Human genetic variation database, a reference database of genetic variations in the Japanese population.
Human genetic variation database, a reference database of genetic variations in the Japanese population.
复制标题
DOI：
10.1038/jhg.2016.12
复制
发表时间：
2016-06
影响因子：
3.5
通讯作者：
Matsuda F
中科院分区：
文献类型：
--
作者：
Higasa K;Miyake N;Yoshimura J;Okamura K;Niihori T;Saitsu H;Doi K;Shimizu M;Nakabayashi K;Aoki Y;Tsurusaki Y;Morishita S;Kawaguchi T;Migita O;Nakayama K;Nakashima M;Mitsui J;Narahara M;Hayashi K;Funayama R;Yamaguchi D;Ishiura H;Ko WY;Hata K;Nagashima T;Yamada R;Matsubara Y;Umezawa A;Tsuji S;Matsumoto N;Matsuda F
使用下一代测序仪进行全基因组和外显子组重测序是鉴定与疾病相关的基因组变异的有力方法。然而，从许多候选人中优先考虑致病变异以解释疾病表型的系统策略还远未建立，因为遗传变异的群体特异性频谱尚未被表征。在这里，我们通过合作收集了1208个日本人的外显子组遗传变异，并将数据汇总到一个流行的目录中。我们总共发现了156，622个以前未报告的变体。大多数（88.8%）的等位基因频率低于0.5%的等位基因频率和预测是功能有害的。此外，我们还构建了日本特定的主要等位基因参考基因组，通过该基因组，我们数据中短读段的唯一映射数量平均增加了0.045%。我们的研究结果说明了构建种族特异性参考基因组以识别罕见变异的重要性。所有收集到的数据都集中到一个新开发的数据库中，作为探索病原变异的有用资源。公众可在http://www.genome.med.kyoto-u.ac.jp/SnpDB/查阅该数据库。
Whole-genome and -exome resequencing using next-generation sequencers is a powerful approach for identifying genomic variations that are associated with diseases. However, systematic strategies for prioritizing causative variants from many candidates to explain the disease phenotype are still far from being established, because the population-specific frequency spectrum of genetic variation has not been characterized. Here, we have collected exomic genetic variation from 1208 Japanese individuals through a collaborative effort, and aggregated the data into a prevailing catalog. In total, we identified 156 622 previously unreported variants. The allele frequencies for the majority (88.8%) were lower than 0.5% in allele frequency and predicted to be functionally deleterious. In addition, we have constructed a Japanese-specific major allele reference genome by which the number of unique mapping of the short reads in our data has increased 0.045% on average. Our results illustrate the importance of constructing an ethnicity-specific reference genome for identifying rare variants. All the collected data were centralized to a newly developed database to serve as useful resources for exploring pathogenic variations. Public access to the database is available at http://www.genome.med.kyoto-u.ac.jp/SnpDB/.