A research group at Tohoku Medical Megabank Organization (ToMMo) has successfully constructed a Japanese population reference panel (1KJPN).
ToMMo identified through this high-coverage sequencing (32.4 × on average), 21.2 million, including 12 million novel, single-nucleotide variants (SNVs) at an estimated false discovery rate of <1.0%. This detailed analysis detected signatures for purifying selection on regulatory elements as well as coding regions. ToMMo also catalogued structural variants, including 3.4 million insertions and deletions, and 25,923 genic copy-number variants. The 1KJPN was effective for imputing genotypes of the Japanese population genome wide. These data demonstrate the value of high-coverage sequencing for constructing population-specific variant panels, which covers 99.0% SNVs of minor allele frequency ≥0.1%, and its value for identifying causal rare variants of complex human disease phenotypes in genetic association studies.

Figure: Properties of genomic variation discovered in 1KJPN. Histograms and scatterplot of diploid copy numbers of AMY1 genes (blue) and region X (red) in 1KJPN. A diagram depicting the positions of AMY1A, Region X, AMY1B and AMY1C on chromosome 1 of GRCh37 is shown in the right top.

Article

Masao Nagasaki, Jun Yasuda, Fumiki Katsuoka, Naoki Nariai, Kaname Kojima, Yosuke Kawai, Yumi Yamaguchi-Kabata, Junji Yokozawa, Inaho Danjoh, Sakae Saito, Yukuto Sato, Takahiro Mimori, Kaoru Tsuda, Rumiko Saito, Xiaoqing Pan, Satoshi Nishikawa, Shin Ito, Yoko Kuroki, Osamu Tanabe, Nobuo Fuse et al.
"Rare variant discovery by deep whole-genome sequencing of 1,070 Japanese individuals"
Nature Communications Volume: 6, Article number: 8018, doi:10.1038/ncomms9018

The member list of ToMMo is available on our website.
We thank GenomeWeb in the United States for reporting our achievement.

Related Links

-Nagasaki Laboratory: Division of Biomedical Information Analysis
-Integrative Genomics
-Integrative Japanese Genome Variation Database
-Japonica Array: Improved genotype imputation by designing a population-specific SNP array with 1,070 Japanese individuals [News: 2015/06/25]