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Hijikata A, Suyama M, Kikugawa S, Matoba R, Naruto T, Enomoto Y, Kurosawa K, Harada N, Yanagi K, Kaname T, Miyako K, Takazawa M, Sasai H, Hosokawa J, Itoga S, Yamaguchi T, Kosho T, Matsubara K, Kuroki Y, Fukami M, Adachi K, Nanba E, Tsuchida N, Uchiyama Y, Matsumoto N, Nishimura K, Ohara O. Exome-wide benchmark of difficult-to-sequence regions using short-read next-generation DNA sequencing. Nucleic Acids Res 2024; 52:114-124. [PMID: 38015437 PMCID: PMC10783491 DOI: 10.1093/nar/gkad1140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 11/03/2023] [Accepted: 11/13/2023] [Indexed: 11/29/2023] Open
Abstract
Next-generation DNA sequencing (NGS) in short-read mode has recently been used for genetic testing in various clinical settings. NGS data accuracy is crucial in clinical settings, and several reports regarding quality control of NGS data, primarily focusing on establishing NGS sequence read accuracy, have been published thus far. Variant calling is another critical source of NGS errors that remains unexplored at the single-nucleotide level despite its established significance. In this study, we used a machine-learning-based method to establish an exome-wide benchmark of difficult-to-sequence regions at the nucleotide-residue resolution using 10 genome sequence features based on real-world NGS data accumulated in The Genome Aggregation Database (gnomAD) of the human reference genome sequence (GRCh38/hg38). The newly acquired metric, designated the 'UNMET score,' along with additional lines of structural information from the human genome, allowed us to assess the sequencing challenges within the exonic region of interest using conventional short-read NGS. Thus, the UNMET score could provide a basis for addressing potential sequential errors in protein-coding exons of the human reference genome sequence GRCh38/hg38 in clinical sequencing.
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Affiliation(s)
- Atsushi Hijikata
- Laboratory of Computational Genomics, School of Life Sciences, Tokyo University of Pharmacy and Life Sciences, Hachioji, Tokyo 192-0392, Japan
| | - Mikita Suyama
- Division of Bioinformatics, Medical Institute of Bioregulation, Kyushu University, Higashi-ku, Fukuoka 812-8582, Japan
| | | | - Ryo Matoba
- DNA Chip Research Inc., Minato-ku, Tokyo 105-0022, Japan
| | - Takuya Naruto
- Clinical Research Institute, Kanagawa Children's Medical Center, Minami-ku, Yokohama, Kanagawa 232-0066, Japan
| | - Yumi Enomoto
- Clinical Research Institute, Kanagawa Children's Medical Center, Minami-ku, Yokohama, Kanagawa 232-0066, Japan
| | - Kenji Kurosawa
- Clinical Research Institute, Kanagawa Children's Medical Center, Minami-ku, Yokohama, Kanagawa 232-0066, Japan
- Division of Medical Genetics, Kanagawa Children's Medical Center, Minami-ku, Yokohama, Kanagawa 232-0066, Japan
| | - Naoki Harada
- Department of Fundamental Cell Technology, Center for iPS Cell Research and Application (CiRA), Kyoto University, Sakyo-ku, Kyoto 606-8507, Japan
| | - Kumiko Yanagi
- Department of Genome Medicine, National Center for Child Health and Development, Setagaya-ku, Tokyo 157-8535, Japan
| | - Tadashi Kaname
- Department of Genome Medicine, National Center for Child Health and Development, Setagaya-ku, Tokyo 157-8535, Japan
| | - Keisuke Miyako
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Masaki Takazawa
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Hideo Sasai
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
- Department of Pediatrics, Graduate School of Medicine, Gifu University, Gifu, Gifu 501-1194, Japan
| | - Junichi Hosokawa
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Sakae Itoga
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
| | - Tomomi Yamaguchi
- Department of Medical Genetics, Shinshu University School of Medicine, Matsumoto, Nagano 390-8621, Japan
- Center for Medical Genetics, Shinshu University Hospital, Matsumoto, Nagano 390-8621, Japan
- Division of Clinical Sequencing, Shinshu University School of Medicine, Matsumoto, Nagano 390-8621, Japan
| | - Tomoki Kosho
- Department of Medical Genetics, Shinshu University School of Medicine, Matsumoto, Nagano 390-8621, Japan
- Center for Medical Genetics, Shinshu University Hospital, Matsumoto, Nagano 390-8621, Japan
- Division of Clinical Sequencing, Shinshu University School of Medicine, Matsumoto, Nagano 390-8621, Japan
| | - Keiko Matsubara
- Division of Collaborative Research, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo 157-8535, Japan
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo 157-8535, Japan
| | - Yoko Kuroki
- Department of Genome Medicine, National Center for Child Health and Development, Setagaya-ku, Tokyo 157-8535, Japan
- Division of Collaborative Research, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo 157-8535, Japan
| | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Setagaya-ku, Tokyo 157-8535, Japan
| | - Kaori Adachi
- Organization for Research Initiative and Promotion, Tottori University, Yonago, Tottori 680-8550, Japan
| | - Eiji Nanba
- Organization for Research Initiative and Promotion, Tottori University, Yonago, Tottori 680-8550, Japan
| | - Naomi Tsuchida
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0027, Japan
- Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Kanagawa 236-0027, Japan
| | - Yuri Uchiyama
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0027, Japan
- Department of Rare Disease Genomics, Yokohama City University Hospital, Yokohama, Kanagawa 236-0027, Japan
| | - Naomichi Matsumoto
- Department of Human Genetics, Yokohama City University Graduate School of Medicine, Kanazawa-ku, Yokohama, Kanagawa 236-0027, Japan
| | | | - Osamu Ohara
- Department of Applied Genomics, Kazusa DNA Research Institute, Kisarazu, Chiba 292-0818, Japan
- Division of Clinical Sequencing, Shinshu University School of Medicine, Matsumoto, Nagano 390-8621, Japan
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Nakano M, Yui H, Kikugawa S, Tokida R, Sakai N, Kondo N, Endo N, Haro H, Shimodaira H, Suzuki T, Kato H, Takahashi J, Nakamura Y. Associations of LRP5 and MTHFR Gene Variants with Osteoarthritis Prevalence in Elderly Women: A Japanese Cohort Survey Randomly Sampled from a Basic Resident Registry. Ther Clin Risk Manag 2021; 17:1065-1073. [PMID: 34616152 PMCID: PMC8488030 DOI: 10.2147/tcrm.s330530] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 09/05/2021] [Indexed: 12/05/2022] Open
Abstract
Objective Osteoarthritis (OA) is a common and degenerative joint disorder in the elderly. A greater importance of understanding the relationship between genetic factors and OA prevalence has emerged with population aging. We therefore investigated the associations of several bone disease-related genetic variants with the prevalence of OA and osteoporosis in Japanese elderly women from the Obuse study cohort, which was randomly sampled from a basic town resident registry. Methods and Results In total, 206 female participants (mean ± standard deviation age: 69.7 ± 11.0 years) who completed OA, bone mineral density, and genotype assessments were included. The number of patients diagnosed as having knee/hip OA and osteoporosis was 59 (28.6%) and 30 (14.6%), respectively. Fisher’s exact testing revealed significant relationships between the minor T allele of LDL receptor related protein 5 (LRP5) rs3736228 and the prevalence of knee/hip OA and osteoporosis. The respective odds ratios (ORs) of the TT genotype for knee/hip OA and osteoporosis were 7.28 (95% confidence interval [CI] 2.22–28.08) and 5.24 (95% CI 0.95–26.98). An additional subgroup analysis for knee OA revealed that the frequency of the common C allele of methylenetetrahydrofolate reductase (MTHFR) rs1801133 had a statistically significant protective association with the prevalence of knee OA (OR 0.58, 95% CI 0.35–0.97). Conclusion In sum, the present study demonstrated significant associations of LRP5 rs3736228 and MTHFR rs1801133 with knee/hip OA and osteoporosis prevalences and knee OA prevalence, respectively, in Japanese elderly women. These results will help further the understanding of OA pathogenesis and related genetic risk factors.
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Affiliation(s)
- Masaki Nakano
- Department of Orthopaedic Surgery, Shinshu University School of Medicine, Matsumoto, Nagano, 390-8621, Japan
| | - Haruka Yui
- Department of Orthopaedic Surgery, Shinshu University School of Medicine, Matsumoto, Nagano, 390-8621, Japan
| | | | - Ryosuke Tokida
- Rehabilitation Center, Shinshu University Hospital, Matsumoto, Nagano, 390-8621, Japan
| | - Noriko Sakai
- Department of Orthopaedic Surgery, New Life Hospital, Obuse, Nagano, 381-0295, Japan
| | - Naoki Kondo
- Division of Orthopedic Surgery, Department of Regenerative and Transplant Medicine, Niigata University Graduate School of Medical and Dental Sciences, Chuo-ku, Niigata, 951-8510, Japan
| | - Naoto Endo
- Division of Orthopedic Surgery, Department of Regenerative and Transplant Medicine, Niigata University Graduate School of Medical and Dental Sciences, Chuo-ku, Niigata, 951-8510, Japan
| | - Hirotaka Haro
- Department of Orthopaedic Surgery, University of Yamanashi Graduate School of Medicine, Chuo, Yamanashi, 409-3898, Japan
| | - Hiroki Shimodaira
- Department of Orthopaedic Surgery, Shinshu University School of Medicine, Matsumoto, Nagano, 390-8621, Japan
| | - Takako Suzuki
- Department of Orthopaedic Surgery, Shinshu University School of Medicine, Matsumoto, Nagano, 390-8621, Japan.,Department of Human Nutrition, Faculty of Human Nutrition, Tokyo Kasei Gakuin University, Chiyoda-ku, Tokyo, 102-8341, Japan
| | - Hiroyuki Kato
- Department of Orthopaedic Surgery, Shinshu University School of Medicine, Matsumoto, Nagano, 390-8621, Japan
| | - Jun Takahashi
- Department of Orthopaedic Surgery, Shinshu University School of Medicine, Matsumoto, Nagano, 390-8621, Japan
| | - Yukio Nakamura
- Department of Orthopaedic Surgery, Shinshu University School of Medicine, Matsumoto, Nagano, 390-8621, Japan
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Murakami K, Kikugawa S, Seki S, Terai H, Suzuki T, Nakano M, Takahashi J, Nakamura Y. Exome Sequencing Reveals De Novo Variants in Congenital Scoliosis. J Pediatr Genet 2021; 11:287-291. [DOI: 10.1055/s-0041-1726282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 02/05/2021] [Indexed: 10/21/2022]
Abstract
AbstractCongenital scoliosis (CS) is a lateral curvature of the spine characterized by the presence of vertebral anomalies. Pathogenic genetic variants in the TBX6 gene are one of the causes of CS. However, since many clinically diagnosed cases of CS are without known TBX6 gene variations, this study aims to uncover new genes related to disease susceptibility of CS by exome sequencing (ES). This study employed ES in a cohort of 5 Japanese patients with CS and their healthy parents or a sister for a total of 16 samples among 5 families. Variant interpretation was performed using SIFT, PolyPhen-2, Mutation Taster, and CADD. Four de novo variants were identified by ES and confirmed by Sanger sequencing: 1 frameshift variant (SHISA3) and 3 missense variants (AGBL5, HDAC4, and PDE2A). ES also uncovered 1 homozygous variant in the MOCOS gene. All of these variants were predicted to be deleterious by SIFT, PolyPhen-2, Mutation Taster, and/or CADD. The number of de novo variants identified in this study was exactly what would be expected by chance. Additional functional studies or gathering matched patients using Gene Matcher are needed.
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Affiliation(s)
- Kohei Murakami
- Department of Orthopaedic Surgery, Shinshu University School of Medicine, Matsumoto, Nagano, Japan
- Laboratory of Immunology, Faculty of Veterinary Medicine, Okayama University of Science, Imabari, Ehime, Japan
| | | | - Shoji Seki
- Department of Orthopedic Surgery, Faculty of Medicine, University of Toyama, Toyama, Japan
| | - Hidetomi Terai
- Department of Orthopedics, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Takako Suzuki
- Department of Orthopaedic Surgery, Shinshu University School of Medicine, Matsumoto, Nagano, Japan
- Department of Human Nutrition, Faculty of Human Nutrition, Tokyo Kasei Gakuin University, Chiyoda, Tokyo, Japan
| | - Masaki Nakano
- Department of Orthopaedic Surgery, Shinshu University School of Medicine, Matsumoto, Nagano, Japan
| | - Jun Takahashi
- Department of Orthopaedic Surgery, Shinshu University School of Medicine, Matsumoto, Nagano, Japan
| | - Yukio Nakamura
- Department of Orthopaedic Surgery, Shinshu University School of Medicine, Matsumoto, Nagano, Japan
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Iwanishi M, Azuma C, Tezuka Y, Yamamoto Y, Ito-Kobayashi J, Washiyama M, Kusakabe T, Kikugawa S. Observation of p.R4810K, a Polymorphism of the Mysterin Gene, the Susceptibility Gene for Moyamoya Disease, in Two Female Japanese Diabetic Patients with Familial Partial Lipodystrophy 1. Intern Med 2020; 59:2529-2537. [PMID: 33055470 PMCID: PMC7662064 DOI: 10.2169/internalmedicine.4042-19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Mysterin, which was recently shown to play an important role in maintaining cellular fat storage, has been identified to be the susceptibility gene for moyamoya disease (MMD). We encountered some female Japanese patients with partial lipodystrophy and MMD-like vascular lesions. This prompted us to examine whether mysterin variants may be present in these patients. We identified a mysterin variant, p.R4810K in two patients with MMD-like vascular lesions, who may fit the category of familial partial lipodystrophy (FPLD) 1. Our cases suggest the possibility that p.R4810K, in addition to atherogenic risk factors, might thus play a role in the development of atherosclerotic lesions in patients with FPLD1 and p.R4810K.
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Affiliation(s)
- Masanori Iwanishi
- Department of Diabetes and Endocrinology, Kusatsu General Hospital, Japan
| | - Choka Azuma
- Department of Diabetes and Endocrinology, Kusatsu General Hospital, Japan
| | - Yuji Tezuka
- Department of Diabetes and Endocrinology, Kusatsu General Hospital, Japan
| | - Yukako Yamamoto
- Department of Diabetes and Endocrinology, Kusatsu General Hospital, Japan
| | - Jun Ito-Kobayashi
- Department of Diabetes and Endocrinology, Kusatsu General Hospital, Japan
| | - Miki Washiyama
- Department of Diabetes and Endocrinology, Kusatsu General Hospital, Japan
| | - Toru Kusakabe
- Department of Endocrinology, Metabolism and Hypertension, Clinical Research Institute, National Hospital Organization Kyoto Medical Center, Japan
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Murakami K, Kikugawa S, Kobayashi Y, Uehara S, Suzuki T, Kato H, Udagawa N, Nakamura Y. Olfactomedin-like protein OLFML1 inhibits Hippo signaling and mineralization in osteoblasts. Biochem Biophys Res Commun 2018; 505:419-425. [PMID: 30266405 DOI: 10.1016/j.bbrc.2018.09.112] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 09/17/2018] [Indexed: 01/06/2023]
Abstract
Congenital scoliosis is a lateral curvature of the spine that is due to the presence of vertebral anomalies. Although genetic and environmental factors are involved in the pathogenesis of congenital scoliosis, the specific cause of only a small number of individuals has been identified to date. We identified a de novo missense mutation in the olfactomedin-like 1 (OLFML1) gene by whole-exome sequencing of a patient with congenital scoliosis. Then, we carried out further functional investigation in mice. An assessment of the tissue distribution of Olfml1 revealed it to be prominently expressed in developing skeletal tissues, specifically osteoblasts. Short hairpin RNA-mediated knockdown of Olfml1 in osteoblasts induced the translocation of Yes-associated protein (YAP) transcriptional coactivator from the cytoplasm to the nucleus, which accelerated the Hippo signaling pathway to promote osteoblast mineralization. In contrast, experimentally induced gain of function of Olfml1 retained YAP in the cytoplasm. There appears to exist a novel cell-autonomous mechanism by which osteoblasts avoid excess mineralization through Olfml1. Our results also indicate that mutation of OLFML1 leads to impaired osteoblast differentiation and abnormal development of bone tissue.
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Affiliation(s)
- Kohei Murakami
- Department of Biochemistry, Matsumoto Dental University, 1780 Gobara, Hiro-oka, Shiojiri, Nagano, 399-0781, Japan; Department of Orthopaedic Surgery, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano, 390-8621, Japan
| | - Shingo Kikugawa
- DNA Chip Research Inc., 1-15-1 Kaigan, Minato-ku, Tokyo, 105-0022, Japan
| | - Yasuhiro Kobayashi
- Institute for Oral Science, Matsumoto Dental University, 1780 Gobara, Hiro-oka, Shiojiri, Nagano, 399-0781, Japan
| | - Shunsuke Uehara
- Department of Biochemistry, Matsumoto Dental University, 1780 Gobara, Hiro-oka, Shiojiri, Nagano, 399-0781, Japan
| | - Takako Suzuki
- Department of Orthopaedic Surgery, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano, 390-8621, Japan
| | - Hiroyuki Kato
- Department of Orthopaedic Surgery, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano, 390-8621, Japan
| | - Nobuyuki Udagawa
- Department of Biochemistry, Matsumoto Dental University, 1780 Gobara, Hiro-oka, Shiojiri, Nagano, 399-0781, Japan
| | - Yukio Nakamura
- Department of Orthopaedic Surgery, Shinshu University School of Medicine, 3-1-1 Asahi, Matsumoto, Nagano, 390-8621, Japan.
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Karasaki T, Nagayama K, Kawashima M, Hiyama N, Murayama T, Kuwano H, Nitadori JI, Anraku M, Sato M, Miyai M, Hosoi A, Matsushita H, Kikugawa S, Matoba R, Ohara O, Kakimi K, Nakajima J. Identification of Individual Cancer-Specific Somatic Mutations for Neoantigen-Based Immunotherapy of Lung Cancer. J Thorac Oncol 2015; 11:324-33. [PMID: 26752676 DOI: 10.1016/j.jtho.2015.11.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 11/19/2015] [Indexed: 11/29/2022]
Abstract
INTRODUCTION Two strategies for selecting neoantigens as targets for non-small cell lung cancer vaccines were compared: (1) an "off-the-shelf" approach starting with shared mutations extracted from global databases and (2) a personalized pipeline using whole-exome sequencing data on each patient's tumor. METHODS The Catalogue of Somatic Mutations in Cancer database was used to create a list of shared missense mutations occurring in more than 1% of patients. These mutations were then assessed for predicted binding affinity to HLA alleles of 15 lung cancer patients, and potential neoantigens (pNeoAgs) for each patient were selected on this basis. In the personalized approach, pNeoAgs were selected from missense mutations detected by whole-exome sequencing of the patient's own samples. RESULTS The list of shared mutations included 22 missense mutations for adenocarcinoma and 18 for squamous cell carcinoma (SCC), resulting in a median of 10 off-the-shelf pNeoAgs for each adenocarcinoma (range 5-13) and 9 (range 5-12) for each SCC. In contrast, a median of 59 missense mutations were identified by whole-exome sequencing (range 33-899) in adenocarcinoma and 164.5 (range 26-232) in SCC. This resulted in a median of 46 pNeoAgs (range 13-659) for adenocarcinoma and 95.5 (range 10-145) for SCC in the personalized set. We found that only one or two off-the-shelf pNeoAgs were included in the set of personalized pNeoAgs-and then in only three patients, with no overlap seen in the remaining 12 patients. CONCLUSIONS Use of an off-the-shelf pipeline is feasible but may not be satisfactory for most patients with non-small cell lung cancer. We recommend identifying personal mutations by comprehensive genome sequencing for developing neoantigen-targeted cancer immunotherapies.
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Affiliation(s)
- Takahiro Karasaki
- Department of Thoracic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kazuhiro Nagayama
- Department of Thoracic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Mitsuaki Kawashima
- Department of Thoracic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Noriko Hiyama
- Department of Thoracic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tomonori Murayama
- Department of Thoracic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hideki Kuwano
- Department of Thoracic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Jun-ichi Nitadori
- Department of Thoracic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masaki Anraku
- Department of Thoracic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masaaki Sato
- Department of Thoracic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Manami Miyai
- Department of Immunotherapeutics, The University of Tokyo Hospital, Tokyo, Japan; MEDINET Co. Ltd., Yokohama, Japan
| | - Akihiro Hosoi
- Department of Immunotherapeutics, The University of Tokyo Hospital, Tokyo, Japan; MEDINET Co. Ltd., Yokohama, Japan
| | - Hirokazu Matsushita
- Department of Immunotherapeutics, The University of Tokyo Hospital, Tokyo, Japan
| | | | | | - Osamu Ohara
- Department of Human Genome Research, Kazusa DNA Research Institute, Kisarazu, Japan
| | - Kazuhiro Kakimi
- Department of Immunotherapeutics, The University of Tokyo Hospital, Tokyo, Japan.
| | - Jun Nakajima
- Department of Thoracic Surgery, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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Nakamura Y, Kikugawa S, Seki S, Takahata M, Iwasaki N, Terai H, Matsubara M, Fujioka F, Inagaki H, Kobayashi T, Kimura T, Kurahashi H, Kato H. PCSK5 mutation in a patient with the VACTERL association. BMC Res Notes 2015; 8:228. [PMID: 26055999 PMCID: PMC4467638 DOI: 10.1186/s13104-015-1166-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 05/12/2015] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND The VACTERL association is a typically sporadic, non-random collection of congenital anomalies that includes vertebral defects, anal atresia, cardiac defects, tracheoesophageal fistula with esophageal atresia, renal anomalies, and limb abnormalities. Although several chromosomal aberrations and gene mutations have been reported as disease-causative, these findings have been sparsely replicated to date. CASE PRESENTATION In the present study, whole exome sequencing of a case with the VACTERL association uncovered a novel frameshift mutation in the PCSK5 gene, which has been reported as one of the causative genes for the VACTERL association. Although this mutation appears potentially pathogenic in its functional aspects, it was also carried by the healthy father. Furthermore, a database survey revealed several other deleterious variants in the PCSK5 gene in the general population. CONCLUSIONS Further studies are necessary to clarify the etiological role of the PCSK5 mutation in the VACTERL association.
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Affiliation(s)
- Yukio Nakamura
- Department of Orthopaedic Surgery, Shinshu University School of Medicine, Matsumoto, Japan.
| | | | - Shoji Seki
- Department of Orthopaedic Surgery, Faculty of Medicine, University of Toyama, Toyama, Japan.
| | - Masahiko Takahata
- Department of Orthopaedic Surgery, Hokkaido University School of Medicine, Sapporo, Japan.
| | - Norimasa Iwasaki
- Department of Orthopaedic Surgery, Hokkaido University School of Medicine, Sapporo, Japan.
| | - Hidetomi Terai
- Department of Orthopaedic Surgery, Osaka City University Graduate School of Medicine, Osaka, Japan.
| | - Mitsuhiro Matsubara
- Department of Orthopaedic Surgery, Nagano Prefectural Children's Hospital, Azumino, Japan.
| | - Fumio Fujioka
- Department of Orthopaedic Surgery, Nagano Prefectural Children's Hospital, Azumino, Japan.
| | - Hidehito Inagaki
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Japan.
| | - Tatsuya Kobayashi
- Endocrine Unit, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
| | - Tomoatsu Kimura
- Department of Orthopaedic Surgery, Faculty of Medicine, University of Toyama, Toyama, Japan.
| | - Hiroki Kurahashi
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Japan.
| | - Hiroyuki Kato
- Department of Orthopaedic Surgery, Shinshu University School of Medicine, Matsumoto, Japan.
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Kikugawa S, Nishikata K, Murakami K, Sato Y, Suzuki M, Altaf-Ul-Amin M, Kanaya S, Imanishi T. PCDq: human protein complex database with quality index which summarizes different levels of evidences of protein complexes predicted from h-invitational protein-protein interactions integrative dataset. BMC Syst Biol 2012; 6 Suppl 2:S7. [PMID: 23282181 PMCID: PMC3521179 DOI: 10.1186/1752-0509-6-s2-s7] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Background Proteins interact with other proteins or biomolecules in complexes to perform cellular functions. Existing protein-protein interaction (PPI) databases and protein complex databases for human proteins are not organized to provide protein complex information or facilitate the discovery of novel subunits. Data integration of PPIs focused specifically on protein complexes, subunits, and their functions. Predicted candidate complexes or subunits are also important for experimental biologists. Description Based on integrated PPI data and literature, we have developed a human protein complex database with a complex quality index (PCDq), which includes both known and predicted complexes and subunits. We integrated six PPI data (BIND, DIP, MINT, HPRD, IntAct, and GNP_Y2H), and predicted human protein complexes by finding densely connected regions in the PPI networks. They were curated with the literature so that missing proteins were complemented and some complexes were merged, resulting in 1,264 complexes comprising 9,268 proteins with 32,198 PPIs. The evidence level of each subunit was assigned as a categorical variable. This indicated whether it was a known subunit, and a specific function was inferable from sequence or network analysis. To summarize the categories of all the subunits in a complex, we devised a complex quality index (CQI) and assigned it to each complex. We examined the proportion of consistency of Gene Ontology (GO) terms among protein subunits of a complex. Next, we compared the expression profiles of the corresponding genes and found that many proteins in larger complexes tend to be expressed cooperatively at the transcript level. The proportion of duplicated genes in a complex was evaluated. Finally, we identified 78 hypothetical proteins that were annotated as subunits of 82 complexes, which included known complexes. Of these hypothetical proteins, after our prediction had been made, four were reported to be actual subunits of the assigned protein complexes. Conclusions We constructed a new protein complex database PCDq including both predicted and curated human protein complexes. CQI is a useful source of experimentally confirmed information about protein complexes and subunits. The predicted protein complexes can provide functional clues about hypothetical proteins. PCDq is freely available at http://h-invitational.jp/hinv/pcdq/.
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Affiliation(s)
- Shingo Kikugawa
- Integrated Databases and Systems Biology Team, Biological Information Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
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Yamasaki C, Murakami K, Fujii Y, Sato Y, Harada E, Takeda JI, Taniya T, Sakate R, Kikugawa S, Shimada M, Tanino M, Koyanagi KO, Barrero RA, Gough C, Chun HW, Habara T, Hanaoka H, Hayakawa Y, Hilton PB, Kaneko Y, Kanno M, Kawahara Y, Kawamura T, Matsuya A, Nagata N, Nishikata K, Noda AO, Nurimoto S, Saichi N, Sakai H, Sanbonmatsu R, Shiba R, Suzuki M, Takabayashi K, Takahashi A, Tamura T, Tanaka M, Tanaka S, Todokoro F, Yamaguchi K, Yamamoto N, Okido T, Mashima J, Hashizume A, Jin L, Lee KB, Lin YC, Nozaki A, Sakai K, Tada M, Miyazaki S, Makino T, Ohyanagi H, Osato N, Tanaka N, Suzuki Y, Ikeo K, Saitou N, Sugawara H, O'Donovan C, Kulikova T, Whitfield E, Halligan B, Shimoyama M, Twigger S, Yura K, Kimura K, Yasuda T, Nishikawa T, Akiyama Y, Motono C, Mukai Y, Nagasaki H, Suwa M, Horton P, Kikuno R, Ohara O, Lancet D, Eveno E, Graudens E, Imbeaud S, Debily MA, Hayashizaki Y, Amid C, Han M, Osanger A, Endo T, Thomas MA, Hirakawa M, Makalowski W, Nakao M, Kim NS, Yoo HS, De Souza SJ, Bonaldo MDF, Niimura Y, Kuryshev V, Schupp I, Wiemann S, Bellgard M, Shionyu M, Jia L, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Zhang Q, Go M, Minoshima S, Ohtsubo M, Hanada K, Tonellato P, Isogai T, Zhang J, Lenhard B, Kim S, Chen Z, Hinz U, Estreicher A, Nakai K, Makalowska I, Hide W, Tiffin N, Wilming L, Chakraborty R, Soares MB, Chiusano ML, Suzuki Y, Auffray C, Yamaguchi-Kabata Y, Itoh T, Hishiki T, Fukuchi S, Nishikawa K, Sugano S, Nomura N, Tateno Y, Imanishi T, Gojobori T. The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. Nucleic Acids Res 2007; 36:D793-9. [PMID: 18089548 PMCID: PMC2238988 DOI: 10.1093/nar/gkm999] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Here we report the new features and improvements in our latest release of the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/), a comprehensive annotation resource for human genes and transcripts. H-InvDB, originally developed as an integrated database of the human transcriptome based on extensive annotation of large sets of full-length cDNA (FLcDNA) clones, now provides annotation for 120 558 human mRNAs extracted from the International Nucleotide Sequence Databases (INSD), in addition to 54 978 human FLcDNAs, in the latest release H-InvDB_4.6. We mapped those human transcripts onto the human genome sequences (NCBI build 36.1) and determined 34 699 human gene clusters, which could define 34 057 (98.1%) protein-coding and 642 (1.9%) non-protein-coding loci; 858 (2.5%) transcribed loci overlapped with predicted pseudogenes. For all these transcripts and genes, we provide comprehensive annotation including gene structures, gene functions, alternative splicing variants, functional non-protein-coding RNAs, functional domains, predicted sub cellular localizations, metabolic pathways, predictions of protein 3D structure, mapping of SNPs and microsatellite repeat motifs, co-localization with orphan diseases, gene expression profiles, orthologous genes, protein-protein interactions (PPI) and annotation for gene families. The current H-InvDB annotation resources consist of two main views: Transcript view and Locus view and eight sub-databases: the DiseaseInfo Viewer, H-ANGEL, the Clustering Viewer, G-integra, the TOPO Viewer, Evola, the PPI view and the Gene family/group.
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Affiliation(s)
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- Japan Biological Information Research Center, Japan Biological Informatics Consortium, Japan
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Kikugawa S, Takehara H, Kuhara S, Kimura M. A Novel Model for Prediction of RNA binding Proteins. CBIJ 2005. [DOI: 10.1273/cbij.5.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Shingo Kikugawa
- Laboratory of Biochemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University
| | - Hideki Takehara
- Laboratory of Molecular Gene Technics, Faculty of Agriculture, Graduate School, Kyushu University
| | - Satoru Kuhara
- Laboratory of Molecular Gene Technics, Faculty of Agriculture, Graduate School, Kyushu University
| | - Makoto Kimura
- Laboratory of Biochemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University
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