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Tamaoka S, Fukuda A, Nakabayashi K, Matsubara K, Ogata-Kawata H, Muranishi Y, Hata K, Kato-Fukui Y, Sakamoto S, Kasahara M, Fukami M. Rare sequence variants associated with the risk of non-syndromic biliary atresia. Hepatol Res 2023; 53:1134-1141. [PMID: 37491771 DOI: 10.1111/hepr.13946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/20/2023] [Accepted: 07/22/2023] [Indexed: 07/27/2023]
Abstract
AIM The etiology of non-syndromic biliary atresia (BA) remains largely unknown. In this study, we performed genome-wide screening of genes associated with the risk of non-syndromic BA. METHODS We analyzed exome data of 15 Japanese patients with non-syndromic BA and 509 control individuals using an optimal sequence kernel association test (SKAT-O), a gene-based association study optimized for small-number subjects. Furthermore, we examined the frequencies of known BA-related single-nucleotide polymorphisms in the BA and control groups. RESULTS SKAT-O showed that rare damaging variants of MFHAS1, a ubiquitously expressed gene encoding a Toll-like receptor-associated protein, were more common in the BA group than in the control group (Bonferroni corrected p-value = 0.0097). Specifically, p.Val106Gly and p.Arg556Cys significantly accumulated in the patient group. These variants resided within functionally important domains. SKAT-O excluded the presence of other genes significantly associated with the disease risk. Of 60 known BA-associated single-nucleotide polymorphisms, only eight were identified in the BA group. In particular, p.Ile3421Met of MYO15A and p.Ala421Thr of THOC2 were more common in the BA group than in the control group. However, the significance of these two variants is questionable, because MYO15A has been linked to deafness, but not to BA, and the p.Ala421Thr of THOC2 represents a relatively common single-nucleotide polymorphism in Asia. CONCLUSIONS The results of this study indicate that rare damaging variants in MFHAS1 may constitute a risk factor for non-syndromic BA, whereas the contribution of other monogenic variants to the disease predisposition is limited.
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Affiliation(s)
- Satoshi Tamaoka
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
- Department of Pediatrics, Keio University School of Medicine, Tokyo, Japan
| | - Akinari Fukuda
- Center for Organ Transplantation, National Center for Child Health and Development, Tokyo, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Keiko Matsubara
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
- Division of Diversity Research, National Center for Child Health and Development, Tokyo, Japan
| | - Hiroko Ogata-Kawata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Yuki Muranishi
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Yuko Kato-Fukui
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Seisuke Sakamoto
- Center for Organ Transplantation, National Center for Child Health and Development, Tokyo, Japan
| | - Mureo Kasahara
- Center for Organ Transplantation, National Center for Child Health and Development, Tokyo, Japan
| | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
- Division of Diversity Research, National Center for Child Health and Development, Tokyo, Japan
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Yamaguchi M, Cotterill S. Association of Mutations in Replicative DNA Polymerase Genes with Human Disease: Possible Application of Drosophila Models for Studies. Int J Mol Sci 2023; 24:ijms24098078. [PMID: 37175782 PMCID: PMC10178534 DOI: 10.3390/ijms24098078] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023] Open
Abstract
Replicative DNA polymerases, such as DNA polymerase α-primase, δ and ε, are multi-subunit complexes that are responsible for the bulk of nuclear DNA replication during the S phase. Over the last decade, extensive genome-wide association studies and expression profiling studies of the replicative DNA polymerase genes in human patients have revealed a link between the replicative DNA polymerase genes and various human diseases and disorders including cancer, intellectual disability, microcephalic primordial dwarfism and immunodeficiency. These studies suggest the importance of dissecting the mechanisms involved in the functioning of replicative DNA polymerases in understanding and treating a range of human diseases. Previous studies in Drosophila have established this organism as a useful model to understand a variety of human diseases. Here, we review the studies on Drosophila that explored the link between DNA polymerases and human disease. First, we summarize the recent studies linking replicative DNA polymerases to various human diseases and disorders. We then review studies on replicative DNA polymerases in Drosophila. Finally, we suggest the possible use of Drosophila models to study human diseases and disorders associated with replicative DNA polymerases.
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Affiliation(s)
| | - Sue Cotterill
- Molecular and Clinical Sciences Research Institute, St George's University of London, London SW17 0RE, UK
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Aganezov S, Yan SM, Soto DC, Kirsche M, Zarate S, Avdeyev P, Taylor DJ, Shafin K, Shumate A, Xiao C, Wagner J, McDaniel J, Olson ND, Sauria MEG, Vollger MR, Rhie A, Meredith M, Martin S, Lee J, Koren S, Rosenfeld JA, Paten B, Layer R, Chin CS, Sedlazeck FJ, Hansen NF, Miller DE, Phillippy AM, Miga KH, McCoy RC, Dennis MY, Zook JM, Schatz MC. A complete reference genome improves analysis of human genetic variation. Science 2022; 376:eabl3533. [PMID: 35357935 DOI: 10.1126/science.abl3533] [Citation(s) in RCA: 123] [Impact Index Per Article: 61.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Compared to its predecessors, the Telomere-to-Telomere CHM13 genome adds nearly 200 million base pairs of sequence, corrects thousands of structural errors, and unlocks the most complex regions of the human genome for clinical and functional study. We show how this reference universally improves read mapping and variant calling for 3202 and 17 globally diverse samples sequenced with short and long reads, respectively. We identify hundreds of thousands of variants per sample in previously unresolved regions, showcasing the promise of the T2T-CHM13 reference for evolutionary and biomedical discovery. Simultaneously, this reference eliminates tens of thousands of spurious variants per sample, including reduction of false positives in 269 medically relevant genes by up to a factor of 12. Because of these improvements in variant discovery coupled with population and functional genomic resources, T2T-CHM13 is positioned to replace GRCh38 as the prevailing reference for human genetics.
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Affiliation(s)
- Sergey Aganezov
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Stephanie M Yan
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Daniela C Soto
- Department of Biochemistry and Molecular Medicine, Genome Center, MIND Institute, University of California, Davis, CA, USA
| | - Melanie Kirsche
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Samantha Zarate
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Pavel Avdeyev
- Genome Informatics Section, National Human Genome Research Institute, Bethesda, MD, USA
| | - Dylan J Taylor
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Kishwar Shafin
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Alaina Shumate
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Chunlin Xiao
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA
| | - Justin Wagner
- National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Jennifer McDaniel
- National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Nathan D Olson
- National Institute of Standards and Technology, Gaithersburg, MD, USA
| | | | - Mitchell R Vollger
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Arang Rhie
- Genome Informatics Section, National Human Genome Research Institute, Bethesda, MD, USA
| | - Melissa Meredith
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Skylar Martin
- Department of Computer Science and Biofrontiers Institute, University of Colorado, Boulder, CO, USA
| | - Joyce Lee
- Bionano Genomics, San Diego, CA, USA
| | - Sergey Koren
- Genome Informatics Section, National Human Genome Research Institute, Bethesda, MD, USA
| | | | - Benedict Paten
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Ryan Layer
- Department of Computer Science and Biofrontiers Institute, University of Colorado, Boulder, CO, USA
| | | | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Nancy F Hansen
- Comparative Genomics Analysis Unit, National Human Genome Research Institute, Rockville, MD, USA
| | - Danny E Miller
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.,Department of Pediatrics, Division of Genetic Medicine, University of Washington and Seattle Children's Hospital, Seattle, WA, USA
| | - Adam M Phillippy
- Genome Informatics Section, National Human Genome Research Institute, Bethesda, MD, USA
| | - Karen H Miga
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - Rajiv C McCoy
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Megan Y Dennis
- Department of Biochemistry and Molecular Medicine, Genome Center, MIND Institute, University of California, Davis, CA, USA
| | - Justin M Zook
- National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Michael C Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.,Department of Biology, Johns Hopkins University, Baltimore, MD, USA.,Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
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