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Accurate Identification of Sites of Origin in Carcinoma of Unknown Primary (CUP) Tumors Using DNA Methylation I

ABSTRACT: Accurate Identification of Sites of Origin in Carcinoma of Unknown Primary (CUP) Tumors Using DNA Methylation I

PROVIDER: PRJNA1050221 | ENA |

REPOSITORIES: ENA

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Accurate Identification of Sites of Origin in Carcinoma of Unknown Primary (CUP) Tumors Using DNA Methylation

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Expression analysis of cancer of unknown primary (CUP) 1

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Project description:This SuperSeries is composed of the SubSeries listed below.

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Cancers of unknown primary (CUP) are characterized by chromosomal instability (CIN) compared to metastasis of know origin.

Project description:Employing genome wide transcriptome analysis,Linear Discriminant Analysis (LDA) and Quadratic Discriminant Analysis (QDA), we created a successful classification model to identify the putative origin of a CUP. Using the classifications of the CUPs enable the comparison of transcriptome profiles from CUPs to the equivalent normal metastasis across the different carcinoma types. Gene Set Enrichment Analysis (GSEA) and Pathway analysis were used to reveal the common biological features characterizing CUPs. The classifier was build using 2208 samples of normal tissue, known primary tumors, metastasis of known origin and tested on 60 CUP samples. 130 of these samples were collected and analyzed as part of the project and submitted to ArrayExpress. The analyses show that CUPs are distinct from metastases of known origin. CUPs exhibit inconsistent expression of conventional cancer biomarkers and QDA derived outlier scores show that CUPs are more distantly related to their primary tumor class than corresponding metastases of known origin. Gene set enrichment analysis showed that CUPs display increased expression of genes involved in DNA damage repair and by employing signatures of chromosome instability (CIN), we found that CUPs are chromosome unstable compared to metastases of known origin.

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Expression analysis of cancer of unknown primary (CUP)

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