Angelica Ochoa
A5075124414- Cancer Genomics and Diagnostics
- Medical Imaging and Pathology Studies
- Occupational and environmental lung diseases
- RNA modifications and cancer
- Bioinformatics and Genomic Networks
- Ferroptosis and cancer prognosis
- Genetics, Bioinformatics, and Biomedical Research
- Epigenetics and DNA Methylation
- Genomics and Phylogenetic Studies
- Lung Cancer Treatments and Mutations
- Genetic factors in colorectal cancer
- Cancer-related molecular mechanisms research
- Genomics and Chromatin Dynamics
- RNA Research and Splicing
- Genomics and Rare Diseases
- Cancer-related Molecular Pathways
- Gene expression and cancer classification
- Radiomics and Machine Learning in Medical Imaging
- Evolution and Genetic Dynamics
- Pancreatic and Hepatic Oncology Research
- DNA Repair Mechanisms
- Cancer Research and Treatments
- Chromosomal and Genetic Variations
- Biomedical and Engineering Education
- Cancer Immunotherapy and Biomarkers
Memorial Sloan Kettering Cancer Center
2017-2025
Kettering University
2017-2025
Molecular Oncology (United States)
2017-2022
Georgetown University
2015
Boston University
2014
Universidad Pontificia Bolivariana
1987
For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical contain key features representing the democratized nature collection process. To ensure proper use this large dataset associated genomic features, we developed standardized named Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major outcome endpoints. In...
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...
Aneuploidy, whole chromosome or arm imbalance, is a near-universal characteristic of human cancers. In 10,522 cancer genomes from The Cancer Genome Atlas, aneuploidy was correlated with TP53 mutation, somatic mutation rate, and expression proliferation genes. Aneuploidy anti-correlated immune signaling genes, due to decreased leukocyte infiltrates in high-aneuploidy samples. Chromosome arm-level alterations show cancer-specific patterns, including loss 3p squamous We applied genome...
Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings tumor-infiltrating lymphocytes (TILs) based on H&E from 13 tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches images. Affinity propagation revealed local spatial structure in patterns correlation with overall survival. map...
Our comprehensive analysis of alternative splicing across 32 The Cancer Genome Atlas cancer types from 8,705 patients detects events and tumor variants by reanalyzing RNA whole-exome sequencing data. Tumors have up to 30% more than normal samples. Association somatic with confirmed known trans associations in SF3B1 U2AF1 identified additional trans-acting (e.g., TADA1, PPP2R1A). Many tumors thousands not detectable samples; on average, we ≈930 exon-exon junctions ("neojunctions") typically...
The Cancer Genome Atlas (TCGA) cancer genomics dataset includes over 10,000 tumor-normal exome pairs across 33 different types, in total >400 TB of raw data files requiring analysis. Here we describe the Multi-Center Mutation Calling Multiple Cancers project, our effort to generate a comprehensive encyclopedia somatic mutation calls for TCGA enable robust cross-tumor-type analyses. Our approach accounts variance and batch effects introduced by rapid advancement DNA extraction,...
Gene fusions represent an important class of somatic alterations in cancer. We systematically investigated 9,624 tumors across 33 cancer types using multiple fusion calling tools. identified a total 25,664 fusions, with 63% validation rate. Integration gene expression, copy number, and annotation data revealed that involving oncogenes tend to exhibit increased whereas tumor suppressors have the opposite effect. For kinases, we found 1,275 intact kinase domain, proportion which varied...
Hippo signaling has been recognized as a key tumor suppressor pathway. Here, we perform comprehensive molecular characterization of 19 core genes in 9,125 samples across 33 cancer types using multidimensional "omic" data from The Cancer Genome Atlas. We identify somatic drivers among and the related microRNA (miRNA) regulators, functional genomic approaches, experimentally characterize YAP TAZ mutation effects miR-590 miR-200a regulation for TAZ. pathway activity is best characterized by...
We characterized the epigenetic landscape of genes encoding long noncoding RNAs (lncRNAs) across 6,475 tumors and 455 cancer cell lines. In stark contrast to CpG island hypermethylation phenotype in cancer, we observed a recurrent hypomethylation 1,006 lncRNA including EPIC1 (epigenetically-induced lncRNA1). Overexpression is associated with poor prognosis luminal B breast patients enhances tumor growth vitro vivo. Mechanistically, promotes cell-cycle progression by interacting MYC through...
Hotspot mutations in splicing factor genes have been recently reported at high frequency hematological malignancies, suggesting the importance of RNA cancer. We analyzed whole-exome sequencing data across 33 tumor types The Cancer Genome Atlas (TCGA), and we identified 119 with significant non-silent mutation patterns, including over-representation, recurrent loss function (tumor suppressor-like), or hotspot profile (oncogene-like). Furthermore, analysis revealed altered events associated...
Highlights•MYC paralogs are significantly amplified (28% of all samples)•MYC antagonists mutated (MGA, 4% samples) or deleted (MNT, 10% alterations mutually exclusive with PIK3CA, PTEN, APC, BRAF alterations•Expression analysis reveals pan-cancer and tumor-specific MYC-associated pathwaysSummaryAlthough the MYC oncogene has been implicated in cancer, a systematic assessment MYC, related transcription factors, co-regulatory proteins, forming proximal network (PMN), across human cancers is...
Abstract International cancer registries make real-world genomic and clinical data available, but their joint analysis remains a challenge. AACR Project GENIE, an international registry collecting from 19 centers, makes >130,000 patients publicly available through the cBioPortal for Cancer Genomics (https://genie.cbioportal.org). For 25,000 patients, additional longitudinal data, including treatment outcome are being collected by GENIE Biopharma Collaborative using PRISSMM curation...
The role of enhancers, a key class non-coding regulatory DNA elements, in cancer development has increasingly been appreciated. Here, we present the detection and characterization large number expressed enhancers genome-wide analysis 8928 tumor samples across 33 types using TCGA RNA-seq data. Compared with matched normal tissues, global enhancer activation was observed most cancers. Across types, activity positively associated aneuploidy, but not mutation load, suggesting hypothesis centered...
Highlights•Classification of metabolic expression subtypes in 33 TCGA cancer types•Metabolic show consistent prognostic patterns across types•Analysis master regulators suggesting therapeutic targets•Metabolic associated with sensitivity to drugs clinical useSummaryMetabolic reprogramming provides critical information for oncology. Using molecular data 9,125 patient samples from The Cancer Genome Atlas, we identified tumor types based on mRNA seven major processes and assessed their...
Long noncoding RNAs (lncRNAs) are commonly dysregulated in tumors, but only a handful known to play pathophysiological roles cancer. We inferred lncRNAs that dysregulate cancer pathways, oncogenes, and tumor suppressors (cancer genes) by modeling their effects on the activity of transcription factors, RNA-binding proteins, microRNAs 5,185 TCGA tumors 1,019 ENCODE assays. Our predictions included hundreds candidate onco- tumor-suppressor lncRNAs) whose somatic alterations account for...
Abstract Driven by the recent advances of next generation sequencing (NGS) technologies and an urgent need to decode complex human diseases, a multitude large-scale studies were conducted recently that have resulted in unprecedented volume whole transcriptome (RNA-seq) data, such as Genotype Tissue Expression project (GTEx) The Cancer Genome Atlas (TCGA). While these data offer new opportunities identify mechanisms underlying disease, comparison from different sources remains challenging,...
BACKGROUND. Adenoid cystic carcinoma (ACC) is a rare malignancy arising in salivary glands and other sites, characterized by high rates of relapse distant spread. Recurrent/metastatic (R/M) ACCs are generally incurable, due to lack active systemic therapies. To improve outcomes, deeper understanding genetic alterations vulnerabilities R/M tumors needed.
Precision oncology uses genomic evidence to match patients with treatment but often fails identify all who may respond. The transcriptome of these "hidden responders" reveal responsive molecular states. We describe and evaluate a machine-learning approach classify aberrant pathway activity in tumors, which aid hidden responder identification. algorithm integrates RNA-seq, copy number, mutations from 33 different cancer types across Cancer Genome Atlas (TCGA) PanCanAtlas project predict...
Cancer classification is foundational for patient care and oncology research. Systems such as International Classification of Diseases Oncology (ICD-O), Systematized Nomenclature Medicine Clinical Terms (SNOMED-CT), National Institute Thesaurus (NCIt) provide large sets cancer terminologies but they lack a dynamic modernized platform that addresses the fast-evolving needs in clinical reporting genomic sequencing results associated research.To meet these needs, we have developed OncoTree, an...
Abstract cBioPortal for Cancer Genomics is a widely used platform exploratory, interactive visualization and analysis of large-scale clinico-genomic datasets. provides range visualizations analyses including cohort exploration, OncoPrints, mutation “lollipop” plots, survival analysis, alteration enrichment detailed patient-level visualizations. also integrates variant annotations from variety sources to facilitate interpretation. The public (https://www.cbioportal.org) accessed by...
Interpretation of genomic variants in tumor samples still presents a challenge research and the clinical setting. A major issue is that information for variant interpretation fragmented across disparate databases, aggregation from these requires building extensive infrastructure. To this end, we have developed Genome Nexus, one-stop shop annotation with user-friendly interface cancer researchers clinicians.Genome Nexus (1) aggregates sources are relevant to applications, (2) allows...