Construction and integration of three de novo Japanese human genome assemblies toward a population-specific reference

Jun Takayama, Shu Tadaka, Kenji Yano, Fumiki Katsuoka, Chinatsu Gocho, Takamitsu Funayama, Satoshi Makino, Yasunobu Okamura, Atsuo Kikuchi, Sachiyo Sugimoto, Junko Kawashima, Akihito Otsuki, Mika Sakurai-Yageta, Jun Yasuda, Shigeo Kure, Kengo Kinoshita (), Masayuki Yamamoto () and Gen Tamiya ()
Additional contact information
Jun Takayama: Tohoku University
Shu Tadaka: Tohoku University
Kenji Yano: Tohoku University
Fumiki Katsuoka: Tohoku University
Chinatsu Gocho: Tohoku University
Takamitsu Funayama: Tohoku University
Satoshi Makino: Tohoku University
Yasunobu Okamura: Tohoku University
Atsuo Kikuchi: Tohoku University Graduate School of Medicine
Sachiyo Sugimoto: Tohoku University
Junko Kawashima: Tohoku University
Akihito Otsuki: Tohoku University
Mika Sakurai-Yageta: Tohoku University
Jun Yasuda: Tohoku University
Shigeo Kure: Tohoku University
Kengo Kinoshita: Tohoku University
Masayuki Yamamoto: Tohoku University
Gen Tamiya: Tohoku University

Nature Communications, 2021, vol. 12, issue 1, 1-14

Abstract: 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.

Date: 2021
References: Add references at CitEc
Citations:

Downloads: (external link)
https://www.nature.com/articles/s41467-020-20146-8 Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-020-20146-8

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/s41467-020-20146-8

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().