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. 2019 Jun 18:6:28.
doi: 10.1038/s41439-019-0059-5. eCollection 2019.

3.5KJPNv2: an allele frequency panel of 3552 Japanese individuals including the X chromosome

Shu Tadaka #  1   2 , Fumiki Katsuoka #  1   2 , Masao Ueki  1   3 , Kaname Kojima  1   2   4 , Satoshi Makino  1   2 , Sakae Saito  1   2 , Akihito Otsuki  1   2 , Chinatsu Gocho  1 , Mika Sakurai-Yageta  1   2 , Inaho Danjoh  1   2 , Ikuko N Motoike  1   2   4 , Yumi Yamaguchi-Kabata  1   2 , Matsuyuki Shirota  1   2   4 , Seizo Koshiba  1   2 , Masao Nagasaki  1   2   4 , Naoko Minegishi  1   2   5 , Atsushi Hozawa  1   2 , Shinichi Kuriyama  1   2   6 , Atsushi Shimizu  7 , Jun Yasuda  1   8 , Nobuo Fuse  1   2 ; Tohoku Medical Megabank Project Study Group; Gen Tamiya  1   3 , Masayuki Yamamoto  1   2   5 , Kengo Kinoshita  1   4   5   9
Affiliations

3.5KJPNv2: an allele frequency panel of 3552 Japanese individuals including the X chromosome

Shu Tadaka et al. Hum Genome Var. .

Abstract

The first step towards realizing personalized healthcare is to catalog the genetic variations in a population. Since the dissemination of individual-level genomic information is strictly controlled, it will be useful to construct population-level allele frequency panels with easy-to-use interfaces. In the Tohoku Medical Megabank Project, we sequenced nearly 4000 individuals from a Japanese population and constructed an allele frequency panel of 3552 individuals after removing related samples. The panel is called the 3.5KJPNv2. It was constructed by using a standard pipeline including the 1KGP and gnomAD algorithms to reduce technical biases and to allow comparisons to other populations. Our database is the first large-scale panel providing the frequencies of variants present on the X chromosome and on the mitochondria in the Japanese population. All the data are available on our original database at https://jmorp.megabank.tohoku.ac.jp.

Keywords: Rare variants; Structural variation.

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Conflict of interest statement

Conflict of interestThe authors declare that they have no conflict of interest.

Figures

Fig. 1
Fig. 1. Heterozygosity of the X chromosome observed by SNP array analysis.
The three regions showing high heterozygosity in (a) are designated par1, XTR, and par2. To perform the variant calls, we used the following regions of GRCh37 corresponding to these three regions: 60,001-2,699,520 (PAR1), 88,456,802-92,375,509 (XTR), and 154,931,044-155,260,560 (PAR2)
Fig. 2
Fig. 2. Comparisons of 3.5KJPNv2 with other genome data.
a Comparison of allele frequencies of variants on chr6 between gnomAD EAS and 3.5KJPNv2. Red dots represent alternative allele frequencies in each population (x-axis: 3.5KJPNv2, y-axis: gnomAD EAS). The green and blue dots show SNVs lacking either in 3.5KJPNv2 or genomAD EAS, respectively. Some outliers denoted by broken circles are described in the text. b Comparison of allele frequencies of variants on chr6 between the RIKEN 2 K panel and 3.5KJPNv2. Colors are used in the same way as in (a). c Comparison of allele frequencies of variants on the X chromosome between gnomAD EAS and 3.5KJPNv2. Colors are used in the same way as in (a). d Distribution of Ts/Tv values for each chromosome. Violin plots were generated from the 3.5KJPNv2 data. The red and green lines are the average values of all 1KGP samples and 1KGP-JPT samples, respectively. In the calculation of Ts/Tv of variants on the X chromosome, only female samples are used. (1KGP ALL: 1271 samples, 1KGP JPT: 48 samples, 3.5KJPNv2: 1999 samples)
Fig. 3
Fig. 3. Population structure of 3.5KJPNv2.
a PCA plot of 3.5KJPNv2 with the East Asian populations CHB, CHS, KHV, and CDX from 1KGP. We observed 12 outliers in the ToMMo samples. b PCA plot of 3.5KJPNv2 only. Black dots correspond to the outliers found in a
See this image and copyright information in PMC

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