Molecular analysis of renal cell carcinoma with unclassfied histology [gene expression]

UID: 10702

Author(s): Chen, Yingbei*, Skanderup, Anders J., Reuter, Victor*, Hsieh, James J.*, Zhao, Jeffrey * MSK affiliated

Core Facilities: Integrated Genomics Operation (IGO)

Description: Summary from the GEO: "Renal cell carcinomas with unclassified histology (uRCC) constitute a significant portion of aggressive non-clear cell RCC (nccRCC) that have no standard therapy. The oncogenic drivers in these tumors are unknown. We performed a molecular analysis of 62 high-grade primary uRCC, incorporating targeted cancer gene sequencing, RNA sequencing, Single Nucleotide Polymorphism array, fluorescence in-situ hybridization, immunohistochemistry, and cell-based assays. We identified recurrent somatic mutations in 29 genes, including NF2 (18%), SETD2 (18%), BAP1 (13%), KMT2C (10%), and MTOR (8%). Integrated analysis revealed distinct molecular subsets, including a subset of 26% uRCC characterized by NF2-loss, dysregulated Hippo-YAP pathway and worse survival.
Analysis of RNA from uRCC with or without NF2-loss."

Subject of Study

Subject(s)

OncoTree Cancer Type(s)

Renal Cell Carcinoma

Access via GEO
GZip and CSV Sequencing Data
Accession #: GSE85897

Access via SRA
RNA Sequence reads for 7 samples.
Accession #: SRP082503

Access via BioProject
Additional information about overall initiative.
Accession #: PRJNA339705
Access Restrictions: Free to All
Access Instructions: The NCBI Gene Expression Omnibus, SRA, and BioProject databases provide open access to these files.
Associated Publications: Chen Y, Xu J, Skanderup A, et al. Molecular analysis of aggressive renal cell carcinoma with unclassified histology reveals distinct subsets. Nature Communications. 2016; 7:13131.
Data Type: Genomic
Equipment Used: Illumina HiSeq 2500
High throughput sequencing system
Dataset Format(s): CSV, SRA, gzip
Dataset Size: 809.6 Kb (CSV), 55.583 Gb (SRA)

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