气候变化领域集成服务门户(CCPortal): Construction and integration of three de novo Japanese human genome assemblies toward a population-specific reference

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DOI	10.1038/s41467-020-20146-8
	Construction and integration of three de novo Japanese human genome assemblies toward a population-specific reference
	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.
发表日期	2021
卷号	12 期号:1
英文摘要	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. © 2021, The Author(s).
语种	英语
scopus关键词	genomic DNA; allele; ancestry; bioinformatics; disease incidence; genetic analysis; genome; male; allele; Article; autosome; chromosome 9; controlled study; genetic variation; haplotype; high throughput sequencing; human; human genome; Japanese (people); karyotype; mate pair sequencing; mitochondrial genome; nanopore sequencing; paired end sequencing; principal component analysis; rare disease; telomere; transposon; whole genome sequencing; X chromosome; Y chromosome; Asian continental ancestry group; cohort analysis; exome; genetics; male; middle aged; single nucleotide polymorphism; Asian Continental Ancestry Group; Cohort Studies; Exome; Genome, Human; Haplotypes; Humans; Male; Middle Aged; Polymorphism, Single Nucleotide; Principal Component Analysis
来源期刊	Nature Communications
文献类型	期刊论文
条目标识符	http://gcip.llas.ac.cn/handle/2XKMVOVA/251559
作者单位	Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan; Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan; Statistical Genetics Team, RIKEN Center for Advanced Intelligence Project, Nihonbashi 1-chome Mitsui Building 15F, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan; Department of Pediatrics, Tohoku University Graduate School of Medicine, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan; Division of Molecular and Cellular Oncology, Miyagi Cancer Center Research Institute, 47-1, Nodayama, Medeshima-Shiode, Natori, Miyagi 981-1293, Japan; Graduate School of Information Sciences, Tohoku University, 6-3-09 Aramaki Aza-Aoba, Aoba-ku, Sendai, Miyagi 980-8579, Japan; Tohoku University Graduate School of Medicine, 2-1, Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
推荐引用方式 GB/T 7714	Takayama J.,Tadaka S.,Yano K.,et al. Construction and integration of three de novo Japanese human genome assemblies toward a population-specific reference[J],2021,12(1).
APA	Takayama J..,Tadaka S..,Yano K..,Katsuoka F..,Gocho C..,...&Tamiya G..(2021).Construction and integration of three de novo Japanese human genome assemblies toward a population-specific reference.Nature Communications,12(1).
MLA	Takayama J.,et al."Construction and integration of three de novo Japanese human genome assemblies toward a population-specific reference".Nature Communications 12.1(2021).