Population structure of Han Chinese in the modern Taiwanese population based on 10,000 participants in the Taiwan Biobank project

Abstract

The Taiwan Biobank (TWB) aims to build a nationwide research database that integrates genomic/epigenomic profiles, lifestyle patterns, dietary habits, environmental exposure history and long-term health outcomes of 300,000 residents of Taiwan. We describe here an investigation of the population structure of Han Chinese on this Pacific island using genotype data of 591,048 SNPs in an initial freeze of 10,801 unrelated TWB participants. In addition to the North-South cline reported in other Han Chinese populations, we find the Taiwanese Han Chinese clustered into three cline groups: 5% were of northern Han Chinese ancestry, 79.9% were of southern Han Chinese ancestry, and 14.5% belonged to a third (T) group. We also find that this T group is genetically distinct from neighbouring Southeast Asians and Austronesian tribes but similar to other southern Han Chinese. Interestingly, high degree of LD between HLA haplotype A*33:03-B*58:01, an MHC allele being of pathological relevance, and SNPs across the MHC region was observed in subjects with T origin, but not in other Han Chinese. This suggested the T group individuals may have experienced evolutionary events independent from the other southern Han Chinese. Based on the newly-discovered population structure, we detect different loci susceptible to type II diabetes in individuals with southern and northern Han Chinese ancestries. Finally, as one of the largest dataset currently available for the Chinese population, genome-wide statistics for the 10,810 subjects are made publicly accessible through Taiwan View (https://taiwanview.twbiobank.org.tw/index; date last accessed October 14, 2016) to encourage future genetic research and collaborations with the island Taiwan.

The rs1277306 Variant of the <b><i>REST</i></b> Gene Confers Susceptibility to Cognitive Aging in an Elderly Taiwanese Population

“…This study incorporated Taiwanese subjects from the Taiwan Biobank, which gathered the information and specimens from participants in recruitment centers across Taiwan [12,13,14]. The study cohort consisted of 634 participants.…”

“…The study cohort consisted of 634 participants. Inclusion criteria were individuals who were aged 60 years or over and self-reported as being of Taiwanese Han Chinese ancestry [14]. Participants with a history of cancer were excluded [14].…”

“…Inclusion criteria were individuals who were aged 60 years or over and self-reported as being of Taiwanese Han Chinese ancestry [14]. Participants with a history of cancer were excluded [14]. Ethical approval for the study was granted by the Internal Review Board of the Taiwan Biobank before conducting the study.…”

Genome‐wide association analysis identifies a GLUL haplotype for familial hepatitis B virus‐related hepatocellular carcinoma

“…17 The TWB chip, which consists of 653,291 SNPs, was specifically customized for the Taiwanese population, who mainly are of the Han-Chinese lineage, by including SNPs with detected polymorphisms in Taiwanese-based genotyping results from the Axiom Genome-Wide CHB 1 Array plate (Affymetrix Inc). 17 The TWB chip, which consists of 653,291 SNPs, was specifically customized for the Taiwanese population, who mainly are of the Han-Chinese lineage, by including SNPs with detected polymorphisms in Taiwanese-based genotyping results from the Axiom Genome-Wide CHB 1 Array plate (Affymetrix Inc).…”

“…Individuals with a family history of HCC have an increased overall risk of developing HCC compared with those without a family history. 16,17 3 Familial HCC cases may have common genetic backgrounds or hereditary genetic factors, whereas sporadic HCC cases most likely result from nonhereditary factors.…”