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

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.

journal_name

Nat Commun

journal_title

Nature communications

authors

Takayama J,Tadaka S,Yano K,Katsuoka F,Gocho C,Funayama T,Makino S,Okamura Y,Kikuchi A,Sugimoto S,Kawashima J,Otsuki A,Sakurai-Yageta M,Yasuda J,Kure S,Kinoshita K,Yamamoto M,Tamiya G

doi

10.1038/s41467-020-20146-8

subject

Has Abstract

pub_date

2021-01-11 00:00:00

pages

226

issue

1

issn

2041-1723

pii

10.1038/s41467-020-20146-8

journal_volume

12

pub_type

杂志文章

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