Dataset Information

Construction of JRG (Japanese reference genome) with single-molecule real-time sequencing.

ABSTRACT: In recent genome analyses, population-specific reference panels have indicated important. However, reference panels based on short-read sequencing data do not sufficiently cover long insertions. Therefore, the nature of long insertions has not been well documented. Here, we assembled a Japanese genome using single-molecule real-time sequencing data and characterized insertions found in the assembled genome. We identified 3691 insertions ranging from 100?bps to ~10,000?bps in the assembled genome relative to the international reference sequence (GRCh38). To validate and characterize these insertions, we mapped short-reads from 1070 Japanese individuals and 728 individuals from eight other populations to insertions integrated into GRCh38. With this result, we constructed JRGv1 (Japanese Reference Genome version 1) by integrating the 903 verified insertions, totaling 1,086,173 bases, shared by at least two Japanese individuals into GRCh38. We also constructed decoyJRGv1 by concatenating 3559 verified insertions, totaling 2,536,870 bases, shared by at least two Japanese individuals or by six other assemblies. This assembly improved the alignment ratio by 0.4% on average. These results demonstrate the importance of refining the reference assembly and creating a population-specific reference genome. JRGv1 and decoyJRGv1 are available at the JRG website.

SUBMITTER: Nagasaki M

PROVIDER: S-EPMC6555796 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Construction of JRG (Japanese reference genome) with single-molecule real-time sequencing.

Nagasaki Masao M Kuroki Yoko Y Shibata Tomoko F TF Katsuoka Fumiki F Mimori Takahiro T Kawai Yosuke Y Minegishi Naoko N Hozawa Atsushi A Kuriyama Shinichi S Suzuki Yoichi Y Kawame Hiroshi H Nagami Fuji F Takai-Igarashi Takako T Ogishima Soichi S Kojima Kaname K Misawa Kazuharu K Tanabe Osamu O Fuse Nobuo N Tanaka Hiroshi H Yaegashi Nobuo N Kinoshita Kengo K Kure Shiego S Yasuda Jun J Yamamoto Masayuki M

Human genome variation 20190607

In recent genome analyses, population-specific reference panels have indicated important. However, reference panels based on short-read sequencing data do not sufficiently cover long insertions. Therefore, the nature of long insertions has not been well documented. Here, we assembled a Japanese genome using single-molecule real-time sequencing data and characterized insertions found in the assembled genome. We identified 3691 insertions ranging from 100 bps to ~10,000 bps in the assembled genome ...[more]

PMID: 31231536

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Dataset Information

Construction of JRG (Japanese reference genome) with single-molecule real-time sequencing.

Publications

Construction of JRG (Japanese reference genome) with single-molecule real-time sequencing.

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