Research summary
Studies span tumor-microenvironment deconvolution from expression data, large-scale human-variation catalogs, and integrated tumor genomic characterization. The ESTIMATE method used gene-expression signatures to infer the fraction of stromal and immune cells in tumor samples and validated the resulting purity score against DNA copy-number-based estimates across samples from 11 tumor types profiled on Agilent and Affymetrix microarrays and by RNA sequencing in The Cancer Genome Atlas [1]. The Exome Aggregation Consortium (ExAC) catalog aggregated and analyzed high-quality protein-coding sequence data from 60,706 individuals of diverse ancestries, containing on average one variant every eight bases of the exome, providing evidence of widespread mutational recurrence and supporting the calculation of objective pathogenicity metrics and the identification of genes under strong selection against truncating variation [2]. The Genome Aggregation Database (gnomAD) extended this approach to 125,748 exomes and 15,708 genomes, identifying 443,769 high-confidence predicted loss-of-function variants after artefact filtering; an improved human mutation-rate model was used to classify protein-coding genes along a spectrum of tolerance to inactivation, with validation from model-organism and engineered human-cell data and application to improving gene-discovery power for common and rare disease [3]. As part of The Cancer Genome Atlas, a comprehensive molecular evaluation of 295 primary gastric adenocarcinomas defined four molecular subtypes: EBV-positive tumors with recurrent PIK3CA mutations, extreme DNA hypermethylation, and amplification of JAK2, CD274 (PD-L1), and PDCD1LG2 (PD-L2); microsatellite-unstable tumors with elevated mutation rates; and two further subgroups distinguished by chromosomal-instability and genomically-stable features, providing a framework that links molecular biology to clinical heterogeneity in gastric cancer [4].
Recent publications
- Integrative genomics viewerDOI
- Inferring tumour purity and stromal and immune cell admixture from expression dataDOI
- Analysis of protein-coding genetic variation in 60,706 humansDOI
- The mutational constraint spectrum quantified from variation in 141,456 humansDOI
- MicroRNA expression profiles classify human cancersDOI
- The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivityDOI
- Integrated Genomic Analysis Identifies Clinically Relevant Subtypes of Glioblastoma Characterized by Abnormalities in PDGFRA, IDH1, EGFR, and NF1DOI
- Comprehensive molecular characterization of gastric adenocarcinomaDOI
- The Immune Landscape of CancerDOI
- Mutational heterogeneity in cancer and the search for new cancer-associated genesDOI
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External profiles
- ORCID: https://orcid.org/0000-0002-0936-0753
- OpenAlex: openalex.org
Profile compiled from public sources (Researchmap, OpenAlex, The University of Tokyo faculty directory). Last refreshed 2026-05. Report incorrect information.