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Single-cell genomic analysis of gastrointestinal cancer

ABSTRACT: Single-cell genomic analysis of gastrointestinal cancer

PROVIDER: PRJNA540551 | ENA |

REPOSITORIES: ENA

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Project description:Synchronous tumors are a rare disease and the underlying mechanism is seldom discussed. Here we present a case study of synchronous primary neoplasms detected in three distinct tissues: mantle cell lymphoma (MCL), clear cell renal cell carcinoma (ccRCC) and gastrointestinal stromal tumor (GIST). MCL is one form of B-cell non-Hodgkin’s lymphoma (NHL) that affects approximately 6% of NHL patients. GIST is thought to be derived from the Interstitial Cells of Cajal, a group of mesenchymal cells in the gastrointestinal tract involved in peristaltic motor activity. ccRCC tumor cells are the most common malignancy of kidney cancer and are characterized by enlarged cytoplasms. Genomic DNA from FFPE tumor sections and control DNA extracted from saliva were heat-fragmentated, labeled, hybridized and scanned following manufacturer’s recommendation for 244K arrays (Agilent). Raw data were background corrected and normalized in R. Nexus v4.1 (Biodiscovery) software was then used to call aberrant regions using Rank Segmentation algorithm from the processed data. Genes within aberrant regions can be indicated as copy number gain or loss accordingly. To identify significantly enriched canonical pathways, upstream and downstream genes for several cancer-related pathways were explored in Ingenuity knowledge base (Ingenuity Systems) and Genespring GX-10 (Agilent) with their copy number change status checked in Nexus. The analysis revealed high copy-number amplifications in gene regions related to an anti-apoptotic and cell-growth promoting pathway in all three cancers. Genomic DNA was isolated from mantle cell lymphoma (MCL), clear cell renal cell carcinoma (ccRCC) and gastrointestinal stromal tumor (GIST) FFPE tumor sections using the WaxFreeTM DNA Extraction Kit (TrimGen). Control DNA extracted from saliva was collected using a saliva self-collecting kit (Oragene). Heat-fragmentation, one-cycle target labeling, hybridization and scanning of the DNA were performed following manufacturer’s recommendation for 244K arrays (Agilent). The arrays were scanned by using the Agilent Scanner G2505B and Agilent Feature Extraction software v10.5 to produce raw data files. Raw data were background corrected and normalized in R. Nexus v4.1 (Biodiscovery) software was then used to call aberrant regions using Rank Segmentation algorithm from the processed data. Genes within aberrant regions can be indicated as copy number gain or loss accordingly.

Dataset Information

Single-cell genomic analysis of gastrointestinal cancer

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