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

IF 1 4区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Genes & genetic systems Pub Date : 2024-10-28 DOI:10.1266/ggs.24-00112
Tomohisa Suzuki, Kota Ninomiya, Takamitsu Funayama, Yasunobu Okamura, Shu Tadaka, Kengo Kinoshita, Masayuki Yamamoto, Shigeo Kure, Atsuo Kikuchi, Gen Tamiya, Jun Takayama
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Abstract

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.

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利用特定人群的人类参考基因组进行下一代测序分析。
下一代测序(NGS)已广泛普及,并在基础研究和临床实践中得到常规应用。参考基因组序列是 NGS 分析的重要资源,最近已构建了几个特定人群的参考基因组,为处理人类样本的巨大遗传多样性提供了选择。然而,支持人群特异性参考的资源不足,使用这些参考基因组进行分析非常繁琐。在此,我们构建了一套资源,支持使用日本参考基因组 JG 进行 NGS 分析。我们创建了用于变异调用、变异效应预测、基因和重复元件注释、读取映射和 RNA-seq 分析的资源。我们还提供了参考坐标转换资源,以进一步丰富注释。然后,我们提供了使用 JG 的变异调用协议。我们的资源为使用特定人群参考基因组准备充足的资源提供了指南,并能促进参考基因组的迁移。
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来源期刊
Genes & genetic systems
Genes & genetic systems 生物-生化与分子生物学
CiteScore
1.50
自引率
0.00%
发文量
22
审稿时长
>12 weeks
期刊介绍: Genes & Genetic Systems , formerly the Japanese Journal of Genetics , is published bimonthly by the Genetics Society of Japan.
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