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A High Quality Asian Genome Assembly Identifies Features of Common Missing Regions

by 1,2,†, 1,2,3,*,†, 4,5,6,*, 4,5, 4,5,7, 3, 1,2, 8, 8, 9, 10,11 and 9,12,13
1
Interdisciplinary Program of Bioinformatics, College of Natural Science, Seoul National University, Seoul 08826, Korea
2
Genome & Health Big Data Laboratory, Department of Health Science, Seoul National University, Seoul 08826, Korea
3
Institute of Health & Environment, Seoul National University, Seoul 08826, Korea
4
DKU-Theragen institute for NGS analysis (DTiNa), Cheonan 31116, Korea
5
Center for Bio-Medical Engineering Core Facility, Dankook University, Cheonan 31116, Korea
6
Department of Microbiology, Dankook University, Cheonan 31116, Korea
7
Department of Nanobiomedical Science, Dankook University, Cheonan 31116, Korea
8
Center for Bio-Analysis, Korea Research Institute of Standards and Science, Daejeon 34113, Korea
9
Bioinformatics Institute, Macrogen Inc., Seoul 08511, Korea
10
Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul 03080, Korea
11
Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea
12
Precision Medicine Center, Seoul National University Bundang Hospital, Seongnam 13605, Korea
13
Gong-Wu Genomic Medicine Institute, Seoul National University Bundang Hospital, Seongnam 13605, Korea
*
Authors to whom correspondence should be addressed.
These authors equally contributed to this manuscript.
Genes 2020, 11(11), 1350; https://doi.org/10.3390/genes11111350
Received: 9 October 2020 / Revised: 6 November 2020 / Accepted: 9 November 2020 / Published: 13 November 2020
(This article belongs to the Section Human Genomics and Genetic Diseases)
The current human reference genome (GRCh38), with its superior quality, has contributed significantly to genome analysis. However, GRCh38 may still underrepresent the ethnic genome, specifically for Asians, though exactly what we are missing is still elusive. Here, we juxtaposed GRCh38 with a high-contiguity genome assembly of one Korean (AK1) to show that a part of AK1 genome is missing in GRCh38 and that the missing regions harbored ~1390 putative coding elements. Furthermore, we found that multiple populations shared some certain parts in the missing genome when we analyzed the “unmapped” (to GRCh38) reads of fourteen individuals (five East-Asians, four Europeans, and five Africans), amounting to ~5.3 Mb (~0.2% of AK1) of the total genomic regions. The recovered AK1 regions from the “unmapped reads”, which were the estimated missing regions that did not exist in GRCh38, harbored candidate coding elements. We verified that most of the common (shared by ≥7 individuals) missing regions exist in human and chimpanzee DNA. Moreover, we further identified the occurrence mechanism and ethnic heterogeneity as well as the presence of the common missing regions. This study illuminates a potential advantage of using a pangenome reference and brings up the need for further investigations on the various features of regions globally missed in GRCh38. View Full-Text
Keywords: missing information; human reference genome; precise ethnic genome; occurrence mechanism missing information; human reference genome; precise ethnic genome; occurrence mechanism
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MDPI and ACS Style

Kim, J.; Sung, J.; Han, K.; Lee, W.; Mun, S.; Lee, J.; Bahk, K.; Yang, I.; Bae, Y.-K.; Kim, C.; Kim, J.-I.; Seo, J.-S. A High Quality Asian Genome Assembly Identifies Features of Common Missing Regions. Genes 2020, 11, 1350. https://doi.org/10.3390/genes11111350

AMA Style

Kim J, Sung J, Han K, Lee W, Mun S, Lee J, Bahk K, Yang I, Bae Y-K, Kim C, Kim J-I, Seo J-S. A High Quality Asian Genome Assembly Identifies Features of Common Missing Regions. Genes. 2020; 11(11):1350. https://doi.org/10.3390/genes11111350

Chicago/Turabian Style

Kim, Jina, Joohon Sung, Kyudong Han, Wooseok Lee, Seyoung Mun, Jooyeon Lee, Kunhyung Bahk, Inchul Yang, Young-Kyung Bae, Changhoon Kim, Jong-Il Kim, and Jeong-Sun Seo. 2020. "A High Quality Asian Genome Assembly Identifies Features of Common Missing Regions" Genes 11, no. 11: 1350. https://doi.org/10.3390/genes11111350

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