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Choi J, Kim S, Kim J, Son HY, Yoo SK, Kim CU, Park YJ, Moon S, Cha B, Jeon MC, Park K, Yun JM, Cho B, Kim N, Kim C, Kwon NJ, Park YJ, Matsuda F, Momozawa Y, Kubo M, Biobank Japan Project, Kim HJ, Park JH, Seo JS, Kim JI, Im SW. A whole-genome reference panel of 14,393 individuals for East Asian populations accelerates discovery of rare functional variants. SCIENCE ADVANCES 2023; 9:eadg6319. [PMID: 37556544 PMCID: PMC10411914 DOI: 10.1126/sciadv.adg6319] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 07/06/2023] [Indexed: 08/11/2023]
Abstract
Underrepresentation of non-European (EUR) populations hinders growth of global precision medicine. Resources such as imputation reference panels that match the study population are necessary to find low-frequency variants with substantial effects. We created a reference panel consisting of 14,393 whole-genome sequences including more than 11,000 Asian individuals. Genome-wide association studies were conducted using the reference panel and a population-specific genotype array of 72,298 subjects for eight phenotypes. This panel yields improved imputation accuracy of rare and low-frequency variants within East Asian populations compared with the largest reference panel. Thirty-nine previously unidentified associations were found, and more than half of the variants were East Asian specific. We discovered genes with rare protein-altering variants, including LTBP1 for height and GPR75 for body mass index, as well as putative regulatory mechanisms for rare noncoding variants with cell type-specific effects. We suggest that this dataset will add to the potential value of Asian precision medicine.
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Affiliation(s)
- Jaeyong Choi
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | | | - Juhyun Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Ho-Young Son
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
| | - Seong-Keun Yoo
- The Marc and Jennifer Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Young Jun Park
- Department of Translational Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sungji Moon
- Interdisciplinary Program in Cancer Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
| | - Bukyoung Cha
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
| | - Min Chul Jeon
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Kyunghyuk Park
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
| | - Jae Moon Yun
- Department of Family Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Belong Cho
- Department of Family Medicine, Seoul National University Hospital, Seoul, Republic of Korea
- Department of Family Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | | | | | | | - Young Joo Park
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, Seoul National University, Seoul, Republic of Korea
| | - Fumihiko Matsuda
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | | | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | | | - Hyun-Jin Kim
- National Cancer Control Institute, National Cancer Center, Goyang, Republic of Korea
| | - Jin-Ho Park
- Department of Family Medicine, Seoul National University Hospital, Seoul, Republic of Korea
- Department of Family Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jeong-Sun Seo
- Macrogen Inc., Seoul, Republic of Korea
- Asian Genome Center, Seoul National University Bundang Hospital, Gyeonggi, Republic of Korea
| | - Jong-Il Kim
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University, Seoul, Republic of Korea
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sun-Wha Im
- Department of Biochemistry and Molecular Biology, Kangwon National University School of Medicine, Gangwon, Republic of Korea
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Khan SY, Ali M, Lee MCW, Ma Z, Biswas P, Khan AA, Naeem MA, Riazuddin S, Riazuddin S, Ayyagari R, Hejtmancik JF, Riazuddin SA. Whole genome sequencing data of multiple individuals of Pakistani descent. Sci Data 2020; 7:350. [PMID: 33051442 PMCID: PMC7555865 DOI: 10.1038/s41597-020-00664-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 09/02/2020] [Indexed: 11/25/2022] Open
Abstract
Here we report whole genome sequencing of four individuals (H3, H4, H5, and H6) from a family of Pakistani descent. Whole genome sequencing yielded 1084.92, 894.73, 1068.62, and 1005.77 million mapped reads corresponding to 162.73, 134.21, 160.29, and 150.86 Gb sequence data and 52.49x, 43.29x, 51.70x, and 48.66x average coverage for H3, H4, H5, and H6, respectively. We identified 3,529,659, 3,478,495, 3,407,895, and 3,426,862 variants in the genomes of H3, H4, H5, and H6, respectively, including 1,668,024 variants common in the four genomes. Further, we identified 42,422, 39,824, 28,599, and 35,206 novel variants in the genomes of H3, H4, H5, and H6, respectively. A major fraction of the variants identified in the four genomes reside within the intergenic regions of the genome. Single nucleotide polymorphism (SNP) genotype based comparative analysis with ethnic populations of 1000 Genomes database linked the ancestry of all four genomes with the South Asian populations, which was further supported by mitochondria based haplogroup analysis. In conclusion, we report whole genome sequencing of four individuals of Pakistani descent. | Measurement(s) | SNV • genome | | Technology Type(s) | whole genome sequencing • DNA sequencing | | Factor Type(s) | individual | | Sample Characteristic - Organism | Homo sapiens | | Sample Characteristic - Location | Pakistan |
Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.12642761
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Affiliation(s)
- Shahid Y Khan
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Muhammad Ali
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Mei-Chong W Lee
- Department of Computer Science, San José State University, San José, CA, 95192, USA
| | - Zhiwei Ma
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Pooja Biswas
- Shiley Eye Institute, University of California San Diego, La Jolla, CA, 92093, USA
| | - Asma A Khan
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, 53700, Pakistan
| | - Muhammad Asif Naeem
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, 53700, Pakistan
| | - Saima Riazuddin
- Department of Otorhinolaryngology-Head & Neck Surgery, University of Maryland School Medicine, Baltimore, MD, 21201, USA
| | - Sheikh Riazuddin
- National Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, 53700, Pakistan.,Allama Iqbal Medical College, University of Health Sciences, Lahore, 54550, Pakistan.,Department of Molecular Biology, Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad, 44080, Pakistan
| | - Radha Ayyagari
- Shiley Eye Institute, University of California San Diego, La Jolla, CA, 92093, USA
| | - J Fielding Hejtmancik
- Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - S Amer Riazuddin
- The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA.
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