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Title: Direct estimation of de novo mutation rates in a chimpanzee parent-offspring trio by ultra-deep whole genome sequencing
Other Titles: チンパンジー親子トリオを用いた超高精度全ゲノム配列決定による新規変異率の直接推定
Authors: Tatsumoto, Shoji
Go, Yasuhiro
Fukuta, Kentaro
Noguchi, Hideki
Hayakawa, Takashi  kyouindb  KAKEN_id
Tomonaga, Masaki  kyouindb  KAKEN_id
Hirai, Hirohisa
Matsuzawa, Tetsuro  kyouindb  KAKEN_id
Agata, Kiyokazu
Fujiyama, Asao
Author's alias: 辰本, 将司
郷, 康広
福多, 賢太郎
野口, 英樹
早川, 卓志
友永, 雅己
平井, 啓久
松沢, 哲郎
阿形, 清和
藤山, 秋佐夫
Keywords: Evolutionary genetics
Genome evolution
Next-generation sequencing
Rare variants
Issue Date: 1-Nov-2017
Publisher: Springer Nature
Journal title: Scientific Reports
Volume: 7
Thesis number: 13561
Abstract: Mutations generate genetic variation and are a major driving force of evolution. Therefore, examining mutation rates and modes are essential for understanding the genetic basis of the physiology and evolution of organisms. Here, we aim to identify germline de novo mutations through the whole-genome surveyance of Mendelian inheritance error sites (MIEs), those not inherited through the Mendelian inheritance manner from either of the parents, using ultra-deep whole genome sequences (>150-fold) from a chimpanzee parent-offspring trio. We identified such 889 MIEs and classified them into four categories based on the pattern of inheritance and the sequence read depth: [i] de novo single nucleotide variants (SNVs), [ii] copy number neutral inherited variants, [iii] hemizygous deletion inherited variants, and [iv] de novo copy number variants (CNVs). From de novo SNV candidates, we estimated a germline de novo SNV mutation rate as 1.48 × 10−8 per site per generation or 0.62 × 10−9 per site per year. In summary, this study demonstrates the significance of ultra-deep whole genome sequencing not only for the direct estimation of mutation rates but also for discerning various mutation modes including de novo allelic conversion and de novo CNVs by identifying MIEs through the transmission of genomes from parents to offspring.
Description: チンパンジー親子トリオ(父親-母親-息子)の 全ゲノム配列を高精度で解明. 京都大学プレスリリース. 2017-11-02.
Rights: © The Author(s) 2017. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit
DOI(Published Version): 10.1038/s41598-017-13919-7
PubMed ID: 29093469
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