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The contribution of common and rare genetic variants to variation in metabolic traits in 288,137 East Asians

Author

Listed:
  • Young Jin Kim

    (National Institute of Health)

  • Sanghoon Moon

    (National Institute of Health)

  • Mi Yeong Hwang

    (National Institute of Health)

  • Sohee Han

    (National Institute of Health)

  • Hye-Mi Jang

    (National Institute of Health)

  • Jinhwa Kong

    (National Institute of Health)

  • Dong Mun Shin

    (National Institute of Health)

  • Kyungheon Yoon

    (National Institute of Health)

  • Sung Min Kim

    (National Institute of Health)

  • Jong-Eun Lee

    (DNALink)

  • Anubha Mahajan

    (Genentech, 1 DNA Way
    University of Oxford)

  • Hyun-Young Park

    (National Institute of Health)

  • Mark I. McCarthy

    (Genentech, 1 DNA Way
    University of Oxford)

  • Yoon Shin Cho

    (Hallym University)

  • Bong-Jo Kim

    (National Institute of Health)

Abstract

Metabolic traits are heritable phenotypes widely-used in assessing the risk of various diseases. We conduct a genome-wide association analysis (GWAS) of nine metabolic traits (including glycemic, lipid, liver enzyme levels) in 125,872 Korean subjects genotyped with the Korea Biobank Array. Following meta-analysis with GWAS from Biobank Japan identify 144 novel signals (MAF ≥ 1%), of which 57.0% are replicated in UK Biobank. Additionally, we discover 66 rare (MAF

Suggested Citation

  • Young Jin Kim & Sanghoon Moon & Mi Yeong Hwang & Sohee Han & Hye-Mi Jang & Jinhwa Kong & Dong Mun Shin & Kyungheon Yoon & Sung Min Kim & Jong-Eun Lee & Anubha Mahajan & Hyun-Young Park & Mark I. McCar, 2022. "The contribution of common and rare genetic variants to variation in metabolic traits in 288,137 East Asians," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-34163-2
    DOI: 10.1038/s41467-022-34163-2
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    as
    1. Tian Ge & Chia-Yen Chen & Yang Ni & Yen-Chen Anne Feng & Jordan W. Smoller, 2019. "Polygenic prediction via Bayesian regression and continuous shrinkage priors," Nature Communications, Nature, vol. 10(1), pages 1-10, December.
    2. Ron Do & Nathan O. Stitziel & Hong-Hee Won & Anders Berg Jørgensen & Stefano Duga & Pier Angelica Merlini & Adam Kiezun & Martin Farrall & Anuj Goel & Or Zuk & Illaria Guella & Rosanna Asselta & Lesli, 2015. "Exome sequencing identifies rare LDLR and APOA5 alleles conferring risk for myocardial infarction," Nature, Nature, vol. 518(7537), pages 102-106, February.
    3. Pradeep Natarajan & Gina M. Peloso & Seyedeh Maryam Zekavat & May Montasser & Andrea Ganna & Mark Chaffin & Amit V. Khera & Wei Zhou & Jonathan M. Bloom & Jesse M. Engreitz & Jason Ernst & Jeffrey R. , 2018. "Deep-coverage whole genome sequences and blood lipids among 16,324 individuals," Nature Communications, Nature, vol. 9(1), pages 1-12, December.
    4. Christopher DeBoever & Yosuke Tanigawa & Malene E. Lindholm & Greg McInnes & Adam Lavertu & Erik Ingelsson & Chris Chang & Euan A. Ashley & Carlos D. Bustamante & Mark J. Daly & Manuel A. Rivas, 2018. "Medical relevance of protein-truncating variants across 337,205 individuals in the UK Biobank study," Nature Communications, Nature, vol. 9(1), pages 1-10, December.
    5. Konrad J. Karczewski & Laurent C. Francioli & Grace Tiao & Beryl B. Cummings & Jessica Alföldi & Qingbo Wang & Ryan L. Collins & Kristen M. Laricchia & Andrea Ganna & Daniel P. Birnbaum & Laura D. Gau, 2020. "The mutational constraint spectrum quantified from variation in 141,456 humans," Nature, Nature, vol. 581(7809), pages 434-443, May.
    6. Eleanor Wheeler & Aaron Leong & Ching-Ti Liu & Marie-France Hivert & Rona J Strawbridge & Clara Podmore & Man Li & Jie Yao & Xueling Sim & Jaeyoung Hong & Audrey Y Chu & Weihua Zhang & Xu Wang & Peng , 2017. "Impact of common genetic determinants of Hemoglobin A1c on type 2 diabetes risk and diagnosis in ancestrally diverse populations: A transethnic genome-wide meta-analysis," PLOS Medicine, Public Library of Science, vol. 14(9), pages 1-30, September.
    7. Shashaank Vattikuti & Juen Guo & Carson C Chow, 2012. "Heritability and Genetic Correlations Explained by Common SNPs for Metabolic Syndrome Traits," PLOS Genetics, Public Library of Science, vol. 8(3), pages 1-8, March.
    8. Clare Bycroft & Colin Freeman & Desislava Petkova & Gavin Band & Lloyd T. Elliott & Kevin Sharp & Allan Motyer & Damjan Vukcevic & Olivier Delaneau & Jared O’Connell & Adrian Cortes & Samantha Welsh &, 2018. "The UK Biobank resource with deep phenotyping and genomic data," Nature, Nature, vol. 562(7726), pages 203-209, October.
    9. Jyh-Yeuan Lee & Lisa N. Kinch & Dominika M. Borek & Jin Wang & Junmei Wang & Ina L. Urbatsch & Xiao-Song Xie & Nikolai V. Grishin & Jonathan C. Cohen & Zbyszek Otwinowski & Helen H. Hobbs & Daniel M. , 2016. "Crystal structure of the human sterol transporter ABCG5/ABCG8," Nature, Nature, vol. 533(7604), pages 561-564, May.
    10. Clara S. Tang & He Zhang & Chloe Y. Y. Cheung & Ming Xu & Jenny C. Y. Ho & Wei Zhou & Stacey S. Cherny & Yan Zhang & Oddgeir Holmen & Ka-Wing Au & Haiyi Yu & Lin Xu & Jia Jia & Robert M. Porsch & Liji, 2015. "Exome-wide association analysis reveals novel coding sequence variants associated with lipid traits in Chinese," Nature Communications, Nature, vol. 6(1), pages 1-9, December.
    11. Kyoko Watanabe & Erdogan Taskesen & Arjen Bochoven & Danielle Posthuma, 2017. "Functional mapping and annotation of genetic associations with FUMA," Nature Communications, Nature, vol. 8(1), pages 1-11, December.
    12. Christian Fuchsberger & Jason Flannick & Tanya M. Teslovich & Anubha Mahajan & Vineeta Agarwala & Kyle J. Gaulton & Clement Ma & Pierre Fontanillas & Loukas Moutsianas & Davis J. McCarthy & Manuel A. , 2016. "The genetic architecture of type 2 diabetes," Nature, Nature, vol. 536(7614), pages 41-47, August.
    13. Joshua D. Backman & Alexander H. Li & Anthony Marcketta & Dylan Sun & Joelle Mbatchou & Michael D. Kessler & Christian Benner & Daren Liu & Adam E. Locke & Suganthi Balasubramanian & Ashish Yadav & Ni, 2021. "Exome sequencing and analysis of 454,787 UK Biobank participants," Nature, Nature, vol. 599(7886), pages 628-634, November.
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    1. Chamlee Cho & Beomsu Kim & Dan Say Kim & Mi Yeong Hwang & Injeong Shim & Minku Song & Yeong Chan Lee & Sang-Hyuk Jung & Sung Kweon Cho & Woong-Yang Park & Woojae Myung & Bong-Jo Kim & Ron Do & Hyon K., 2024. "Large-scale cross-ancestry genome-wide meta-analysis of serum urate," Nature Communications, Nature, vol. 15(1), pages 1-17, December.

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