Next-generation sequencing analysis with a population-specific human reference genome

被引：0

作者：

Suzuki, Tomohisa ^{[1
,2
]}

Ninomiya, Kota ^{[1
]}

Funayama, Takamitsu ^{[3
,4
]}

Okamura, Yasunobu ^{[3
,5
]}

Tadaka, Shu ^{[3
]}

Tohoku Med Megabank Project Study Grp, Kengo

Yamamoto, Masayuki ^{[3
,7
]}

Kure, Shigeo ^{[2
,8
]}

Kikuchi, Atsuo ^{[2
]}

Tamiya, Gen ^{[1
,3
,4
]}

Takayama, Jun ^{[1
,3
,4
]}

机构：

[1] Tohoku Univ, Dept AI & Innovat Med, Sch Med, Sendai, Miyagi 9808573, Japan

[2] Tohoku Univ, Sch Med, Dept Pediat, Sendai, Miyagi 9808574, Japan

[3] Tohoku Univ, Dept Integrat Genom, Tohoku Med Megabank Org, Sendai, Miyagi 9808573, Japan

[4] RIKEN Ctr Adv Intelligence Project, Chuo Ku, Tokyo 1030027, Japan

[5] Tohoku Univ, Adv Res Ctr Innovat Next Generat Med, Sendai, Miyagi 9808573, Japan

[6] Tohoku Univ, Inst Dev Aging & Canc, Dept Silico Anal, Sendai, Miyagi 9808575, Japan

[7] Tohoku Univ, Dept Biochem & Mol Biol, Tohoku Med Megabank Org, Sendai, Miyagi 9808573, Japan

[8] Miyagi Childrens Hosp, Sendai, Miyagi 9893126, Japan

来源：

GENES & GENETIC SYSTEMS | 2024年 / 99卷

关键词：

population-specific reference genome; Japanese reference genome; genome resource; next-generation sequencing data analysis; variant calling; DISCOVERY;

D O I：

10.1266/ggs.24-00112

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Next-generation sequencing (NGS) has become widely available and is routinely used in basic research and clinical practice. The reference genome sequence is an essential resource for NGS analysis, and several population-specific reference genomes have recently been constructed to provide a choice to deal with the vast genetic diversity of human samples. However, resources supporting population- specific references are insufficient, and it is burdensome to perform analysis using these reference genomes. Here, we constructed a set of resources to support NGS analysis using the Japanese reference genome, JG. We created resources for variant calling, variant effect prediction, gene and repeat element annotations, read mappability and RNA-seq analysis. We also provide a resource for reference coordinate conversion for further annotation enrichment. We then provide a variant calling protocol with JG. Our resources provide a guide to prepare sufficient resources for the use of population-specific reference genomes and can facilitate the migration of reference genomes.

引用

页数：8

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