms (InDels) and their combination with adjacent single nucleotide polymorphisms (SNPs) to form compound markers. These markers can improve the polymorphism of microhaplotypes (MHs) within the same length range, and thus, boost the efficiency of DNA mixture analysis. In this study, we screened InDels and SNPs across the whole genome and selected highly polymorphic markers composed of InDels and/or SNPs within 300 bp. Further, we successfully developed and evaluated an NGS-based panel comprising 55 loci, of which 24 were composed of both SNPs and InDels. Analysis of 124 unrelated Southern Han Chinese revealed an average effective number of alleles (Ae ) of 7.52 for this panel. The cumulative power of discrimination and cumulative probability of exclusion values of the 55 loci were 1-2.37 × 10-73 and 1-1.19 × 10-28 , respectively. Additionally, this panel exhibited high allele detection rates of over 97% in each of the 21 artificial mixtures involving from two to six contributors at different mixing ratios. We used EuroForMix to calculate the likelihood ratio (LR) and evaluate the evidence strength provided by this panel, and it could assess evidence strength with LR, distinguishing real and noncontributors. In conclusion, our panel holds great potential for detecting and analyzing DNA mixtures in forensic applications, with the capability to enhance routine mixture analysis.

Large fragment Sanger sequencing identifies the newly encountered variant that caused null alleles in parentage testing

Short tandem repeat (STR) is regarded as a crucial tool for personal identification as well as parentage testing. Thus, genotyping errors of STRs could have negative effects on the reliability of forensic identification. A null allele at the combined DNA index system (CODIS) core loci D2S1338 was found in a father-daughter pair with the AGCU Expressmarker 22 kit which was a commonly used commercial kit during our daily laboratory work. This null allele caused the father and daughter to not conform to the laws of inheritance, thus potentially generating erroneous conclusions that excluded parentage. To figure out the reason for this phenomenon, re-amplification with new primers and then large fragment Sanger sequencing was conducted. We found a G to G/T variation at the position which is fifty-nine bases away from the 3' end of the core repeat in both samples. This probably could be considered a novel variant at the primer binding region which had not been reported that resulted in the emergence of the null allele. We also found that there was more than one single-nucleotide polymorphism (SNP) with minor allele frequency (MAF) greater than 0.1 in the upstream and downstream sequences of D2S1338. When designing primers for amplification of D2S1338, the possible adverse results of these SNPs should be taken into account and avoided.

Influence of Interpersonal and Institutional Trust on the Participation Willingness of Farmers in E-Commerce Poverty Alleviation

To explore the influence of interpersonal trust and institutional trust on the participation willingness of farmers in e-commerce poverty alleviation in China, a questionnaire survey of 320 farmers in Chongqing Ecological Tourism District was adopted for data collection, and a binary logistic model was used for data analysis. The results showed that (1) both interpersonal trust and institutional trust had a positive influence on the participation behavior of farmers in e-commerce poverty alleviation, and the priority ranking from high to low was: trust in government, trust in relatives, trust in neighbors, and trust in village cadres. (2) Institutional trust had a greater impact on the participation behavior of farmers than interpersonal trust, especially in the poverty-stricken areas where economic development was relatively backward. (3) Individual attributes, household attributes, and rural resource attributes had a significant positive impact on the participation intention of farmers. Among these, the role of rural e-business service platform was particularly important. The role of institutional trust at the village level still did not perform well in promoting the participation willingness of farmers. Based on empirical analysis, the suggestions for promoting the active cooperation of farmers and participating in the cooperation of e-business were put forward, such as enhancing the interpersonal network of farmers, improving the rural e-commerce information service platform, and strengthening the construction of the rural business environment.

Genetic variation of 20 autosomal STR loci in the Han nationality in Central Yunnan, Southwest China

A total of 20 autosomal short tandem repeat (STR) loci from 2220 unrelated healthy individuals of Han population living in the central area of Yunnan province, Southwest China were amplified with the PowerPlex® 21 System. After Hardy-Weinberg equilibrium examination, the allele frequencies and forensic statistical parameters of 20 STR loci were evaluated. A total of 298 alleles and 1225 genotypes were observed for all the 20 loci. The allele frequencies varied from 0.0002 to 0.5130. The combined power of discrimination and the combined probability of exclusion of all 20 STR loci were 0.99999999521565 and 0.999999999999999999999999637, respectively. Meanwhile, genetic distances between Central Yunnan Han and 17 previously published populations were compared and a neighbor-joining (NJ) phylogenetic tree was developed and visualized by using MEGA 7 based on Nei's standard genetic distance. The results demonstrated that these loci were highly polymorphic in the Han nationality in Central Yunnan, Southwest China and could be applied in forensic medicine and population genetics.

Evaluation genotypes of cancer cell lines HCC1954 and SiHa by short tandem repeat (STR) analysis and DNA sequencing

Cancer cell lines are used worldwide in biomedical researches, and data interpretation solely depends on unambiguous attribution of those respective cell lines to its original sources. Approximately one-third of all cell lines have an origin other than that assumed, leading to invalid results. It is necessary to characterize the origin of cell lines. Short-tandem-repeat (STR) fingerprinting (DNA fingerprinting) is the method for characterization of genetic identity in cultured cell lines under certain experimental conditions. We showed the fingerprinting profiles in a summed and unidentified human cancer cell line comparison to HCC1954 cell line, revealing marked alterations in DNA fingerprinting profiles up to fourteen STR loci from 16 loci. Furthermore, Sanger DNA sequencing showed no c.3140A > G heterozygous mutation in the PIK3CA gene of this suspected HCC1954 cell line. In addition, we showed the fingerprinting profiles in an unidentified cancer cell line comparison to SiHa cervical cell line, revealing same DNA fingerprinting profiles. In conclusion, we have successfully authenticated and identified both suspected HCC1954 and SiHa cell lines by STR analysis and DNA sequencing. STR analysis combined DNA sequencing may be very useful to evaluate genotypes of cancer cell lines in our cancer studies, as well as in judicial authentication and forensic sciences.