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SG10K Pilot - Large-scale whole-genome sequencing of three diverse Asian populations in Singapore

ABSTRACT: Underrepresentation of Asian genomes has hindered population and medical genetics research on Asians, leading to population disparities in precision medicine. By whole-genome sequencing of 4,810 Singapore Chinese, Malays, and Indians, we found 98.3 million SNPs and small insertions/deletions, over half of which are novel. Population structure analysis demonstrated great representation of Asian genetic diversity by three ethnicities in Singapore, and revealed a Malay-related novel ancestry component. Furthermore, demographic inference suggested that Malays split from Chinese ~24,800 years ago, and experienced significant admixture with East Asians ~1,700 years ago, coinciding with the Austronesian expansion. Additionally, we identified 20 candidate loci for natural selection, among which 14 harbored robust associations with complex traits and diseases. Finally, we showed that our data can substantially improve genotype imputation in diverse Asian and Oceanian populations. These results highlight the value of our data as a resource to empower human genetics discovery across broad geographic regions.

PROVIDER: EGAS00001003875 | EGA |

REPOSITORIES: EGA

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Ethnicity-specific Skeletal Muscle Transcriptional Signatures and Their Relevance to Insulin Resistance in Singapore

Project description:Context: Insulin resistance (IR) and obesity differ between ethnic groups in Singapore, with discordant rates of obesity and IR between several ethnic groups. However, the molecular basis underlying these differences are not clear. Objective: As the skeletal muscle (SM) is metabolically relevant to IR, we investigated molecular pathways in SM that are associated with ethnic differences in IR, obesity and related traits. Design, Setting and Main Outcome measures: We integrated transcriptomic, genomic and phenotypic analyses in 156 healthy subjects representing three major ethnicities in the Singapore Adult Metabolism Study. Patients: The study contains Chinese (n=63), Malay (n=51) and Asian-Indian (n=42) males, aged 21-40 years, without systemic diseases. Results: We found remarkable diversity in the SM transcriptome between the three ethnicities with >8,000 differentially expressed genes (40% of all genes expressed in SM). Comparison with blood transcriptome from a separate Singaporean cohort showed that >95% of SM expression differences between ethnicities were unique to SM. We identified a network of 46 genes that were specifically down-regulated in Malays, suggesting dysregulation of components of cellular respiration in SM of Malay individuals. We also report 28 differentially expressed gene-clusters, four of which were also enriched for genes that were found in GWAS of metabolic traits and disease and correlated with variation in IR, obesity and related traits. Conclusion: We identified extensive gene expression changes in SM between the three Singaporean ethnicities, and report specific genes and molecular pathways that might underpin and explain the differences in IR between these ethnic groups.

2019-07-23 | GSE117339 | GEO

SG Peranakan Project: Genetic admixture in the culturally unique Peranakan Chinese population in Southeast Asia

Project description:The Peranakan Chinese are culturally unique descendants of immigrants from China who settled in the Malay Archipelago ~300-500 years ago. Today, among large communities in Southeast Asia, the Peranakans have preserved Chinese traditions with strong influence from the local indigenous Malays. Yet, whether or to what extent genetic admixture co-occurred with the cultural mixture has been a topic of ongoing debate. We performed whole-genome sequencing (WGS) on 177 Singapore (SG) Peranakans and analyzed the data jointly with WGS data of Asian and European populations. We estimated that Peranakan Chinese inherited ~5.62% (95% confidence interval [CI]: 4.75-6.46%) Malay ancestry, much higher than that in SG Chinese (1.08%, 0.69-1.53%), southern Chinese (0.86%, 0.57-1.31%), and northern Chinese (0.25%, 0.18-0.33%). A sex-biased admixture history, in which the Malay ancestry was contributed primarily by females, was supported by X chromosomal variants, and mitochondrial (MT) and Y haplogroups. Finally, we identified an ancient admixture event shared by Peranakan Chinese and SG Chinese ~1,612 (95% CI: 1,345-1,923) years ago, coinciding with the settlement history of Han Chinese in southern China, apart from the recent admixture event with Malays unique to Peranakan Chinese ~190 (159-213) years ago. These findings greatly advance our understanding of the dispersal history of Chinese and their interaction with indigenous populations in Southeast Asia.

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Microarray analysis of the Asian seabass (Lates calcarifer) gonads

Project description:In this study, we attempt to characterize the transcriptomic profile of the Asian seabass gonads at various developmental stages. The protandric Asian seabass or barramundi (Lates calcarifer) typically matures as a male at approximately 2–4 years of age and then changes sex to a female in later years. For this experiment, Asian seabass of several ages were collected from the Marine Aquaculture Center of the Agri-Food & Veterinary Authority of Singapore and from farms around Singapore. There were no treatments carried out in this experiment. The gonads were examined by histology and classified according to sexual maturation status as described by Guiguen and colleagues (Guiguen et al. Environmental Biology of Fishes, 1994). Altogether, we analyzed 22 gonadal samples that could be classified into six different types of gonads.

2015-01-08 | GSE53898 | GEO

Microarray analysis of the Asian seabass (Lates calcarifer) gonads

Project description:In this study, we attempt to characterize the transcriptomic profile of the Asian seabass gonads at various developmental stages. The protandric Asian seabass or barramundi (Lates calcarifer) typically matures as a male at approximately 2M-bM-^@M-^S4 years of age and then changes sex to a female in later years. For this experiment, Asian seabass of several ages were collected from the Marine Aquaculture Center of the Agri-Food & Veterinary Authority of Singapore and from farms around Singapore. There were no treatments carried out in this experiment. The gonads were examined by histology and classified according to sexual maturation status as described by Guiguen and colleagues (Guiguen et al. Environmental Biology of Fishes, 1994). Altogether, we analyzed 22 gonadal samples that could be classified into six different types of gonads. Total 22 samples: Adult Ovaries (F3-stage; 5 years old fish) : 4 Adult Testes (M3-stage; 5 years old fish) : 4 Early Testes (M3-stage; 8-9 months old fish) : 3 Early Transforming Gonads (>2 years old fish) : 3 Late Transforming Gonads (>2 years old fish) : 4 Undifferentiated Gonads (4.5 months old fish) : 4

2015-01-08 | E-GEOD-53898 | biostudies-arrayexpress

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Project description:The history of human settlement in Southeast Asia has been complex and involved several distinct dispersal events. Here we report the analyses of 1825 individuals from Southeast Asia including new genome-wide genotype data for 146 individuals from three Mainland Southeast Asian (Burmese, Malay and Vietnamese) and four Island Southeast Asian (Dusun, Filipino, Kankanaey and Murut) populations. While confirming the presence of previously recognized major ancestry components in the Southeast Asian population structure, we highlight the Kankanaey Igorots from the highlands of the Philippine Mountain Province as likely the closest living representatives of the source population that may have given rise to the Austronesian expansion. This conclusion rests on independent evidence from various analyses of autosomal data and uniparental markers.

2016-02-04 | GSE77508 | GEO

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2022-10-04 | GSE182409 | GEO

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Project description:The discovery of blood-based proteomics biomarkers is recently a popular topic in AD studies due to its advantage to relate external environmental factors with the development of AD. In this study, a proteomic study based on Malaysian Chinese and Malay prospects was conducted. Differentially expressed proteins (DEPs) in AD patients and normal controls for Chinese and Malays were identified. The dissimilarities of dysregulated proteins identified in Chinese and Malays samples suggested the differences of pathways involved in this pathological condition for each respective ethnicity: the Chinese group was involved to Aβ/tau protein-related, oxidative stress and inflammation whereas neuroinflammation was related to the Malays. These findings served as a preliminary understanding in the molecular studies of AD especially in multi-ethnic population.

2024-06-10 | PXD040566 | Pride

Microarray analysis of the Asian seabass (Lates calcarifer) brains

Project description:In this study, we attempt to characterize the transcriptomic profile of the Asian seabass brains collected from the male and female sexes. The objective is to identify genes that show sexually dimorphic expression in the brain of this species. For this experiment, Asian seabass were collected from the Marine Aquaculture Center of the Agri-Food & Veterinary Authority of Singapore. There were no treatments carried out in this experiment. Four brains from adult male seabass (5 years old) with M3-type testis and four brains from adult female seabass (5 years old) with F3-type ovaries were used in this experiment. (Gonads were examined by histology and classified according to sexual maturation status as described by Guiguen and colleagues (Guiguen et al. Environmental Biology of Fishes, 1994)). Total 8 samples. Male Brain : 4 Female Brain : 4

2015-01-08 | E-GEOD-53901 | biostudies-arrayexpress

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