Autosomal DIPs for population genetic structure and differentiation analyses of Chinese Xinjiang Kyrgyz ethnic group

Systematical explorations of forensic feature and population genetic diversity of the Chinese Mongolian group from northwest China via a self-constructed Multi-InDel panel

This study aimed to investigate the genetic polymorphisms and population characteristics of Chinese Mongolian group from northwest China (NCM) through a self-developed panel including 43 autosomal insertion/deletion (A-InDel) polymorphism genetic markers. Herein, 288 unrelated healthy individuals from the NCM group were employed to obtain the genetic data of 43 A-InDels through multiplex PCR amplification and InDel genotyping using capillary electrophoresis platform. In addition, multiplex population genetic analyses were performed between the NCM group and 27 reference populations. There were no deviations at 43 loci from Hardy-Weinberg equilibrium in the NCM group. The observed heterozygosity (Ho) values ranged from 0.312 8 to 0.559 2, and the combined power of discrimination (CPD) and cumulative probability of exclusion (CPE) values in the NCM group were 0.999 999 999 999 999 998 77 and 0.999 814, respectively. The forensic parameter values indicated that this panel was polymorphic and informative in the NCM group and could be used as an effective tool for forensic personal identification. Furthermore, the results of pairwise genetic distances, principal component analysis, multidimensional scaling analysis, phylogenetic tree construction, and admixture analysis among the NCM group and 27 reference populations revealed that there were closer genetic relationships between the NCM group and East Asian populations, especially Chinese Hui group (CHH) from the northwest China, which is consistent with the geographical location. These present findings contributed to the ongoing genetic explorations and insights into the genetic architecture of the NCM group.

MultiWaverX: modeling latent sex-biased admixture history

Sex-biased gene flow has been common in the demographic history of modern humans. However, the lack of sophisticated methods for delineating the detailed sex-biased admixture process prevents insights into complex admixture history and thus our understanding of the evolutionary mechanisms of genetic diversity. Here, we present a novel algorithm, MultiWaverX, for modeling complex admixture history with sex-biased gene flow. Systematic simulations showed that MultiWaverX is a powerful tool for modeling complex admixture history and inferring sex-biased gene flow. Application of MultiWaverX to empirical data of 17 typical admixed populations in America, Central Asia, and the Middle East revealed sex-biased admixture histories that were largely consistent with the historical records. Notably, fine-scale admixture process reconstruction enabled us to recognize latent sex-biased gene flow in certain populations that would likely be overlooked by much of the routine analysis with commonly used methods. An outstanding example in the real world is the Kazakh population that experienced complex admixture with sex-biased gene flow but in which the overall signature has been canceled due to biased gene flow from an opposite direction.

Genetic Admixture History and Forensic Characteristics of Guizhou Sui People Inferred From Autosomal Insertion/Deletion and Genome-Wide Single-Nucleotide Polymorphisms

Insertion-deletion (Indel) serves as one of the important markers in forensic personal identification and parentage testing, especially for cases with degraded samples. However, the genetic diversity and forensic features in ethnolinguistically diverse southwestern Chinese populations remain to be explored. Sui, one Tai-Kadai-speaking population residing in Guizhou, has a complex genetic history based on linguistic, historic, and anthropological evidence. In this study, we genotyped 30 Indels from 511 Guizhou Sui individuals and obtained approximately 700,000 genome-wide single-nucleotide polymorphisms (SNPs) in 15 representative Sui individuals to comprehensively characterize the genetic diversity, forensic characteristics, and genomic landscape of Guizhou Sui people. The estimated forensic statistically allele frequency spectrum and parameters demonstrated that this Indels panel was polymorphic and informative in Tai-Kadai populations in southern China. Results of principal component analysis (PCA), STRUCTURE, and phylogenetic trees showed that Guizhou Sui had a close genetic relationship with geographically close Tai-Kadai and Hmong-Mien people. Furthermore, genomic analysis based on the Fst and f4-statistics further suggested the genetic affinity within southern Chinese Tai-Kadai-speaking populations and a close relationship with geographically adjoining Guizhou populations. Admixture models based on the ADMIXTURE, f4, three-way qpAdm, and ALDER results demonstrated the interaction between the common ancestor for Tai-Kadai/Austronesian, Hmong-Mien, and Austroasiatic speaking populations played a significant role in the formation of modern Tai-Kadai people. We observed a sex-biased influence in Sui people by finding that the dominant Y chromosomal type was a Hmong-Mien specific lineage O2a2a1a2a1a2-N5 but the mtDNA lineages were commonly found in Tai-Kadai populations. The additional southward expansion of millet farmers in the Yellow River Basin has impacted the gene pool of southern populations including Tai-Kadai. The whole-genome sequencing in the future will shed more light on the finer genetic profile of Guizhou populations.

Genetic Background of Kirgiz Ethnic Group From Northwest China Revealed by Mitochondrial DNA Control Region Sequences on Massively Parallel Sequencing

The mitochondrial DNA (mtDNA) has been used to trace population evolution and apply to forensic identification due to the characteristics including lack of recombination, higher copy number and matrilineal inheritance comparing with nuclear genome DNA. In this study, mtDNA control region sequences of 91 Kirgiz individuals from the Northwest region of China were sequenced to identify genetic polymorphisms and gain insight into the genetic background of the Kirgiz ethnic group. MtDNA control region sequences of Kirgiz individuals presented relatively high genetic polymorphisms. The 1,122 bp sequences of mtDNA control region could differ among unrelated Kirgiz individuals, which suggested the mtDNA control region sequences have a good maternal pedigree tracing capability among different Kirgiz individuals. The neutrality test, mismatch distribution, Bayesian phylogenetic inference, Bayesian skyline analysis, and the median network analyses showed that the Kirgiz group might occurred population expansion, and the expansion could be observed at about ∼53.41 kilo years ago (kya) when ancestries of modern humans began to thrive in Eurasia. The pairwise population comparisons, principal component analyses, and median network analyses were performed based on haplogroup frequencies or mtDNA control region sequences of 5,886 individuals from the Kirgiz group and the 48 reference populations all over the world. And the most homologous haplotypes were found between Kirgiz individuals and the East Asian individuals, which indicated that the Kirgiz group might have gene exchanges with the East Asian populations.

Myopia prevalence and ocular biometry: a cross-sectional study among minority versus Han schoolchildren in Xinjiang Uygur autonomous region, China

Objectives

To describe and compare the prevalence of refractive error and its associated ocular biometric parameters in a large multi-racial sample of schoolchildren from Xinjiang.

Methods

A total of 67,102 school children of five ethnicity groups aged 6–23 years from 46 schools in Xinjiang participated in this study. The children underwent a comprehensive eye examination for vision screening, including uncorrected visual acuity and standardized refraction. Refractive error was determined by autorefractors and subjective refraction. Refraction was recorded in spherical equivalent (SE). The age- and sex- adjusted prevalence of myopia (SE ≤ −0.5 D), low myopia (−6 D < SE ≤ −0.5 D), high myopia (SE ≤ −6.0 D), astigmatism (cylinder < −0.5 D), and anisometropia (difference in SE between two eyes of 1.0 D) in the five ethnic groups were calculated. Ocular biometric parameters including axial length (AL) and corneal radius of curvature (CR) were measured by AL-scan optical biometer.

Results

The age- and sex- adjusted prevalence of myopia in the Han, Hui, Uyghur, Kyrgyz and Kazakh were 65.8% (95% confidence interval [CI] 65.4, 66.3); 59.1% (95% CI 57.8, 60.4); 30.1% (95% CI 29.2, 30.9); 30.2 (95% CI 28.9, 31.4); and 30.0% (95% CI 27.6, 32.3), respectively. The Han and Hui children also had longer ALs (Han, 23.8; Hui, 23.6, Uyghur, 23.1; Kyrgyz, 23.1; Kazakh, 23.3 mm) and larger AL/CR (Han, 3.04; Hui, 3.00; Uyghur, 2.95; Kyrgyz, 2.96; Kazakh, 2.97) values than the other three minorities (P < 0.01). Overall, girls had shorter ALs, steeper corneas, and smaller AL/CR values than boys (P < 0.01).

Conclusions

Significant ethnic difference in the prevalence of myopia was observed in this study on school-aged children in Xinjiang (Han > Hui > Kyrgyz > Uyghur > Kazakh). This study among different ethnic groups in a multiethnic population is valuable for enriching the ethnical information resources for refractive errors and ocular biometry parameters, as well as facilitating further research on myopia-related diseases and risks.

Autosomal deletion/insertion polymorphisms for global stratification analyses and ancestry origin inferences of different continental populations by machine learning methods

A lot of population data of 30 deletion/insertion polymorphisms (DIPs) of the Investigator DIPplex kit in different continental populations have been reported. Here, we assessed genetic distributions of these 30 DIPs in different continental populations to pinpoint candidate ancestry informative DIPs. Besides, the effectiveness of machine learning methods for ancestry analysis was explored. Pairwise informativeness (In) values of 30 DIPs revealed that six loci displayed relatively high In values (>0.1) among different continental populations. Besides, more loci showed high population-specific divergence (PSD) values in African population. Based on the pairwise In and PSD values of 30 DIPs, 17 DIPs in the Investigator DIPplex kit were selected to ancestry analyses of African, European, and East Asian populations. Even though 30 DIPs provided better ancestry resolution of these continental populations based on the results of PCA and population genetic structure, we found that 17 DIPs could also distinguish these continental populations. More importantly, these 17 DIPs possessed more balanced cumulative PSD distributions in these populations. Six machine learning methods were used to perform ancestry analyses of these continental populations based on 17 DIPs. Obtained results revealed that naïve Bayes manifested the greatest performance; whereas, k nearest neighbor showed relatively low performance. To sum up, these machine learning methods, especially for naïve Bayes, could be used as the valuable tool for ancestry analysis.

Genetic structure analyses and ancestral information inference of Chinese Kyrgyz group via a panel of 39 AIM-DIPs

Ancestry informative markers have extensive uses and advantages in inferring ancestral origins and estimating ancestral genetic information components of admixed populations. With the characteristics of highly cultural exchange and the admixed genetic structure of the Kyrgyz group, it is essential to enrich the genetic data of the Kyrgyz group. In this study, we used a self-developed ancestry informative marker-deletion/insertion polymorphic (AIM-DIP) panel to explore ancestral components of Chinese Kyrgyz group and population genetic relationships between the Kyrgyz group and reference populations. Results showed that all AIM-DIP loci were conformed to Hardy-Weinberg equilibrium. There were 36 AIM-DIP loci that contributed significantly to genetic information inference. Multiple statistical analyses revealed that Chinese Kyrgyz group had a closer genetic relationship with Chinese Uyghur group. The ancestral components of the Kyrgyz group, being mostly composed of genetic components of European and East Asian populations, were more similar to the ancestral components of Chinese Uyghur group.

Association of polymorphism genes , , and with risk of hyperinsulinism and insulin resistance in the Kazakh population

Hyperinsulinism and insulin resistance are closely associated with several common diseases including type 2 of diabetes, cardiovascular diseases, and metabolic syndrome. The present study aimed to determine the association between hyperinsulinism, insulin resistance and the polymorphism of genes, including angiotensin II receptor type 1 (AGTR1), angiotensinogen (AGT), β2-adrenoreceptor (ADRB2) and lipoprotein lipase (LPL), in the Kazakh population. The design of the current research was a case-control study, involving 460 subjects (age range, 18-65 years). For every subject, plasma glucose, insulin, total cholesterol, triglycerides, high-density lipoprotein, low-density lipoprotein, apolipoprotein B and apolipoprotein A1 were examined. Moreover, reverse transcription-quantitative PCR was conducted to detect the polymorphism genes LPL Ser447Ter, ADRB2 Gln27Glu, AGT Thr174Met and AGTR1 A1166C. Hyperinsulinism was considered when the insulin level was elevated >24.9 IU/ml. The homeostasis model assessment insulin resistance (HOMA-IR) was used to evaluate insulin resistance. The subjects were divided into hyperinsulinism (17 men and 24 women) and normal level insulin (214 men and 205 women) groups, which were also split into insulin resistance group (HOMA-IR >2.7; 80 men and 105 women) and those without insulin resistance group (151 men and 124 women). The results suggested that LPL Ser447Ter (rs328) allele G was associated with a lower risk of hyperinsulinism (P=0.037). Furthermore, polymorphisms of genes ADRB2 Gln27Glu (rs1042714), AGT Thr174Met (rs4762) and AGTR1 A1166C (rs5186) were not associated with hyperinsulinism and insulin resistance in the Kazakh population. No interaction was identified between LPL Ser447Ter, ADRB2 Gln27Glu, AGT Thr174Met and AGTR1 A1166C. Therefore, the results indicated that haplotype combinations were not associated with insulin resistance.

Forensic characteristic and population structure dissection of Shaanxi Han population in the light of diallelic deletion/insertion polymorphism data

The genetic polymorphisms of diallelic deletion/insertion polymorphic (DIP) loci in the Shaanxi Han population are still not clearly characterized. Herein, allele frequencies and forensic application efficiencies for 30 diallelic DIP loci were investigated in 506 unrelated healthy Han individuals from Chinese Shaanxi province. Based on population data of the same 30 diallelic DIP loci, the genetic differentiations, hierarchical clustering relationships and population architectures among Shaanxi Han and other 50 populations were further dissected through genetic and bioinformatics analyses. Results indicated that most of the 30 diallelic DIP loci were relatively high polymorphisms in the Shaanxi Han population; and there were the genetically intimate relationships between Shaanxi Han and the East Asian populations. In summary, this study provided significant insights into genetic background of Shaanxi Han population, and the multiplex amplification of these 30 diallelic DIP loci was appropriate for forensic individual identification and population genetic research in Shaanxi Han population.

Joint Genetic Analyses of Mitochondrial and Y-Chromosome Molecular Markers for a Population from Northwest China

The genetic markers on mitochondria DNA (mtDNA) and Y-chromosome can be applied as a powerful tool in population genetics. We present a study to reveal the genetic background of Kyrgyz group, a Chinese ethnic group living in northwest China, and genetic polymorphisms of 60 loci on maternal inherited mtDNA and 24 loci on paternal inherited Y-chromosome short tandem repeats (Y-STRs) were investigated. The relationship between the two systems was tested, and the result indicated that they were statistically independent from each other. The genetic distances between Kyrgyz group and 11 reference populations for mtDNA, and 13 reference populations for Y-STRs were also calculated, respectively. The present results demonstrated that the Kyrgyz group was genetically closer to East Asian populations than European populations based on the mtDNA loci but the other way around for the Y-STRs. The genetic analyses could largely strengthen the understanding for the genetic background of the Kyrgyz group.

Genetic structure and forensic characteristics of the Kyrgyz population from Kizilsu Kirghiz autonomous prefecture based on autosomal DIPs

Living in the heart of Eurasia, the Kyrgyz ethnic minority have a complex human evolutionary and migration history. However, the genetic architecture of the Kyrgyz population has not been fully explored. We studied 526 Kyrgyz samples from Kizilsu Kirghiz Autonomous Prefecture in Xinjiang using the Investigator® DIPplex kit. All loci followed Hardy-Weinberg equilibrium (HWE). The combined power of discrimination (CPD) and combined power of paternity exclusion (CPE) was 0.9999999999988 and 0.9936, respectively. Compared with 90 reference populations, five InDels (HLD99, HLD81, HLD64, HLD118, and HLD111) have the potential to distinguish the Kyrgyz/Uyghur/Kazak population from other East Asian populations. Our results suggested a close genetic relationship between the Kyrgyz population and the Uyghur/Kazak populations, followed by South Asian populations. This was in accordance with the inland migration hypothesis or modern human migration influenced by warfare. Overall, this system can be used as a powerful tool in forensic individual identification and as a complementary tool in paternity cases and biogeographic ancestry analyses.

An innovative panel containing a set of insertion/deletion loci for individual identification and its forensic efficiency evaluations in Chinese Hui ethnic minority

BACKGROUND

Individual identification is one of the most important tasks in the field of forensic genetics. Insertion/Deletion (InDel) polymorphism marker has been a promising marker for individual identification. However, a part of InDel loci in commonly used commercial kit show low polymorphisms in Chinese populations.

METHODS

We evaluated a panel of 35 InDel loci constructed previously for individual identifications in Hui group. Subsequently, population data of three Chinese populations from 1,000 Genomes Project database were used to evaluate individual identification performance of these 35 InDels. Forensic parameters, such as heterozygosity, power of exclusion, match probability and power of discrimination, were calculated to evaluate the forensic efficiency of these loci in Hui group. The heatmap of insertion allelic frequencies, Nei's genetic distances, pairwise fixation index values, principal component analyses and admixture analyses were used to analyze the genetic differentiations and structure between Hui group and other populations.

RESULTS

In studied Hui group, besides rs3054057, polymorphism information content values of the remaining loci were greater than 0.3. Values of expected heterozygosity of these loci were close to 0.5. The combined power of discrimination and power of exclusion values were 0.99999999999999659609 and 0.998682, respectively. Analyses of population genetics revealed that Chinese Hui group had closer genetic relationships with East Asian populations than other intercontinental populations.

CONCLUSION

The forensic statistical analyses revealed these loci showed relatively high genetic polymorphisms in Chinese Hui group, and could be served as a useful tool for individual identifications in Hui group. Population genetic evaluations indicated that Chinese Hui group had close genetic relationships with East Asian populations.

A surrogate FRAX model for the Kyrgyz Republic

The hip fracture rates from Kazakhstan were used to create a surrogate FRAX® model for the Kyrgyz Republic.

INTRODUCTION

The International Society for Clinical Densitometry and International Osteoporosis Foundation recommend utilizing a surrogate FRAX model, based on the country-specific risk of death, and fracture data based on a country where fracture rates are considered to be representative of the index country.

OBJECTIVE

This paper describes a surrogate FRAX model for the Kyrgyz Republic.

METHODS

The FRAX model used the incidence of hip fracture from the neighbouring country of Kazakhstan and the death risk for the Kyrgyz Republic.

RESULTS

Compared with the model for Kazakhstan, the surrogate model gave somewhat higher 10-year fracture probabilities for men between 60 and 80 years of age and lower probabilities for men above the age of 80. For women the probabilities were similar up to the age of 75-80 years and then lower. There were very close correlations in fracture probabilities between the surrogate and authentic models (1.00) so that the use of the Kyrgyz model had little impact on the rank order of risk. It was estimated that 2752 hip fractures arose in 2015 in individuals over the age of 50 years in the Kyrgyz Republic, with a predicted increase by 207% to 8435 in 2050.

CONCLUSION

The surrogate FRAX model for the Kyrgyz Republic provides the opportunity to determine fracture probability among the Kyrgyz population and help guide decisions about treatment.

Prevalence and Correlation of Metabolic Syndrome: A Cross-Sectional Study of Nearly 10 Million Multi-Ethnic Chinese Adults

PURPOSE

This study aimed to examine the prevalence and correlates of metabolic syndrome (MetS) in multi-ethnic populations of Northwest China based on Large-scale provincial health checking data.

PATIENTS AND METHODS

A total of 9,745,640 Chinese aged ≥18 years in Xinjiang, the largest autonomous region of multi-ethnic in China, were enrolled from Feb. to Sep. 2019. MetS was defined by modified Adult Treatment Panel (ATP III) criteria.

RESULTS

The overall prevalence of MetS was 20.85% [Sex: 20.06% female, 21.56% male; Age: 39.22% 60-years and above, 26.32% 40- to 59-years and 9.56% 18- to 39-years; Ethnicity: 28.19% Hui followed by Han (26.39%), Uyghur (18.56%), Other (18.61%), Kazak (17.98%), Mongolian (17.87%), Kyrgyz (14.44%)]. People living in cities and towns (23.03%) or North (24.78%) had higher prevalence of MetS than rural (19.94%) and South (17.66%). Although the prevalence of hypertension, smoking, drinking and lack of physical activity were higher in Kyrgyz, Mongolian and Kazak than those of other ethnic groups, the risk of MetS was lower.

CONCLUSION

The results indicated that a high prevalence of MetS in Hui and Han groups and people living in cities and towns. Living in North Xinjiang and elder population tend to have higher prevalence of MetS. The prevention and management of MetS in these populations should be prioritized.

Genetic diversity and phylogenetic analysis of Chinese Han and Li ethnic populations from Hainan Island by 30 autosomal insertion/deletion polymorphisms

With the characteristics of low mutation rate, length variation and short amplicon size, insertion/deletion polymorphisms (InDels) have the advantages of both short tandem repeats (STRs) and single nucleotide polymorphisms (SNPs). Herein, people of two ethnicities from Hainan Island were genotyped for the first time using the Investigator DIPplex kit. We investigated the forensic parameters of the 30 InDels and the phylogenetic relationships among different populations. The accumulated powers of discrimination and powers of exclusion were 0.999 999 999 9646 and 0.9897 in the Hainan Han population and 0.999 999 999 9292 and 0.9861 in the Hainan Li population, respectively. Additionally, population comparisons among geographically, ethnically and linguistically diverse populations via cluster heatmap, multidimensional scaling, principal component analysis, phylogenetic tree and STRUCTURE analyses demonstrated that the Hainan Han population had genetic similarities to the other Han, She and Tujia populations, while the Hainan Li population had close genetic relationships to the Zhuang and Miao groups; both populations had a high degree of genetic differentiation from most Turkic-speaking populations. Aforementioned results suggested that the 30 autosomal InDels are highly polymorphic and informative, which are suitable for human identification and population genetics.

Four hundred and forty-five Chinese individuals from two ethnicities (Hainan Han and Hainan Li) were firstly analyzed by 30 autosomal InDels included in the Investigator DIPplex panel.

Forensic parameters of the 30 InDels in the two populations showed high polymorphism and universality for human identification purposes.

The Investigator DIPplex panel had a certain capacity of differentiating intercontinental populations and different language populations.

Forensic characteristics and population genetics of Chinese Kazakh ethnic minority with an efficient STR panel

On the purpose of enhancing the forensic efficiency of CODIS STR loci, new STR loci have been gradually discovered and developed into some commercial multiplex systems. Recently, 22 STR loci including 18 non-CODIS STR loci and four CODIS STR loci were investigated in 501 unrelated healthy individuals of Kazakh ethnic group. Seven to 20 alleles at the different loci were identified and altogether 276 alleles for 22 selected loci were detected with the corresponding allelic frequencies ranging from 0.0010 to 0.3623. No significant deviation was observed from the Hardy-Weinberg equilibrium test for any of the 22 STRs. The value of cumulative power of discrimination in Kazakh group was 1-1.00E^-28. Analyses of population differentiations and genetic distances between Kazakh and other Chinese groups presented that the Kazakh group with the Uygur group. These 22 STR loci evenly distributed on 22 different autosomal chromosomes were characterized by high genetic diversities and therefore could be utilized in the forensic cases to further increase the discrimination performance.

Genetic distribution analyses and population background explorations of Gansu Yugur and Guizhou Miao groups via InDel markers

Insertion and deletion markers (InDels) have gained considerable attentions in population genetics and forensic research. In this study, we investigated genetic distributions of 30 InDels in Gansu Yugur and Guizhou Miao groups and evaluated their forensic application values. Genetic relationship analyses between Gansu Yugur, Guizhou Miao groups and other published populations were conducted based on these 30 InDels. Power of discrimination and power of exclusion in trio and duo cases of 30 InDels ranged from 0.3528 to 0.6247, 0.0937 to 0.1873, and 0.0219 to 0.1247 in Gansu Yugur group; and they ranged from 0.2579 to 0.6247, 0.0671 to 0.1874, and 0.0105 to 0.1247 in Guizhou Miao group. Obtained cumulative power of discrimination values indicated these InDels could be used for forensic individual identifications in both ethnic groups. Principal component analysis and phylogenetic reconstruction revealed that Gansu Yugur and Guizhou Miao groups had close affinities with their neighboring populations. Genetic structure analyses among these populations also indicated that studied Gansu Yugur and Guizhou Miao groups showed similar genetic structure with their neighboring populations. Further analyses of Y-STR, mtDNA, and ancestry informative markers should be conducted to better understand genetic backgrounds of Gansu Yugur and Guizhou Miao groups in the future.