Genetic polymorphism of 19 autosomal STR loci in the Yi ethnic minority of Liangshan Yi autonomous prefecture from Sichuan province in China

Genetic polymorphism analysis and forensic application evaluation of 57 insertion/deletion polymorphisms from Yi ethnic group in Yunnan

BACKGROUND

As a new kind of diallelic genetic marker, insertion/deletion (InDel) polymorphisms have recently been used in forensic science. However, there are relatively few studies on the forensic evaluation of InDel genetic polymorphisms from different populations.

AIM

The aim of the present work is to assess the genetic polymorphism and forensic applicability of 57 InDels from the Yi ethnic group and explore the genetic background of this group.

SUBJECTS AND METHODS

A total sample of 122 unrelated individuals of Yi group from the Yunnan province were genotyped by the AGCU indel 60 Kit. Multiplex population genetic analyses on the same 57 InDels were carried out among the Yunnan Yi group and 29 reference populations.

RESULTS

The average allele frequency of these loci in the Yi ethnic group was 0.485. Heterozygosity, polymorphism information content, and the power of discrimination were 0.477, 0.362, and 0.612, respectively. The combined power of discrimination and the combined power of exclusion reached to 0.99999999999999999669 and 0.999962965, respectively. The results showed that 57 InDels polymorphisms have high genetic polymorphisms in the Yi ethnic group.

CONCLUSIONS

The 57 InDels could be used for forensic individual identification, paternity testing, and intercontinental population discrimination, with the potential for use in biogeographic ancestry inference.

A forensic population database of autosomal STR and X-STR markers in the Qiang ethnic minority of China

The Qiang ethnic group is one of the oldest ethnic groups in China and is the most active ethnic group among all the populations along the Tibetan-Yi corridor. They have had a profound impact nationally and internationally. The paternal and maternal genetic feature of the Qiang ethnic group has been revealed, leaving the question of the genetic characteristics from autosomes and X chromosome not answered. The aim of this study was to explore the potential of 36 A-STR (Microreader™ 36A ID System) and 19 X-STR (Microreader™ 19X System) for application in the Qiang population and to elucidate their genetic diversity in southwest China. The cumulative probability of exclusion (CPE) for autosomal STRs is 1-1.3814 × 10-15 and the mean paternity exclusion chance (MEC) for X-STRs is 1-1.7323 × 10-6. Forensic parameters suggest that the STRs analyzed here are well-suited for forensic applications. The results of phylogenetic, interpopulation differentiation, and principal coordinates analysis (PCoA) indicate that the Qiang people have extensive connections with ethnic minorities in China, supporting the view that the Qiang people are the oldest group in the entire Sino-Tibetan language family. The Qiang appeared genetically more associated with most ethnic groups in China, especially the Han. The calculation of random matching probability (RMP) was improved by Fst correction of allele frequencies to make RMP more accurate and reasonable. This study can fill in the gaps in the Qiang STR reference database, providing valuable frequency data for forensic applications and evidence for the Qiang's genetic pattern as an important ancestral position in the Sino-Tibetan populations.

Genetic Polymorphism Analysis of 24 Y-STRs in a Han Chinese Population in Luzhou, Southwest China

Han is the largest of China's 56 ethnic groups and the most populous ethnic group in the world. The Luzhou region is located in southwest China, at the junction of three provinces. The unique historical factors contribute to the genetic polymorphism information. Short tandem repeats (STRs) are highly polymorphic, but the polymorphism of the Y chromosomal STRs (Y-STRs) loci in the Luzhou region is still unclear. It is of great significance to provide Y-STRs genetic data for the Han population from the Luzhou areas of southwest China. A total of 910 unrelated male individuals of the Han population from the Luzhou area were recruited, and 24 Y-STRs were analyzed. The population structure and phylogenetic relationships were compared with those of another 11 related Han populations. A total of 893 different haplotypes were achieved from 910 samples, of which 877 (98.21%) haplotypes were unique. Haplotype diversity and discrimination were 0.999956 and 0.981319, respectively. The lowest genetic diversity of DYS437 is 0.4321, and the highest genetic diversity of DYS385a/b is 0.9642. Pair-to-pair genetic distance and relative probability values indicate that Luzhou Han people are close to Sichuan Han people, Guangdong Han people, and Hunan Han people, which is consistent with geographical distribution, historical influence, and economic development. The 24 Y-STR markers of the southwest Luzhou Han population were highly polymorphic, which provided us with genetic polymorphism information and enriched the population genetic database. Therefore, it is of great value to our forensic applications and population genetics research.

Comorbidity and drug resistance of smear-positive pulmonary tuberculosis patients in the yi autonomous prefecture of China: a cross-sectional study

BACKGROUND

Tuberculosis (TB) has a high morbidity and mortality rate, and its prevention and treatment focus is on impoverished areas. The Liangshan Yi Autonomous Prefecture is a typical impoverished area in western China with insufficient medical resources and high HIV positivity. However, there have been few reports of TB and drug resistance in this area.

METHODS

We collected the demographic and clinical data of inpatients with sputum smear positive TB between 2015 and 2021 in an infectious disease hospital in the Liangshan Yi Autonomous Prefecture. Descriptive analyses were used for the epidemiological data. The chi-square test was used to compare categorical variables between the drug-resistant and drug-susceptible groups, and binary logistic regression was used to analyse meaningful variables.

RESULTS

We included 2263 patients, 79.9% of whom were Yi patients. The proportions of HIV (14.4%) and smoking (37.3%) were higher than previously reported. The incidence of extrapulmonary TB (28.5%) was high, and the infection site was different from that reported previously. When drug resistance gene detection was introduced, the proportion of drug-resistant patients became 10.9%. Patients aged 15-44 years (OR 1.817; 95% CI 1.162-2.840; P < 0.01) and 45-59 years (OR 2.175; 95% CI 1.335-3.543; P < 0.01) had significantly higher incidences of drug resistance than children and the elderly. Patients with a cough of ≥ 2 weeks had a significantly higher chance of drug resistance than those with < 2 weeks or no cough symptoms (OR 2.069; 95% CI 1.234-3.469; P < 0.01). Alcoholism (OR 1.741; 95% CI 1.107-2.736; P < 0.05) and high bacterial counts on sputum acid-fast smears (OR 1.846; 95% CI 1.115-3.058; P < 0.05) were significant in the univariate analysis.

CONCLUSIONS

Sputum smear-positive TB predominated in Yi men (15-44 years) with high smoking, alcoholism, and HIV rates. Extrapulmonary TB, especially abdominal TB, prevailed. Recent drug resistance testing revealed higher rates in 15-59 age group and ≥ 2 weeks cough duration. Alcohol abuse and high sputum AFB counts correlated with drug resistance. Strengthen screening and supervision to curb TB transmission and drug-resistant cases in the region.

Comprehensive insights into the genetic background of Chinese populations using Y chromosome markers

China is located in East Asia. With a high genetic and cultural diversity, human migration in China has always been a hot topic of genetics research. To explore the origins and migration routes of Chinese males, 3333 Chinese individuals (Han, Hui, Mongolia, Yi and Kyrgyz) with 27 Y-STRs and 143 Y-SNPs from published literature were analysed. Our data showed that there are five dominant haplogroups (O2-M122, O1-F265, C-M130, N-M231, R-M207) in China. Combining analysis of haplogroup frequencies, geographical positions and time with the most recent common ancestor (TMRCA), we found that haplogroups C-M130, N-M231 and R1-M173 and O1a-M175 probably migrated into China via the northern route. Interestingly, we found that haplogroup C*-M130 in China may originate in South Asia, whereas the major subbranches C2a-L1373 and C2b-F1067 migrated from northern China. The results of BATWING showed that the common ancestry of Y haplogroup in China can be traced back to 17 000 years ago, which was concurrent with global temperature increases after the Last Glacial Maximum.

Genetic Polymorphism and Population Genetic Structure Analysis of 21 Autosomal STR Loci for a Han-Chinese Population from Luzhou of Southwest China

The Han nationality is an ancient and populous people, and different places in China may have their distinct group relationships. Luzhou area, as a crossroads of several provinces in Southwest China, lacks autosomal short tandem repeat (STR) research and population genetics research. In this study, 21 autosomal STR loci were evaluated in 1959 Han-Chinese individuals from Luzhou area. There was no substantial linkage disequilibrium (LD) among the 21 autosomal STR markers, and all markers were in Hardy-Weinberg equilibrium (HWE). The total discrimination power (TDP) and cumulative probability of exclusion (CPE) of the 21 autosomal STR loci were calculated to be 1-9.8505 × 10^-16 and 1-1.9406 × 10^-9, respectively. There were 333 alleles for 21 STRs with allelic frequencies ranging from 0.00026 to 0.51302, and the number of alleles ranged from 7 in locus TPOX to 29 in locus Penta E. According to the results of population comparison and population differentiation, historical influences, geographical distribution, cultural integration, and economic development may have an impact on the Luzhou Han population and other Chinese populations. These 21 STR loci were found to enrich autosomal STR information in forensic databases and provide highly informative polymorphisms for our forensic practice in China, including personal identification and parentage testing.

Novel, heterozygous, de novo pathogenic variant (c.4963delA: p.Thr1656Glnfs*42) of the NF1 gene in a Chinese family with neurofibromatosis type 1

Neurofibromatosis type 1 (NF1) presents an autosomal dominant, haploinsufficient, and multisystemic disorder with patches of skin café-au-lait spots, lisch nodules in the iris, even tumors in the peripheral nervous system or fibromatous skin. In this study, a Chinese young woman who suffered from NF1 disease with first-trimester spontaneous abortion was recruited. Analysis for whole exome sequencing (WES), Sanger sequencing, short tandem repeat (STR), and co-segregation was carried out. As results, a novel, heterozygous, de novo pathogenic variant (c.4963delA:p.Thr1656Glnfs*42) of the NF1 gene in the proband was identified. This pathogenic variant of the NF1 gene produced a truncated protein that lost more than one-third of the NF1 protein at the C-terminus including half of the CRAL-TRIO lipid-binding domain and nuclear localization signal (NLS), thus leading to pathogenicity (ACMG criteria: PVS1 + PM2 + PM2). Analysis for NF1 conservation in species revealed high conservation in different species. Analysis of NF1 mRNA levels in different human tissues showed low tissue specificity, which may affect multiple organs presenting other symptoms or phenotypes. Moreover, prenatal NF1 gene diagnosis showed both alleles as wild types. Thus, this NF1 novel variant probably underlays the NF1 pathogenesis in this pedigree, which would help for the diagnosis, genetic counseling, and clinical management of this disorder.

FST estimates of 94 populations in China based on STR markers

The proper assessment of DNA evidence in cases of personal identification is a recurring theme in forensics. It is common practice to evaluate the strength of DNA evidence using the likelihood ratio (LR). The accurate use of population allele frequencies is a crucial problem in LR calculation. Allele frequency differences among different populations could be estimated by the F_ST values. Thus, F_ST would also affect LR values by correcting the allele frequencies. In this study, Chinese population allele frequency data were selected from population reports published in Chinese and English journals. The population-specific F_ST values of each population, the overall F_ST values of each province, each region, and the whole country, and the locus-specific F_ST values of different loci were calculated. The LRs using different allele frequencies and different F_ST values were compared based on the combination of simulated genotypes. As a result, the F_ST values of 94 populations, 19 provinces, 7 regions, and the whole country were obtained. The LR was overestimated using allele frequencies of the combined population containing multiple populations rather than using allele frequencies of a population, and the LRs after F_ST correction were lower than those without correction. Conclusively, the correction in conjunction with corresponding F_ST values can make the LRs more accurate and reasonable.

Developmental Validation of the Novel Five-Dye-Labeled Multiplex Autosomal STR Panel and Its Forensic Efficiency Evaluation

Short tandem repeats (STRs) are the most frequently used genetic markers in forensic genetics due to their high genetic diversities and abundant distributions in the human genome. Currently, the combined DNA index system is commonly incorporated into various commercial kits for forensic research. Some novel STRs that are different from the combined DNA index system were not only used to assess complex paternity cases but also could provide more genetic information and higher forensic efficiency in combination with those commonly used STRs. In this study, we validated forensic performance of a novel multiplex amplification STR panel to evaluate its sensitivity, species specificity, forensic application values, and so on. Obtained results revealed that the kit showed high sensitivity, and the complete allelic profile could be observed at 0.125 ng DNA sample. In addition, the kit possessed high species specificity, good tolerance to common inhibitors, and accurate genotyping ability. More importantly, STRs out of the kit displayed high discrimination power and probability of exclusion. To sum up, the novel kit presented in this study can be viewed as a promising tool for forensic human identification and complex paternity analysis.