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Article
Inherited CARD9 Deficiency Due to a Founder Effect in East Asia
Autosomal recessive CARD9 deficiency can underly deep and superficial fungal diseases. We identified two Japanese patients, suffering from superficial and invasive Candida albicans diseases, carrying biallelic va...
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Article
Open AccessCorrection to: Tumor budding and fibrotic focus—proposed grading system for tumor budding in invasive carcinoma no special type of the breast
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Article
Open AccessLong-read sequencing reveals the complex structure of extra dic(21;21) chromosome and its biological effects
Complex congenital chromosome abnormalities are rare but often cause severe symptoms. However, the structures and biological impacts of such abnormalities have seldomly been analyzed at the molecular level. Pr...
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Article
Open AccessNarcolepsy type I-associated DNA methylation and gene expression changes in the human leukocyte antigen region
Narcolepsy type 1 (NT1) is caused by a loss of hypothalamic orexin-producing cells, and autoreactive CD4+ and CD8+ T cells have been suggested to play a role in the autoimmune mechanism. Although NT1 showed a str...
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Article
Open AccessLocalized assembly for long reads enables genome-wide analysis of repetitive regions at single-base resolution in human genomes
Long-read sequencing technologies have the potential to overcome the limitations of short reads and provide a comprehensive picture of the human genome. However, the characterization of repetitive sequences by...
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Article
Comprehensive analysis of microsatellite polymorphisms in human populations
Microsatellites (MS) are tandem repeats of short units, and have been used for population genetics, individual identification, and medical genetics. However, studies of MS on a whole-genome level are limited, ...
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Article
Open AccessTumor budding and fibrotic focus—proposed grading system for tumor budding in invasive carcinoma no special type of the breast
Tumor budding grade is a very useful histological prognostic indicator for colorectal cancer patients. Recently, it has been also reported as a significant prognostic indicator in invasive breast carcinoma pat...
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Article
Open AccessImmunogenomic pan-cancer landscape reveals immune escape mechanisms and immunoediting histories
Immune reactions in the tumor microenvironment are an important hallmark of cancer, and emerging immune therapies have been proven effective against several types of cancers. To investigate cancer genome-immun...
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Article
Characterization of intermediate-sized insertions using whole-genome sequencing data and analysis of their functional impact on gene expression
Intermediate-sized insertions are one of the structural variants contributing to genome diversity. However, due to technical difficulties in identifying them, their importance in disease pathogenicity and gene...
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Article
Open AccessClinical benefit of treatment after trastuzumab emtansine for HER2-positive metastatic breast cancer: a real-world multi-centre cohort study in Japan (WJOG12519B)
Trastuzumab emtansine (T-DM1) treatment for human epidermal growth factor receptor-2 (HER2)-positive metastatic breast cancer after taxane with trastuzumab and pertuzumab is standard therapy. However, treatmen...
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Article
Open AccessWhole-genome sequencing with long reads reveals complex structure and origin of structural variation in human genetic variations and somatic mutations in cancer
Identification of germline variation and somatic mutations is a major issue in human genetics. However, due to the limitations of DNA sequencing technologies and computational algorithms, our understanding of ...
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Article
Open AccessAberrant (pro)renin receptor expression induces genomic instability in pancreatic ductal adenocarcinoma through upregulation of SMARCA5/SNF2H
(Pro)renin receptor [(P)RR] has a role in various diseases, such as cardiovascular and renal disorders and cancer. Aberrant (P)RR expression is prevalent in pancreatic ductal adenocarcinoma (PDAC) which is the...
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Article
Open AccesseVIDENCE: a practical variant filtering for low-frequency variants detection in cell-free DNA
Plasma cell-free DNA (cfDNA) testing plays an increasingly important role in precision medicine for cancer. However, circulating cell-free tumor DNA (ctDNA) is highly diluted by cfDNA from non-cancer cells, co...
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Article
Open AccessIdentification of intermediate-sized deletions and inference of their impact on gene expression in a human population
Next-generation sequencing has allowed for the identification of different genetic variations, which are known to contribute to diseases. Of these, insertions and deletions are the second most abundant type of...
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Article
Open AccessClinical utility of androgen receptor gene aberrations in circulating cell-free DNA as a biomarker for treatment of castration-resistant prostate cancer
The therapeutic landscape of castration-resistant prostate cancer (CRPC) has rapidly expanded. There is a need to develop noninvasive biomarkers to guide treatment. We established a highly sensitive method for...
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Article
Open AccessPublisher Correction: IMSindel: An accurate intermediate-size indel detection tool incorporating de novo assembly and gapped global-local alignment with split read analysis
A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has not been fixed in the paper.
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Article
Open AccessIMSindel: An accurate intermediate-size indel detection tool incorporating de novo assembly and gapped global-local alignment with split read analysis
Insertions and deletions (indels) have been implicated in dozens of human diseases through the radical alteration of gene function by short frameshift indels as well as long indels. However, the accurate detec...
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Chapter and Conference Paper
A Rare Piece Diffusion Method Using Rateless Coding on BitTorrent-Like Distribution System
In P2P content distribution systems, frequent join and leave operations of users make some content pieces extremely hard to be available. In the worst case, a certain piece is completely lost. Exchanging piece...
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Article
Erratum: Whole-genome mutational landscape and characterization of noncoding and structural mutations in liver cancer
Nat. Genet.; 10.1038/ng.3547; corrected online 18 April 2016 In the version of this article initially published online, the mutation category plots in the top panel of Figure 1 were not correctly aligned with ...
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Article
Open AccessSystematic analysis of mutation distribution in three dimensional protein structures identifies cancer driver genes
Protein tertiary structure determines molecular function, interaction and stability of the protein, therefore distribution of mutation in the tertiary structure can facilitate the identification of new driver ...
