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

the Tohoku Medical Megabank Project Study Group

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71 Citations (Scopus)


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.

Original languageEnglish
Article number28
JournalHuman Genome Variation
Issue number1
Publication statusPublished - 2019 Dec 1

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Genetics


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