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Takayama J, Tadaka S, Yano K, Katsuoka F, Gocho C, Funayama T, Makino S, Okamura Y, Kikuchi A, Sugimoto S, Kawashima J, Otsuki A, Sakurai-Yageta M, Yasuda J, Kure S, Kinoshita K, Yamamoto M, Tamiya G. Construction and integration of three de novo Japanese human genome assemblies toward a population-specific reference. Nat Commun 2021; 12:226. [PMID: 33431880 PMCID: PMC7801658 DOI: 10.1038/s41467-020-20146-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 11/17/2020] [Indexed: 12/21/2022] Open
Abstract
The complete human genome sequence is used as a reference for next-generation sequencing analyses. However, some ethnic ancestries are under-represented in the reference genome (e.g., GRCh37) due to its bias toward European and African ancestries. Here, we perform de novo assembly of three Japanese male genomes using > 100× Pacific Biosciences long reads and Bionano Genomics optical maps per sample. We integrate the genomes using the major allele for consensus and anchor the scaffolds using genetic and radiation hybrid maps to reconstruct each chromosome. The resulting genome sequence, JG1, is contiguous, accurate, and carries the Japanese major allele at most loci. We adopt JG1 as the reference for confirmatory exome re-analyses of seven rare-disease Japanese families and find that re-analysis using JG1 reduces total candidate variant calls versus GRCh37 while retaining disease-causing variants. These results suggest that integrating multiple genomes from a single population can aid genome analyses of that population.
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Affiliation(s)
- Jun Takayama
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
- Statistical Genetics Team, RIKEN Center for Advanced Intelligence Project, Nihonbashi 1-chome Mitsui Building 15F, 1-4-1 Nihonbashi, Chuo-ku, Tokyo, 103-0027, Japan
| | - Shu Tadaka
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
| | - Kenji Yano
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
- Statistical Genetics Team, RIKEN Center for Advanced Intelligence Project, Nihonbashi 1-chome Mitsui Building 15F, 1-4-1 Nihonbashi, Chuo-ku, Tokyo, 103-0027, Japan
| | - Fumiki Katsuoka
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
| | - Chinatsu Gocho
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
| | - Takamitsu Funayama
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
| | - Satoshi Makino
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
| | - Yasunobu Okamura
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
| | - Atsuo Kikuchi
- Department of Pediatrics, Tohoku University Graduate School of Medicine, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8575, Japan
| | - Sachiyo Sugimoto
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
| | - Junko Kawashima
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
| | - Akihito Otsuki
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
| | - Mika Sakurai-Yageta
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
| | - Jun Yasuda
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
- Division of Molecular and Cellular Oncology, Miyagi Cancer Center Research Institute, 47-1, Nodayama, Medeshima-Shiode, Natori, Miyagi, 981-1293, Japan
| | - Shigeo Kure
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan
- Department of Pediatrics, Tohoku University Graduate School of Medicine, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8575, Japan
| | - Kengo Kinoshita
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan.
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan.
- Graduate School of Information Sciences, Tohoku University, 6-3-09 Aramaki Aza-Aoba, Aoba-ku, Sendai, Miyagi, 980-8579, Japan.
| | - Masayuki Yamamoto
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan.
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan.
| | - Gen Tamiya
- Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan.
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8573, Japan.
- Statistical Genetics Team, RIKEN Center for Advanced Intelligence Project, Nihonbashi 1-chome Mitsui Building 15F, 1-4-1 Nihonbashi, Chuo-ku, Tokyo, 103-0027, Japan.
- Tohoku University Graduate School of Medicine, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi, 980-8575, Japan.
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5
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Yamamoto G, Miyabe I, Tanaka K, Kakuta M, Watanabe M, Kawakami S, Ishida H, Akagi K. SVA retrotransposon insertion in exon of MMR genes results in aberrant RNA splicing and causes Lynch syndrome. Eur J Hum Genet 2020; 29:680-686. [PMID: 33293698 DOI: 10.1038/s41431-020-00779-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 10/30/2020] [Accepted: 11/17/2020] [Indexed: 11/10/2022] Open
Abstract
Lynch syndrome is an autosomal dominant hereditary cancer syndrome in which many cancers develop, the main one being colorectal cancer. Germline pathogenic variants in one of four mismatch repair (MMR) genes are known to be causative of this disease. Accurate diagnosis using genetic testing can greatly benefit the health of those affected. Recently, owing to the improvement of sequence techniques, complicated variants affecting the functions of MMR genes were discovered. In this study, we analyzed insertions of a retrotransposon-like sequence in exon 5 of the MSH6 gene and exon 3 of the MSH2 gene found in Japanese families suspected of having Lynch syndrome. Both of these insertions induced aberrant splicing, and these variants were successfully identified by mRNA sequencing or visual observation of mapping results, although a standard DNA-seq analysis pipeline failed to detect them. The insertion sequences were ~2.5 kbp in length and were found to have the structure of an SVA retrotransposon (SVA). One SVA sequence was not present in the hg19 or hg38 reference genome, but was in a Japanese-specific reference sequence (JRGv2). Our study illustrates the difficulties of identifying SVA insertions in disease genes, and that the possibility of polymorphic insertions should be considered when analyzing mobile elements.
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Affiliation(s)
- Gou Yamamoto
- Department of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, 780 Komuro, Ina-machi, Kitaadachi-gun, Saitama, 362-0806, Japan
| | - Izumi Miyabe
- Department of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, 780 Komuro, Ina-machi, Kitaadachi-gun, Saitama, 362-0806, Japan
| | - Keisuke Tanaka
- Department of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, 780 Komuro, Ina-machi, Kitaadachi-gun, Saitama, 362-0806, Japan
| | - Miho Kakuta
- Department of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, 780 Komuro, Ina-machi, Kitaadachi-gun, Saitama, 362-0806, Japan
| | - Motoko Watanabe
- Department of Clinical Genetics, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Satoru Kawakami
- Department of Urology, Saitama Medical Center, Saitama Medical University, Kawagoe, Saitama, Japan
| | - Hideyuki Ishida
- Department of Digestive Tract and General Surgery, Saitama Medical Center, Saitama Medical University, Kawagoe, Saitama, Japan
| | - Kiwamu Akagi
- Department of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, 780 Komuro, Ina-machi, Kitaadachi-gun, Saitama, 362-0806, Japan.
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