UALCAN: A Portal for Facilitating Tumor Subgroup Gene Expression and Survival Analyses

Neoplasia, Journal Year: 2017, Volume and Issue: 19(8), P. 649 - 658

Published: July 18, 2017

Genomics data from The Cancer Genome Atlas (TCGA) project has led to the comprehensive molecular characterization of multiple cancer types. large sample numbers in TCGA offer an excellent opportunity address questions associated with tumo heterogeneity. Exploration by researchers and clinicians is imperative unearth novel therapeutic/diagnostic biomarkers. Various computational tools have been developed aid carrying out specific analyses; however there need for resources facilitate study gene expression variations survival associations across tumors. Here, we report UALCAN, easy use, interactive web-portal perform in-depth analyses data. UALCAN uses level 3 RNA-seq clinical 31 portal's user-friendly features allow perform: 1) analyze relative a query gene(s) tumor normal samples, as well various sub-groups based on individual stages, grade, race, body weight or other clinicopathologic features, 2) estimate effect patient survival; 3) identify top over- under-expressed (up down-regulated) genes This resource serves platform silico validation target identifying sub-group candidate Thus, could be extremely helpful accelerating research. publicly available at http://ualcan.path.uab.edu.

Language: Английский

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Breast cancer

Nature Reviews Disease Primers, Journal Year: 2019, Volume and Issue: 5(1)

Published: Sept. 23, 2019

Language: Английский

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OncoKB: A Precision Oncology Knowledge Base

JCO Precision Oncology, Journal Year: 2017, Volume and Issue: 1, P. 1 - 16

Published: July 7, 2017

With prospective clinical sequencing of tumors emerging as a mainstay in cancer care, there is an urgent need for support tool that distills the implications associated with specific mutation events into standardized and easily interpretable format. To this end, we developed OncoKB, expert-guided precision oncology knowledge base.

Language: Английский

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A Living Biobank of Breast Cancer Organoids Captures Disease Heterogeneity

Cell, Journal Year: 2017, Volume and Issue: 172(1-2), P. 373 - 386.e10

Published: Dec. 7, 2017

Language: Английский

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The somatic mutation profiles of 2,433 breast cancers refine their genomic and transcriptomic landscapes

Nature Communications, Journal Year: 2016, Volume and Issue: 7(1)

Published: May 10, 2016

Abstract The genomic landscape of breast cancer is complex, and inter- intra-tumour heterogeneity are important challenges in treating the disease. In this study, we sequence 173 genes 2,433 primary tumours that have copy number aberration (CNA), gene expression long-term clinical follow-up data. We identify 40 mutation-driver (Mut-driver) genes, determine associations between mutations, driver CNA profiles, clinical-pathological parameters survival. assess clonal states Mut-driver estimate levels using mutant-allele fractions. Associations PIK3CA mutations reduced survival identified three subgroups ER-positive (defined by amplification 17q23, 11q13–14 or 8q24). High general associated with a worse outcome, but highly aggressive low heterogeneity. These results emphasize importance genome-based stratification cancer, implications for designing therapeutic strategies.

Language: Английский

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Association analysis identifies 65 new breast cancer risk loci

Nature, Journal Year: 2017, Volume and Issue: 551(7678), P. 92 - 94

Published: Oct. 20, 2017

Language: Английский

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Landscape of Microsatellite Instability Across 39 Cancer Types

JCO Precision Oncology, Journal Year: 2017, Volume and Issue: 1, P. 1 - 15

Published: Oct. 3, 2017

Microsatellite instability (MSI) is a pattern of hypermutation that occurs at genomic microsatellites and caused by defects in the mismatch repair system. Mismatch deficiency leads to MSI has been well described several types human cancer, most frequently colorectal, endometrial, gastric adenocarcinomas. known be both predictive prognostic, especially colorectal cancer; however, current clinical guidelines only recommend testing for endometrial cancers. Therefore, less about prevalence extent among other cancer.Using our recently published MSI-calling software, MANTIS, we analyzed whole-exome data from 11,139 tumor-normal pairs The Cancer Genome Atlas Therapeutically Applicable Research Generate Effective Treatments projects external sources across 39 cancer types. Within subset these types, assessed mutation burden, mutational signatures, somatic variants associated with MSI.We identified 3.8% all cancers assessed-present 27 tumor types-most notably adrenocortical carcinoma (ACC), cervical (CESC), mesothelioma, which not yet described. In addition, MSI-high ACC CESC tumors were observed have higher average burden than microsatellite-stable tumors.We provide evidence as-yet-unappreciated cancer. These findings support an expanded role multiple as patients MSI-positive are predicted benefit novel immunotherapies trials.

Language: Английский

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The chromatin accessibility landscape of primary human cancers

Science, Journal Year: 2018, Volume and Issue: 362(6413)

Published: Oct. 26, 2018

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 identified, noncoding mutations associated clinical prognosis discovered. Science , this issue p. eaav1898 ; see also 401

Language: Английский

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Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors

Nature Communications, Journal Year: 2017, Volume and Issue: 8(1)

Published: Oct. 31, 2017

Whole-exome sequencing of cell-free DNA (cfDNA) could enable comprehensive profiling tumors from blood but the genome-wide concordance between cfDNA and tumor biopsies is uncertain. Here we report ichorCNA, software that quantifies content in 0.1× coverage whole-genome data without prior knowledge mutations. We apply ichorCNA to 1439 samples 520 patients with metastatic prostate or breast cancers. In earliest tested sample for each patient, 34% have ≥10% tumor-derived cfDNA, sufficient standard whole-exome sequencing. Using sequencing, validate clonal somatic mutations (88%), copy number alterations (80%), mutational signatures, neoantigens matched 41 content. summary, provide methods identify eligible profiling, revealing its applicability many patients, demonstrate high

Language: Английский

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The Genomic Landscape of Endocrine-Resistant Advanced Breast Cancers

Cancer Cell, Journal Year: 2018, Volume and Issue: 34(3), P. 427 - 438.e6

Published: Sept. 1, 2018

Language: Английский

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