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A database of 5305 healthy Korean individuals reveals genetic and clinical implications for an East Asian population.

ABSTRACT: Despite substantial advances in disease genetics, studies to date have largely focused on individuals of European descent. This limits further discoveries of novel functional genetic variants in other ethnic groups. To alleviate the paucity of East Asian population genome resources, we established the Korean Variant Archive 2 (KOVA 2), which is composed of 1896 whole-genome sequences and 3409 whole-exome sequences from healthy individuals of Korean ethnicity. This is the largest genome database from the ethnic Korean population to date, surpassing the 1909 Korean individuals deposited in gnomAD. The variants in KOVA 2 displayed all the known genetic features of those from previous genome databases, and we compiled data from Korean-specific runs of homozygosity, positively selected intervals, and structural variants. In doing so, we found loci, such as the loci of ADH1A/1B and UHRF1BP1, that are strongly selected in the Korean population relative to other East Asian populations. Our analysis of allele ages revealed a correlation between variant functionality and evolutionary age. The data can be browsed and downloaded from a public website ( https://www.kobic.re.kr/kova/ ). We anticipate that KOVA 2 will serve as a valuable resource for genetic studies involving East Asian populations.

SUBMITTER: Lee J

PROVIDER: S-EPMC9628380 | biostudies-literature | 2022 Nov

REPOSITORIES: biostudies-literature

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A database of 5305 healthy Korean individuals reveals genetic and clinical implications for an East Asian population.

Lee Jeongeun J Lee Jean J Jeon Sungwon S Lee Jeongha J Jang Insu I Yang Jin Ok JO Park Soojin S Lee Byungwook B Choi Jinwook J Choi Byung-Ok BO Gee Heon Yung HY Oh Jaeseong J Jang In-Jin IJ Lee Sanghyuk S Baek Daehyun D Koh Youngil Y Yoon Sung-Soo SS Kim Young-Joon YJ Chae Jong-Hee JH Park Woong-Yang WY Bhak Jong Hwa JH Choi Murim M

Experimental & molecular medicine 20221102 11

Despite substantial advances in disease genetics, studies to date have largely focused on individuals of European descent. This limits further discoveries of novel functional genetic variants in other ethnic groups. To alleviate the paucity of East Asian population genome resources, we established the Korean Variant Archive 2 (KOVA 2), which is composed of 1896 whole-genome sequences and 3409 whole-exome sequences from healthy individuals of Korean ethnicity. This is the largest genome database ...[more]

PMID: 36323850

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Project description:ImportanceMost previous genome-wide association studies (GWAS) of depression have used data from individuals of European descent. This limits the understanding of the underlying biology of depression and raises questions about the transferability of findings between populations.ObjectiveTo investigate the genetics of depression among individuals of East Asian and European descent living in different geographic locations, and with different outcome definitions for depression.Design, setting, and participantsGenome-wide association analyses followed by meta-analysis, which included data from 9 cohort and case-control data sets comprising individuals with depression and control individuals of East Asian descent. This study was conducted between January 2019 and May 2021.ExposuresAssociations of genetic variants with depression risk were assessed using generalized linear mixed models and logistic regression. The results were combined across studies using fixed-effects meta-analyses. These were subsequently also meta-analyzed with the largest published GWAS for depression among individuals of European descent. Additional meta-analyses were carried out separately by outcome definition (clinical depression vs symptom-based depression) and region (East Asian countries vs Western countries) for East Asian ancestry cohorts.Main outcomes and measuresDepression status was defined based on health records and self-report questionnaires.ResultsThere were a total of 194 548 study participants (approximate mean age, 51.3 years; 62.8% women). Participants included 15 771 individuals with depression and 178 777 control individuals of East Asian descent. Five novel associations were identified, including 1 in the meta-analysis for broad depression among those of East Asian descent: rs4656484 (β = -0.018, SE = 0.003, P = 4.43x10-8) at 1q24.1. Another locus at 7p21.2 was associated in a meta-analysis restricted to geographically East Asian studies (β = 0.028, SE = 0.005, P = 6.48x10-9 for rs10240457). The lead variants of these 2 novel loci were not associated with depression risk in European ancestry cohorts (β = -0.003, SE = 0.005, P = .53 for rs4656484 and β = -0.005, SE = 0.004, P = .28 for rs10240457). Only 11% of depression loci previously identified in individuals of European descent reached nominal significance levels in the individuals of East Asian descent. The transancestry genetic correlation between cohorts of East Asian and European descent for clinical depression was r = 0.413 (SE = 0.159). Clinical depression risk was negatively genetically correlated with body mass index in individuals of East Asian descent (r = -0.212, SE = 0.084), contrary to findings for individuals of European descent.Conclusions and relevanceThese results support caution against generalizing findings about depression risk factors across populations and highlight the need to increase the ancestral and geographic diversity of samples with consistent phenotyping.

Project description:There is increasing interest in clarifying how different face emotion expressions are perceived by people from different cultures, of different ages and sex. However, scant availability of well-controlled emotional face stimuli from non-Western populations limit the evaluation of cultural differences in face emotion perception and how this might be modulated by age and sex differences. We present a database of East Asian face expression stimuli, enacted by young and older, male and female, Taiwanese using the Facial Action Coding System (FACS). Combined with a prior database, this present database consists of 90 identities with happy, sad, angry, fearful, disgusted, surprised and neutral expressions amounting to 628 photographs. Twenty young and 24 older East Asian raters scored the photographs for intensities of multiple-dimensions of emotions and induced affect. Multivariate analyses characterized the dimensionality of perceived emotions and quantified effects of age and sex. We also applied commercial software to extract computer-based metrics of emotions in photographs. Taiwanese raters perceived happy faces as one category, sad, angry, and disgusted expressions as one category, and fearful and surprised expressions as one category. Younger females were more sensitive to face emotions than younger males. Whereas, older males showed reduced face emotion sensitivity, older female sensitivity was similar or accentuated relative to young females. Commercial software dissociated six emotions according to the FACS demonstrating that defining visual features were present. Our findings show that East Asians perceive a different dimensionality of emotions than Western-based definitions in face recognition software, regardless of age and sex. Critically, stimuli with detailed cultural norms are indispensable in interpreting neural and behavioral responses involving human facial expression processing. To this end, we add to the tools, which are available upon request, for conducting such research.

Project description:BackgroundShaanxi province, located in the upper Yellow River, has been evidenced as the geographic origin of Chinese civilization, Sino-Tibetan-speaking language, and foxtail or broomcorn millet farmers via the linguistic phylogenetic spectrum, archeological documents, and genetic evidence. Nowadays, Han Chinese is the dominant population in this area. The formation process of modern Shaanxi Han population reconstructed via the ancient DNA is on the way, however, the patterns of genetic relationships of modern Shaanxi Han, allele frequency distributions of high mutated short tandem repeats (STRs) and corresponding forensic parameters are remained to be explored.MethodsHere, we successfully genotyped 23 autosomal STRs in 630 unrelated Shaanxi male Han individuals using the recently updated Huaxia Platinum PCR amplification system. Forensic allele frequency and parameters of all autosomal STRs were assessed. And comprehensive population genetic structure was explored via various typical statistical technologies.ResultsPopulation genetic analysis based on the raw-genotype dataset among 15,803 Eurasian individuals and frequency datasets among 56 populations generally illustrated that linguistic stratification is significantly associated with the genetic substructure of the East Asian population. Principal component analysis, multidimensional scaling plots and phylogenetic tree further demonstrated that Shaanxi Han has a close genetic relationship with geographically close Shanxi Han, and showed that Han Chinese is a homogeneous population during the historic and recent admixture from the STR variations. Except for Sinitic-speaking populations, Shaanxi Han harbored more alleles sharing with Tibeto-Burman-speaking populations than with other reference populations. Focused on the allele frequency correlation and forensic parameters, all loci are in accordance with the minimum requirements of HWE and LD. The observed combined probability of discrimination of 8.2201E-28 and the cumulative power of exclusion of 0.9999999995 in Shaanxi Han demonstrated that the studied STR loci are informative and polymorphic, and this system can be used as a powerful routine forensic tool in personal identification and parentage testing.ConclusionBoth the geographical and linguistic divisions have shaped the genetic structure of modern East Asian. And more forensic reference data should be obtained for ethnically, culturally, geographically and linguistically different populations for better routine forensic practice and population genetic studies.

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A database of 5305 healthy Korean individuals reveals genetic and clinical implications for an East Asian population.

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A database of 5305 healthy Korean individuals reveals genetic and clinical implications for an East Asian population.

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