Hidewaki Nakagawa
A5081957766- Cancer Genomics and Diagnostics
- Genetic factors in colorectal cancer
- Prostate Cancer Treatment and Research
- RNA modifications and cancer
- Molecular Biology Techniques and Applications
- Epigenetics and DNA Methylation
- Cancer, Hypoxia, and Metabolism
- Genomics and Phylogenetic Studies
- Genetic Associations and Epidemiology
- Cancer, Lipids, and Metabolism
- Cholangiocarcinoma and Gallbladder Cancer Studies
- Cancer-related molecular mechanisms research
- Pancreatic and Hepatic Oncology Research
- Cancer Immunotherapy and Biomarkers
- Prostate Cancer Diagnosis and Treatment
- Genomic variations and chromosomal abnormalities
- DNA Repair Mechanisms
- Monoclonal and Polyclonal Antibodies Research
- RNA Research and Splicing
- Hepatocellular Carcinoma Treatment and Prognosis
- Genomics and Rare Diseases
- Cancer-related Molecular Pathways
- Cancer-related gene regulation
- Colorectal Cancer Treatments and Studies
- Immunotherapy and Immune Responses
RIKEN Center for Integrative Medical Sciences
2016-2025
Yokohama City University
2024
The University of Tokyo
2006-2023
Tokyo University of Science
2005-2023
Cancer Genomics Centre
2023
University of Miyazaki
2022
RIKEN
2010-2021
National Center for Geriatrics and Gerontology
2021
National Institute for Japanese Language and Linguistics
2021
Aichi Cancer Center
2018
Abstract Somatic mutations in cancer genomes are caused by multiple mutational processes, each of which generates a characteristic signature 1 . Here, as part the Pan-Cancer Analysis Whole Genomes (PCAWG) Consortium 2 International Cancer Genome (ICGC) and The Atlas (TCGA), we characterized signatures using 84,729,690 somatic from 4,645 whole-genome 19,184 exome sequences that encompass most types cancer. We identified 49 single-base-substitution, 11 doublet-base-substitution, 4...
Germ-line mutations in the mismatch-repair genes MLH1, MSH2, MSH6, and PMS2 lead to development of Lynch syndrome (hereditary nonpolyposis colorectal cancer), conferring a strong susceptibility cancer. We assessed frequency such patients with cancer examined strategies for molecular screening identify syndrome.Patients new diagnosis adenocarcinoma at major hospitals metropolitan Columbus, Ohio, were eligible study. Genotyping tumor microsatellite instability was primary method. Among whose...
Tobacco smoking increases the risk of at least 17 classes human cancer. We analyzed somatic mutations and DNA methylation in 5243 cancers types for which tobacco confers an elevated risk. Smoking is associated with increased mutation burdens multiple distinct mutational signatures, contribute to different extents cancers. One these mainly found derived from tissues directly exposed smoke, attributable misreplication damage caused by carcinogens. Others likely reflect indirect activation...
Abstract A key mutational process in cancer is structural variation, which rearrangements delete, amplify or reorder genomic segments that range size from kilobases to whole chromosomes 1–7 . Here we develop methods group, classify and describe somatic variants, using data the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium International Cancer Genome (ICGC) The Atlas (TCGA), aggregated whole-genome sequencing 2,658 cancers across 38 tumour types 8 Sixteen signatures variation...
Abstract Endometrial cancer is the most common in women with Lynch syndrome. The identification of individuals syndrome desirable because they can benefit from increased surveillance. purpose this study was to determine feasibility and desirability molecular screening for all endometrial patients. Unselected patients (N = 543) were studied. All tumors underwent microsatellite instability (MSI) testing. Patients MSI-positive testing germ line mutations MLH1, MSH2, MSH6, PMS2. Of 543 studied,...
Chromothripsis is a mutational phenomenon characterized by massive, clustered genomic rearrangements that occurs in cancer and other diseases. Recent studies selected types have suggested chromothripsis may be more common than initially inferred from low-resolution copy-number data. Here, as part of the Pan-Cancer Analysis Whole Genomes (PCAWG) Consortium International Cancer Genome (ICGC) The Atlas (TCGA), we analyze patterns across 2,658 tumors 38 using whole-genome sequencing We find...
The discovery of drivers cancer has traditionally focused on protein-coding genes
Abstract About half of all cancers have somatic integrations retrotransposons. Here, to characterize their role in oncogenesis, we analyzed the patterns and mechanisms retrotransposition 2,954 cancer genomes from 38 histological subtypes within framework Pan-Cancer Analysis Whole Genomes (PCAWG) project. We identified 19,166 somatically acquired events, which affected 35% samples spanned a range event types. Long interspersed nuclear element (LINE-1; L1 hereafter) insertions emerged as first...
Mitochondria are essential cellular organelles that play critical roles in cancer. Here, as part of the International Cancer Genome Consortium/The Atlas Pan-Cancer Analysis Whole Genomes Consortium, which aggregated whole-genome sequencing data from 2,658 cancers across 38 tumor types, we performed a multidimensional, integrated characterization mitochondrial genomes and related RNA data. Our analysis presents most definitive mutational landscape identifies several hypermutated cases....
Abstract Here, as part of the Pan-Cancer Analysis Whole Genomes (PCAWG) Consortium, for which whole-genome and—for a subset—whole-transcriptome sequencing data from 2,658 cancers across 38 tumor types was aggregated, we systematically investigated potential viral pathogens using consensus approach that integrated three independent pipelines. Viruses were detected in 382 genome and 68 transcriptome datasets. We found high prevalence known tumor-associated viruses such Epstein–Barr virus...
Highlights•Biliary tract cancers are clinically and genetically heterogeneous.•32 significantly mutated genes were identified, some negatively affecting prognosis.•A novel deletion of MUC17 at 7q22.1 was detected.•Cell-of-origin predictions suggest hepatocyte-origin hepatitis-related ICCs.•Deleterious germline mutations cancer-predisposing detected in 11% patients with BTC.Graphical abstractAbstractBackground & AimsBiliary (BTCs) pathologically heterogeneous respond poorly to treatment....
Abstract As whole-genome sequencing for cancer genome analysis becomes a clinical tool, full understanding of the variables affecting output is required. Here using tumour-normal sample pairs from two different types cancer, chronic lymphocytic leukaemia and medulloblastoma, we conduct benchmarking exercise within context International Cancer Genome Consortium. We compare methods, pipelines validation methods. show that PCR-free methods increasing depth to ∼100 × shows benefits, as long...
Recent genome-wide association studies reported strong and reproducible associations of multiple genetic variants in a large "gene-desert" region chromosome 8q24 with susceptibility to prostate cancer (PC). However, the causative or functional these loci their biological mechanisms associated PC remain unclear should be investigated. Here, focusing on its most centromeric (so-called Region 2: Chr8: 128.14-128.28 Mb) among 8q24, we performed fine mapping re-sequencing this critical identified...
Chromatin is folded into successive layers to organize linear DNA. Genes within the same topologically associating domains (TADs) demonstrate similar expression and histone-modification profiles, boundaries separating different have important roles in reinforcing stability of these features. Indeed, domain disruptions human cancers can lead misregulation gene expression. However, frequency remains unclear. Here, as part Pan-Cancer Analysis Whole Genomes (PCAWG) Consortium International...
Intrahepatic cholangiocarcinoma and combined hepatocellular show varying degrees of biliary epithelial differentiation, which can be defined as liver cancer displaying phenotype (LCB). LCB is second in the incidence for cancers with without chronic hepatitis background more aggressive than carcinoma (HCC). To gain insight into its molecular alterations, we performed whole-genome sequencing analysis on 30 LCBs. Here show, genome-wide substitution patterns LCBs developed livers overlapped...
Exosome-mediated signal transportation plays a variety of critical roles in cancer progression and metastasis. From the aspect diagnosis, circulating exosomes are ideal resources biomarkers because molecular features tumor cells transcribed on them. However, isolating pure from body fluids is time-consuming still major challenge to be addressed for comprehensive profiling exosomal proteins miRNAs. Here we constructed anti-CD9 antibody-coupled highly porous monolithic silica microtips which...
Abstract Long non-coding RNAs (lncRNAs) are a growing focus of cancer genomics studies, creating the need for resource lncRNAs with validated roles. Furthermore, it remains debated whether mutated can drive tumorigenesis, and such functions could be conserved during evolution. Here, as part ICGC/TCGA Pan-Cancer Analysis Whole Genomes (PCAWG) Consortium, we introduce Cancer LncRNA Census (CLC), compilation 122 GENCODE causal roles in phenotypes. In contrast to existing databases, CLC requires...