scholarly journals Screening and selection of 21 novel microhaplotype markers for ancestry inference in ten Chinese Subpopulations

2021 ◽  
Author(s):  
Xing Zou ◽  
Guanglin He ◽  
Jing Liu ◽  
Lirong Jiang ◽  
Mengge Wang ◽  
...  
Keyword(s):  
Massively Parallel Sequencing ◽  
East Asian ◽  
Principal Component ◽  
Amplification Efficiency ◽  
East Asians ◽  
Chinese Populations ◽  
Asian Populations ◽  
Continental Population ◽  
High Discriminatory Power ◽  
Ancestry Inference

Genetic findings suggested that ethnolinguistically diverse populations in China harbor differentiated genetic structure and complex evolutionary admixture history, which provide the genetic basis and theoretical foundation for forensic biogeographical ancestry inference (BGAI). Forensic assays for BGAI among intracontinental eastern Eurasians were previously conducted mainly based on the SNPs or InDels. Microhaplotypes, as a set of closely linked SNPs within 200 base pairs, possess the advantages of both STR and SNP and have great potential in forensic ancestry inference. However, the developed forensic assay based on the ancestry informative microhaplotypes in the BGAI remained to be comprehensively explored, especially in China with enriching genetic diversity. Here, we described a new BGAI panel based on 21 novel identified ancestry informative microhaplotypes that focused on dissected finer-scale ancestry composition of Chinese populations. We initially screened all possible microhaplotypes with high Fst values among five East Asian populations and finally employed 21 candidate microhaplotypes in two multiplex SNaPshot assays. Forensic amplification efficiency and statistically/physically phased haplotypes of the 21 microhaplotypes were validated using both SNaPshot and massively parallel sequencing (MPS) platforms. Followingly, we validated the efficiency of these microhaplotypes for BGAI in 764 individuals from ten Chinese populations. Fine-scale ancestry source and ancestry proportion estimated by the principal component analysis (PCA), multidimensional scaling (MDS), phylogenetic tree and model-based STRUCTURE among worldwide populations and East Asians showed that our customized panel could provide a higher discrimination resolution in both continental population stratification and East Asian regional substructure. East Asian populations could be further classified into linguistically/geographically different intracontinental subpopulations (Tibeto-Burman, Tai-Kadai and others). Finally, we obtained a higher estimated accuracy using training and tested datasets in the microhaplotype-based panel than traditional SNP-based panels. Generally, the above results demonstrated that this microhaplotype panel was robust and suitable for forensic BGAI in Chinese populations, which not only provided a high discriminatory power for continental populations but also discriminated East Asians into linguistically restricted subpopulations.

scholarly journals Genetic Structural Differentiation Analyses of Intercontinental Populations and Ancestry Inference of the Chinese Hui Group Based on a Novel Developed Autosomal AIM-InDel Genotyping System

2020 ◽  
Vol 2020 ◽  
pp. 1-12
Author(s):  
Tong Xie ◽  
Chunmei Shen ◽  
Xiaoye Jin ◽  
Qiong Lan ◽  
Yating Fang ◽  
...  
Keyword(s):  
Genetic Relationships ◽  
East Asian ◽  
Fixation Index ◽  
Scaling Analysis ◽  
Component Ratio ◽  
Ancestry Informative Marker ◽  
Structural Differentiation ◽  
Chinese Han ◽  
Asian Populations ◽  
Ancestry Inference

In the present study, we investigated the genetic polymorphisms of 39 ancestry informative marker-insertion/deletion (AIM-InDel) loci in the Chinese Hui group using a previously self-developed panel, further clarified the genetic relationships between the Hui group and other reference populations, and assessed the ancestry inference efficiency of the AIM-InDel panel based on the worldwide population data from 1000 Genomes Phase 3. The results of the locus-specific informativeness (In) and pairwise fixation index (Fst) values, multidimensional scaling analysis, and success ratio of estimation with cross-validation showed that the novel panel could well reveal the genetic structural differentiations of the East Asian, European, African, and South Asian populations. Besides, the biogeographical ancestry origin inference both at the individual and population levels was conducted on the Chinese Hui group by principal component analysis and STRUCTURE analysis, and the results revealed that the Hui group had the East Asian origin, and the East Asian component ratio of Hui group was approximately 88.87%. Furthermore, the population genetic analyses among the Hui group and reference populations were performed based on the insertion allele frequency heat map, population pairwise Fst values and phylogenetic tree, and the results indicated that the Hui group was genetically closer to East Asian populations, especially two Chinese Han populations (CHS and CHB populations).

scholarly journals The history and evolution of the Denisovan-EPAS1 haplotype in Tibetans

2020 ◽  
Author(s):  
Xinjun Zhang ◽  
Kelsey Witt ◽  
Amy Ko ◽  
Kai Yuan ◽  
Shuhua Xu ◽  
...  
Keyword(s):  
South Asians ◽  
East Asian ◽  
Ancestral Population ◽  
The Tibetan Plateau ◽  
East Asians ◽  
Adaptive Introgression ◽  
Asian Populations ◽  
Introgressed Segment ◽  
Introgression Event ◽  
Selection Event

AbstractRecent studies suggest that admixture with archaic hominins played an important role in facilitating biological adaptations to new environments. For example, interbreeding with Denisovans facilitated the adaptation to high altitude environments on the Tibetan Plateau. Specifically, the EPAS1 gene, a transcription factor that regulates the response to hypoxia, exhibits strong signatures of both positive selection and introgression from Denisovans in Tibetan individuals. Interestingly, despite being geographically closer to the Denisova cave, East Asian populations do not harbor as much Denisovan ancestry as populations from Melanesia. Recently, two studies have suggested two independent waves of Denisovan admixture into East Asians, one of which is shared with South Asians and Oceanians. Here we leverage data from EPAS1 in 78 Tibetan individuals to interrogate which of these two introgression events introduced the EPAS1 beneficial sequence into the ancestral population of Tibetans, and we use the distribution of introgressed segment lengths at this locus to infer the timing of the introgression and selection event. We find that the introgression event unique to East Asians most likely introduced the beneficial haplotype into the ancestral population of Tibetans around 43,000 (15,700–60,000) years ago, and selection started 12,000 (1,925-50,000) years ago. Our estimates suggest that one of the most convincing examples of adaptive introgression is in fact selection acting on standing archaic variation.

scholarly journals Carrier frequency and incidence estimation of Smith–Lemli–Opitz syndrome in East Asian populations by Genome Aggregation Database (gnomAD) based analysis

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Jong Eun Park ◽  
Taeheon Lee ◽  
Kyeongsu Ha ◽  
Chang-Seok Ki
Keyword(s):  
Carrier Frequency ◽  
East Asian ◽  
Pathogenic Variant ◽  
Facial Features ◽  
Multiple Congenital Anomalies ◽  
East Asians ◽  
Asian Populations ◽  
Incidence Estimation ◽  
Opitz Syndrome ◽  
Genetics And Genomics

Abstract Background Smith–Lemli–Opitz syndrome (SLOS) is an autosomal, recessively inherited congenital malformation syndrome characterized by multiple congenital anomalies such as microcephaly with mental defects, distinctive facial features, genital abnormalities, and 2–3 syndactyly of the toes. SLOS is caused by defective 7-dehydrocholesterol reductase, which is encoded by the DHCR7 gene. This study aimed to analyze the carrier frequency and expected incidence of SLOS in East Asians and Koreans using exome data from the Genome Aggregation Database (gnomAD) through the 2015 American College of Medical Genetics and Genomics and the Association for Molecular Pathology guideline (2015 ACMG-AMP guideline). Methods We analyzed 9197 exomes for East Asian populations from gnomAD, comprising 1909 Korean, 76 Japanese, and 7212 other East Asian populations. All identified variants were classified according to the 2015 ACMG-AMP guideline. Results According to the 2015 ACMG-AMP guideline, 15 pathogenic variant/likely pathogenic variant (PV/LPV) cases were identified in 33 East Asian individuals (33/9191 = 0.4%). Among them, four PVs/LPVs were identified in 19 Korean individuals (19/1909 = 1.0%). The predicted incidence, based upon the carrier rates of PV/LPV of DHCR7 alleles, is 1 in 310,688 in East Asians and l in 40,380 in Koreans. Conclusions This study is the first to identify carrier frequencies in East Asians and Koreans using gnomAD. It was confirmed that East Asians (0.4%) had a lower carrier frequency than did other ethnicities (1–3%) and Koreans (1.0%) had similar or lower carrier frequencies than other ethnicities. The variant spectrums of DHCR7 in East Asian and Korean populations differed greatly from those of other ethnic groups.

scholarly journals Carrier Frequency and Incidence Estimation of Smith–Lemli–Opitz syndrome in East Asian Populations by Genome Aggregation Database (gnomAD) Based Analysis

2021 ◽  
Author(s):  
Jong Eun Park ◽  
Taeheon Lee ◽  
Kyeongsu Ha ◽  
Chang-Seok Ki
Keyword(s):  
Carrier Frequency ◽  
East Asian ◽  
Pathogenic Variant ◽  
Facial Features ◽  
Multiple Congenital Anomalies ◽  
East Asians ◽  
Asian Populations ◽  
Incidence Estimation ◽  
Opitz Syndrome ◽  
Genetics And Genomics

Abstract Background: Smith–Lemli–Opitz syndrome (SLOS) is an autosomal, recessively inherited congenital malformation syndrome characterized by multiple congenital anomalies such as microcephaly with mental defects, distinctive facial features, genital abnormalities, and 2-3 syndactyly of the toes. SLOS is caused by defective 7-dehydrocholesterol reductase, which is encoded by the DHCR7 gene. This study aimed to analyze the carrier frequency and expected incidence of SLOS in East Asians and Koreans using exome data from the Genome Aggregation Database (gnomAD) through the 2015 American College of Medical Genetics and Genomics and the Association for Molecular Pathology guideline (2015 ACMG-AMP guideline).Methods: We analyzed 9,197 exomes for East Asian populations from gnomAD, comprising 1,909 Korean, 76 Japanese, and 7,212 other East Asian populations. All identified variants were classified according to 2015 ACMG-AMP guideline.Results: According to the 2015 ACMG-AMP guideline, 15 pathogenic variant/likely pathogenic variant (PV/LPV) cases were identified in 33 East Asian individuals (39/9,191 = 0.4%). Among them, four PVs/LPVs were identified in 19 Korean individuals (19/1,909 = 1.0%). The estimated incidence of SLOS is 1 in 310,688 in East Asians and l in 40,380 in Koreans. Conclusions: This study is the first to identify carrier frequencies in East Asians and Koreans using gnomAD. It was confirmed that East Asians had a lower carrier frequency than did other ethnicities, and Koreans had lower or similar carrier frequencies. The variant spectrums of DHCR7 in East Asian and Korean populations differed greatly from those of other ethnic groups.

scholarly journals The impact of evolutionary processes in shaping the genetics of complex traits in East Asia and Europe: a specific contribution from Denisovan and Neanderthal introgression

2021 ◽  
Author(s):  
Dora Koller ◽  
Frank R Wendt ◽  
Gita Pathak ◽  
Antonella De Lillo ◽  
Flavio De Angelis ◽  
...  
Keyword(s):  
Complex Traits ◽  
East Asian ◽  
Limited Information ◽  
Evolutionary Processes ◽  
East Asians ◽  
European Descent ◽  
Asian Populations ◽  
The Uk ◽  
The Impact ◽  
Specific Contribution

Evidence of how human evolution shaped the polygenicity of human traits and diseases has been extensively studied in populations of European descent. However, limited information is currently available about its impact on other ancestry groups. Here, we investigated how different evolutionary processes affected the common variant heritability of traits and diseases in East Asians. Leveraging genome-wide association statistics from the Biobank Japan (up to 158,284 participants), we assessed natural selection (negative and positive), archaic introgression from Neanderthal and Denisova, and several genomic functional categories with respect to the heritability of physiological and pathological conditions. Similar to reports in European descent populations, the heritability estimates for East Asian traits were ubiquitously enriched for negative selection annotations (false discovery rate, FDR q<0.05). Enrichment of Denisovan introgression was identified in coronary artery disease (1.69-fold enrichment, p=0.003). We followed up these enrichments by conducting a phenome-wide association study (PheWAS) of Denisovan and Neanderthal alleles in participants of six ancestral backgrounds from the UK Biobank. In East Asians, Denisovan-inherited alleles were associated with 22 phenotypes, including metabolic, immunological, cardiovascular, endocrine, and dermatological traits. The strongest association was observed for the Denisovan-inherited locus rs59185462 with rheumatoid arthritis (beta=0.82, p=1.91x10-105). In summary, our study provides the first evidence regarding the impact of evolutionary processes on the genetics of complex traits in worldwide populations, highlighting the specific contribution of Denisovan introgression in East Asian populations.

scholarly journals The history and evolution of the Denisovan-EPAS1 haplotype in Tibetans

2021 ◽  
Vol 118 (22) ◽  
pp. e2020803118
Author(s):  
Xinjun Zhang ◽  
Kelsey E. Witt ◽  
Mayra M. Bañuelos ◽  
Amy Ko ◽  
Kai Yuan ◽  
...  
Keyword(s):  
South Asians ◽  
East Asian ◽  
Ancestral Population ◽  
The Tibetan Plateau ◽  
East Asians ◽  
Adaptive Introgression ◽  
Asian Populations ◽  
Introgressed Segment ◽  
Introgression Event ◽  
Selection Event

Recent studies suggest that admixture with archaic hominins played an important role in facilitating biological adaptations to new environments. For example, interbreeding with Denisovans facilitated the adaptation to high-altitude environments on the Tibetan Plateau. Specifically, the EPAS1 gene, a transcription factor that regulates the response to hypoxia, exhibits strong signatures of both positive selection and introgression from Denisovans in Tibetan individuals. Interestingly, despite being geographically closer to the Denisova Cave, East Asian populations do not harbor as much Denisovan ancestry as populations from Melanesia. Recently, two studies have suggested two independent waves of Denisovan admixture into East Asians, one of which is shared with South Asians and Oceanians. Here, we leverage data from EPAS1 in 78 Tibetan individuals to interrogate which of these two introgression events introduced the EPAS1 beneficial sequence into the ancestral population of Tibetans, and we use the distribution of introgressed segment lengths at this locus to infer the timing of the introgression and selection event. We find that the introgression event unique to East Asians most likely introduced the beneficial haplotype into the ancestral population of Tibetans around 48,700 (16,000–59,500) y ago, and selection started around 9,000 (2,500–42,000) y ago. Our estimates suggest that one of the most convincing examples of adaptive introgression is in fact selection acting on standing archaic variation.

scholarly journals A set of novel SNP loci for differentiating continental populations and three Chinese populations

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6508 ◽  
Author(s):  
Xiao-Ye Jin ◽  
Yuan-Yuan Wei ◽  
Qiong Lan ◽  
Wei Cui ◽  
Chong Chen ◽  
...  
Keyword(s):  
Multinomial Logistic Regression ◽  
East Asian ◽  
Principal Component ◽  
Nucleotide Polymorphisms ◽  
Ancestry Informative Marker ◽  
Chinese Populations ◽  
Forensic Research ◽  
Bayes Analysis ◽  
Biogeographical Regions ◽  
Two Populations

In recent years, forensic geneticists have begun to develop some ancestry informative marker (AIM) panels for ancestry analysis of regional populations. In this study, we chose 48 single nucleotide polymorphisms (SNPs) from SPSmart database to infer ancestry origins of continental populations and Chinese subpopulations. Based on the genetic data of four continental populations (African, American, East Asian and European) from the CEPH-HGDP database, the power of these SNPs for differentiating continental populations was assessed. Population genetic structure revealed that distinct ancestry components among these continental populations could be discerned by these SNPs. Another novel population set from 1000 Genomes Phase 3 was treated as testing populations to further validate the efficiency of the selected SNPs. Twenty-two populations from CEPH-HGDP database were classified into three known populations (African, East Asian, and European) based on their biogeographical regions. Principal component analysis and Bayes analysis of testing populations and three known populations indicated these testing populations could be correctly assigned to their corresponding biogeographical origins. For three Chinese populations (Han, Mongolian, and Uygur), multinomial logistic regression analyses indicated that these 48 SNPs could be used to estimate ancestry origins of these populations. Therefore, these SNPs possessed the promising potency in ancestry analysis among continental populations and some Chinese populations, and they could be used in population genetics and forensic research.

scholarly journals The apolipoprotein E (APOE) gene and the risk of diabetic nephropathy (DN): a meta-analysis in East Asian populations

2010 ◽  
Vol 4 (2) ◽  
pp. 329-335 ◽  
Author(s):  
Jie Feng ◽  
Gang Wan ◽  
Xiaoquan Zhu ◽  
Binyou Wang ◽  
Ze Yang
Keyword(s):  
Risk Factor ◽  
Meta Analysis ◽  
East Asian ◽  
Apoe Gene ◽  
Case Control Studies ◽  
East Asians ◽  
Asian Populations ◽  
Increased Risk ◽  
Ε4 Allele ◽  
Fail Safe

Abstract Background: Several studies have examined the association between DN and the APOE gene, but the results have been inconsistent. Objective: Determine whether APOE is a risk factor for DN by a meta-analysis. Methods: A meta-analysis was performed using all findings of 16 similar case-control studies in East Asian to evaluate the effect of APOE as a risk factor for DN. Several electronic databases were searched for relevant articles up to 2009. After data collection, a meta-analysis was used to assess heterogeneity, combine results and evaluate variations by using software STATA SE 9.0. Publication bias was examined by the Egger’s linear regression test and fail-safe number. Results: The meta-analysis showed that the ε2 allele almost doubled the risk of DN in East Asians (pooled ORs [95% CI]: 1.85 [1.49-2.29]). In contrast, studies relating the ε4 allele to DN risk were very heterogeneous and the pooled ORs were 1.05 [95% CI: 0.72-1.52]. In the subgroup meta-analysis, ε4 was substantially related to an increased risk for DN in studies conducted in China (pooled ORs [95% CI]: 1.51 [1.11-2.06]), which was different from previous results. However, the higher risk of DN associated with ε4 was not found in Japanese or Korean populations (pooled ORs [95% CI]: 0.46 [0.27-0.80] and 0.58 [0.09-3.55], respectively). Conclusion: The ε2 allele conferred a higher risk of DN in East Asians, and no significant result was obtained with the ε4 allele.

1188-P: Glycemic Efficacy of Sitagliptin in East Asian Populations: A Pooled Analysis

Diabetes ◽  
2019 ◽  
Vol 68 (Supplement 1) ◽  
pp. 1188-P
Author(s):  
JOAO M. CONCEICAO ◽  
CLAUDIO D. GONZALEZ ◽  
SAMUEL S. ENGEL ◽  
JONGHO AHN ◽  
SHIGERU TOKITA ◽  
...  
Keyword(s):  
East Asian ◽  
Pooled Analysis ◽  
Asian Populations

Complications of Asian Double Eyelid Surgery: Prevention and Management

2020 ◽  
Vol 36 (05) ◽  
pp. 592-601
Author(s):  
Stephanie Ming Young ◽  
Yoon-Duck Kim
Keyword(s):  
East Asian ◽  
Eyelid Surgery ◽  
Patient Dissatisfaction ◽  
Optimal Outcomes ◽  
Asian Populations ◽  
Underlying Causes ◽  
Double Eyelid

AbstractDouble eyelid surgery remains one of the most popular aesthetic surgeries, especially among East Asian populations. Complications related to double eyelid surgery can be divided into various categories: (1) patient dissatisfaction, (2) problems with the eyelid crease, (3) problems with the eyelid height, (4) suture-related complications, and (5) complications related to eyelid surgery in general. As with all eyelid surgeries, it is important to understand and appreciate the normal and abnormal function and anatomy of the Asian eyelid to reduce the risk of complications. It is also important to recognize the various complications and their underlying causes so that the surgeon can confidently revise the surgery to achieve optimal outcomes.

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