Combination of Genome-Wide Polymorphisms and Copy Number Variations of Pharmacogenes in Koreans

Han, Nayoung; Oh, Jung Mi; Kim, In‐Wha

doi:10.3390/jpm11010033

Cited by 6 publications

(6 citation statements)

References 64 publications

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“…DNA genotyping of both the discovery and replication GWAS populations was performed using the Korea Biobank Array, which was designed by the Center for Genome Science, Korea National Institute of Health, South Korea, and referred to as the KoreanChip (KCHIP; Seoul, South Korea). The KCHIP array included a total of 833,535 single nucleotide variants for autosomal chromosomes ( Han et al, 2021 ). The location of the genes was assigned according to the National Center for Biotechnology Information Human Genome Build 37 (hg19).…”

Section: Methodsmentioning

confidence: 99%

A Genome-Wide Association Study of Novel Genetic Variants Associated With Anthropometric Traits in Koreans

2021

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Most previous genome-wide association studies (GWAS) have identified genetic variants associated with anthropometric traits. However, most of the evidence were reported in European populations. Anthropometric traits such as height and body fat distribution are significantly affected by gender and genetic factors. Here we performed GWAS involving 64,193 Koreans to identify the genetic factors associated with anthropometric phenotypes including height, weight, body mass index, waist circumference, hip circumference, and waist-to-hip ratio. We found nine novel single-nucleotide polymorphisms (SNPs) and 59 independent genetic signals in genomic regions that were reported previously. Of the 19 SNPs reported previously, eight genetic variants at RP11-513I15.6 and one genetic variant at the RP11-977G19.10 region and six Asian-specific genetic variants were newly found. We compared our findings with those of previous studies in other populations. Five overlapping genetic regions (PAN2, ANKRD52, RNF41, HGMA1, and C6orf106) had been reported previously but none of the SNPs were independently identified in the current study. Seven of the nine newly found novel loci associated with height in women revealed a statistically significant skeletal expression of quantitative trait loci. Our study provides additional insight into the genetic effects of anthropometric phenotypes in East Asians.

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Section: Methodsmentioning

confidence: 99%

A Genome-Wide Association Study of Novel Genetic Variants Associated With Anthropometric Traits in Koreans

2021

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“…For imputation, 8,699,350 variants from the East Asian population of 1000 Genomes Project Phase 3 with MAF ≥ 1% in East Asians were used as the reference to estimate the genomic coverage for common variants 16 . All variants applied to the following exclusion criteria for quality control process 17,18 : (i) subjects with < 5% missing genotype were included in the analysis, (ii) markers showing signi cant deviations from the Hardy-Weinberg equilibrium (P < 1.0×10 − 4 ), (iii) genotyping accuracy less than 96-99%, and ( ) minor allele frequency < 0.01. After the quality control (QC) evaluations, the remaining 317,290 variants were subjected to further analyses.…”

Section: Genotyping and Genetic Instrument Variant Selectionmentioning

confidence: 99%

A bidirectional causality between type 2 diabetes and hypertension in Korean general population: A Mendelian Randomization Study

Jeon,

Jung,

Kimm

et al. 2023

Preprint

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We deeply validated if the bidirectional causality between type 2 diabetes and hypertension is concordance with a previous Europian study in Korean large biobank. Five MR methods were applied using the weighted genetic risk score from 91 and 68 variants extracted from the genome-wide association study (GWAS) of the large Korean biobank (p-value <1.0×10-8), including a 2-stage least squares (2SLS) regression method, inverse-variance weighted (IVW) method, 2 median-based methods (simple and weighted) and MR-Egger were used to assess the bidirectional causal association between fasting blood sugar (FBS) and systolic blood pressure (SBP) in the Korean population. Using the 2SLS regression method, we showed that FBS genetically 0.5 mmol/L elevation caused an increased 1.63 mm/Hg SBP (p=0.0070), and genetically determined 10 mm/Hg elevation of SBP caused an increased 0.63 mmol/L FBS (p<0.0001). That bidirectional causal relationship was particularly strong among men. Under the other four methods, bidirectional causality was found also, and there was no horizontal pleiotropy The bidirectional causality different from previous studies between type 2 diabetes and hypertension was proved in the Asian general population, and. The underlying detailed mechanisms remain to be elucidated.

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“…Genotyping procedures for the KoGES (Han et al, 2021) and the BBJ (Nakatochi et al, 2019) are described in detail elsewhere. Brie y, in the KoGES, 72,299 participants were genotyped using Affymetrix or Illumina platforms.…”

Section: Genetic Variants As Instrumental Variablesmentioning

confidence: 99%

Body mass index increases uric acid in East Asian population: a Mendelian randomization study

Ryu

Lee²,

Yoon³

et al. 2022

Preprint

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Background: Previous observational and Mendelian randomization studies suggested that the increase in serum uric acid causes adiposity, not vice versa. However, most findings came from data on European ancestry. Among East Asian populations, both directions in the causal relationship between adiposity and uric acid have been suggested by observational studies and a few MR studies. In this study, we tested the hypothesis of the causal effect of body mass index (BMI) on serum uric acid in East Asian populations.Methods: Summary statistics from two large, publicly available biobanks from South Korea (72,299 participants in the Korean Genome and Epidemiology Study) and Japan (158,284 participants in the Biobank Japan) were utilized to conduct a two-sample Mendelian randomization study.Results: We found that genetically determined BMI has a positive causal effect on serum uric acid in various Mendelian randomization methods (inverse-variance weighted: B [95% CI] = 0.029 [-0.006, 0.065]; simple mode: a [95% CI] = 0.053 [0.009, 0.097]); weighted mode: c [95% CI] = 0.036 [0.005, 0.067]); weighted median: k [95% CI] = 0.042 [0.019, 0.065]). Multiple robustness checks such as a funnel plot, leave-one-out analyses, and an MR-Egger regression did not suggest directional horizontal pleiotropy. Conclusions: Genetically determined BMI increases serum uric acid in East Asian populations. Our findings from the South Korean and Japanese populations are consistent with previous observations in the European population.

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Combination of Genome-Wide Polymorphisms and Copy Number Variations of Pharmacogenes in Koreans

Cited by 6 publications

References 64 publications

A Genome-Wide Association Study of Novel Genetic Variants Associated With Anthropometric Traits in Koreans

A Genome-Wide Association Study of Novel Genetic Variants Associated With Anthropometric Traits in Koreans

A bidirectional causality between type 2 diabetes and hypertension in Korean general population: A Mendelian Randomization Study

Body mass index increases uric acid in East Asian population: a Mendelian randomization study

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