•Journal•ISSN: 2054-345X
Human genome variation
Nature Portfolio
About: Human genome variation is an academic journal published by Nature Portfolio. The journal publishes majorly in the area(s): Medicine & Biology. It has an ISSN identifier of 2054-345X. It is also open access. Over the lifetime, 439 publications have been published receiving 3222 citations.
Topics: Medicine, Biology, Gene, Missense mutation, Exome sequencing
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TL;DR: A new database provides information on the frequency of genetic variations within 3552 Japanese individuals, and facilitates comparisons with other populations, and is the first large-scale panel providing the frequencies of variants present on the X chromosome and on the mitochondria in the Japanese population.
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.
109 citations
TL;DR: The integrative Japanese Genome Variation Database (iJGVD) provides genomic variation data detected by whole-genome sequencing of Japanese individuals that contains variants detected by WGS of 1,070 individuals who participated in a genome cohort study of the Tohoku Medical Megabank Project.
Abstract: The integrative Japanese Genome Variation Database (iJGVD; http://ijgvd.megabank.tohoku.ac.jp/) provides genomic variation data detected by whole-genome sequencing (WGS) of Japanese individuals. Specifically, the database contains variants detected by WGS of 1,070 individuals who participated in a genome cohort study of the Tohoku Medical Megabank Project. In the first release, iJGVD includes >4,300,000 autosomal single nucleotide variants (SNVs) whose minor allele frequencies are >5.0%.
104 citations
TL;DR: In this paper, a population-specific genome for the indigenous Arab population of Qatar (QTRG) was constructed by incorporating allele frequency data from sequencing of 1,161 Qataris, representing 0.4% of the population.
Abstract: Reaching the full potential of precision medicine depends on the quality of personalized genome interpretation. In order to facilitate precision medicine in regions of the Middle East and North Africa (MENA), a population-specific genome for the indigenous Arab population of Qatar (QTRG) was constructed by incorporating allele frequency data from sequencing of 1,161 Qataris, representing 0.4% of the population. A total of 20.9 million single nucleotide polymorphisms (SNPs) and 3.1 million indels were observed in Qatar, including an average of 1.79% novel variants per individual genome. Replacement of the GRCh37 standard reference with QTRG in a best practices genome analysis workflow resulted in an average of 7* deeper coverage depth (an improvement of 23%) and 756,671 fewer variants on average, a reduction of 16% that is attributed to common Qatari alleles being present in QTRG. The benefit for using QTRG varies across ancestries, a factor that should be taken into consideration when selecting an appropriate reference for analysis.
63 citations
TL;DR: A germline nonsense mutation within the extracellular domain of the RING finger ubiquitin ligase RNF43 is reported, segregating with a severe form of serrated polyposis within a kindred, providing evidence that inherited R NF43 mutations define a familial cancer syndrome.
Abstract: We report a germline nonsense mutation within the extracellular domain of the RING finger ubiquitin ligase RNF43, segregating with a severe form of serrated polyposis within a kindred. The finding provides evidence that inherited RNF43 mutations define a familial cancer syndrome.
52 citations
TL;DR: An integrative multi-omics database that provides whole-DNA methylation, whole-genome, and whole-transcriptome data for CD4+ T-lymphocytes, monocytes, and neutrophils collected from approximately 100 subjects is launched.
Abstract: We launched an integrative multi-omics database, iMETHYL (
http://imethyl.iwate-megabank.org
). iMETHYL provides whole-DNA methylation (~24 million autosomal CpG sites), whole-genome (~9 million single-nucleotide variants), and whole-transcriptome (>14 000 genes) data for CD4+ T-lymphocytes, monocytes, and neutrophils collected from approximately 100 subjects. These data were obtained from whole-genome bisulfite sequencing, whole-genome sequencing, and whole-transcriptome sequencing, making iMETHYL a comprehensive database.
51 citations