A5015458809- Cancer Genomics and Diagnostics
- Cancer Immunotherapy and Biomarkers
- Bladder and Urothelial Cancer Treatments
- Epigenetics and DNA Methylation
- Multiple and Secondary Primary Cancers
- RNA modifications and cancer
- Cancer-related molecular mechanisms research
- Urinary and Genital Oncology Studies
- Genomics and Chromatin Dynamics
- Ferroptosis and cancer prognosis
- Genetic factors in colorectal cancer
- Ovarian cancer diagnosis and treatment
- DNA Repair Mechanisms
- Lung Cancer Treatments and Mutations
- Pancreatic and Hepatic Oncology Research
- Cancer, Hypoxia, and Metabolism
- Cancer-related Molecular Pathways
- Bioinformatics and Genomic Networks
- Immune Cell Function and Interaction
- MicroRNA in disease regulation
- Single-cell and spatial transcriptomics
- Cancer-related gene regulation
- RNA Research and Splicing
- Genomics and Phylogenetic Studies
- Renal cell carcinoma treatment
The University of Texas MD Anderson Cancer Center
2012-2025
Van Andel Institute
2016-2025
Zhongnan Hospital of Wuhan University
2016-2025
Wuhan University
2013-2025
China Pharmaceutical University
2021-2025
McGill University
2025
Wenzhou Medical University
2025
Second Military Medical University
2023-2025
Yuhuangding Hospital
2025
Qingdao University
2025
We analysed primary breast cancers by genomic DNA copy number arrays, methylation, exome sequencing, messenger RNA microRNA sequencing and reverse-phase protein arrays. Our ability to integrate information across platforms provided key insights into previously defined gene expression subtypes demonstrated the existence of four main cancer classes when combining data from five platforms, each which shows significant molecular heterogeneity. Somatic mutations in only three genes (TP53, PIK3CA...
Infiltrating stromal and immune cells form the major fraction of normal in tumour tissue not only perturb signal molecular studies but also have an important role cancer biology. Here we describe 'Estimation STromal Immune MAlignant Tumours using Expression data' (ESTIMATE)—a method that uses gene expression signatures to infer samples. ESTIMATE scores correlate with DNA copy number-based purity across samples from 11 different types, profiled on Agilent, Affymetrix platforms or based RNA...
Gastric cancer is a leading cause of deaths, but analysis its molecular and clinical characteristics has been complicated by histological aetiological heterogeneity. Here we describe comprehensive evaluation 295 primary gastric adenocarcinomas as part The Cancer Genome Atlas (TCGA) project. We propose classification dividing into four subtypes: tumours positive for Epstein–Barr virus, which display recurrent PIK3CA mutations, extreme DNA hypermethylation, amplification JAK2, CD274 (also...
The American Joint Committee on Cancer (AJCC) staging manual has become the benchmark for classifying patients with cancer, defining prognosis, and determining best treatment approaches. Many view primary role of tumor, lymph node, metastasis (TNM) system as that a standardized classification evaluating cancer at population level in terms extent disease, both initial presentation after surgical treatment, overall impact improvements treatment. rapid evolution knowledge biology discovery...
We performed an extensive immunogenomic analysis of more than 10,000 tumors comprising 33 diverse cancer types by utilizing data compiled TCGA. Across types, we identified six immune subtypes—wound healing, IFN-γ dominant, inflammatory, lymphocyte depleted, immunologically quiet, and TGF-β dominant—characterized differences in macrophage or signatures, Th1:Th2 cell ratio, extent intratumoral heterogeneity, aneuploidy, neoantigen load, overall proliferation, expression immunomodulatory genes,...
Urothelial carcinoma of the bladder is a common malignancy that causes approximately 150,000 deaths per year worldwide. So far, no molecularly targeted agents have been approved for treatment disease. As part The Cancer Genome Atlas project, we report here an integrated analysis 131 urothelial carcinomas to provide comprehensive landscape molecular alterations. There were statistically significant recurrent mutations in 32 genes, including multiple genes involved cell-cycle regulation,...
Highlights•Alteration map of 10 signaling pathways across 9,125 samples from 33 cancer types•Reusable, curated pathway templates that include a catalogue driver genes•57% tumors have at least one potentially actionable alteration in these pathways•Co-occurrence alterations suggests combination therapy opportunitiesSummaryGenetic control cell-cycle progression, apoptosis, and cell growth are common hallmarks cancer, but the extent, mechanisms, co-occurrence differ between individual tumor...
Understanding the interactions between tumor and host immune system is critical to finding prognostic biomarkers, reducing drug resistance, developing new therapies. Novel computational methods are needed estimate tumor-infiltrating cells understand tumor–immune in cancers. We analyze over 10,000 RNA-seq samples across 23 cancer types from The Cancer Genome Atlas (TCGA). Our computationally inferred infiltrates associate much more strongly with patient clinical features, viral infection...
Determining how somatic copy number alterations (SCNAs) promote cancer is an important goal. We characterized SCNA patterns in 4,934 cancers from The Cancer Genome Atlas Pan-Cancer data set. Whole-genome doubling, observed 37% of cancers, was associated with higher rates every other type SCNA, TP53 mutations, CCNE1 amplifications and the PPP2R complex. SCNAs that were internal to chromosomes tended be shorter than telomere-bounded SCNAs, suggesting different mechanisms underlying their...
Papillary renal-cell carcinoma, which accounts for 15 to 20% of carcinomas, is a heterogeneous disease that consists various types renal cancer, including tumors with indolent, multifocal presentation and solitary an aggressive, highly lethal phenotype. Little known about the genetic basis sporadic papillary no effective forms therapy advanced exist.We performed comprehensive molecular characterization 161 primary using whole-exome sequencing, copy-number analysis, messenger RNA microRNA...
Cancer chromatin accessibility landscape The Genome Atlas (TCGA) provides a high-quality resource of molecular data on large variety human cancers. Corces et al. used recently modified assay to profile determine the accessible in 410 TCGA samples from 23 cancer types (see Perspective by Taipale). When were integrated with other omics available for same tumor samples, inherited risk loci predisposition revealed, transcription factors and enhancers driving subtypes patient survival differences...
<h2>Summary</h2> DNA damage repair (DDR) pathways modulate cancer risk, progression, and therapeutic response. We systematically analyzed somatic alterations to provide a comprehensive view of DDR deficiency across 33 types. Mutations with accompanying loss heterozygosity were observed in over 1/3 genes, including <i>TP53</i> <i>BRCA1/2</i>. Other prevalent included epigenetic silencing the direct genes <i>EXO5</i>, <i>MGMT</i>, <i>ALKBH3</i> ∼20% samples. Homologous recombination (HRD) was...
Polycomb group proteins (PCGs) are involved in repression of genes that required for stem cell differentiation. Recently, it was shown promoters PCG target (PCGTs) 12-fold more likely to be methylated cancer than non-PCGTs. Age is the most important demographic risk factor cancer, and we hypothesized its carcinogenic potential may referred by irreversibly stabilizing features. To test this, analyzed methylation status over 27,000 CpGs mapping ∼14,000 whole blood samples from 261...
Illumina Infinium DNA Methylation BeadChips represent the most widely used genome-scale methylation assays. Existing strategies for masking probes overlapping repeats or single nucleotide polymorphisms (SNPs) are based largely on ad hoc assumptions and subjective criteria. In addition, recently introduced MethylationEPIC (EPIC) array expands utility of this platform, but has not yet been well characterized. We present in paper an extensive characterization EPIC HM450 microarrays, including...