Panel of 16 genes for hereditary cancer-predisposing syndrome
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB43823 | ENA |
REPOSITORIES: ENA
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Project description: Not available
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Project description:Heredity is a major risk factor for ovarian cancer, but many families escape detection. Refined diagnosis of ovarian cancers linked to the breast and ovarian cancer (HBOC) syndrome and the hereditary nonpolyposis colorectal cancer (HNPCC) syndrome would allow cancer prevention in high risk families. In order to delineate genetic profiles of hereditary ovarian cancer, we applied genome wide array comparative genomic hybridization to 24 sporadic tumors, 12 HBOC associated tumors (BRCA1 mutations) and eight HNPCC associated tumors (mismatch repair gene mutations). Unsupervised cluster analysis identified two distinctive clusters related to genetic complexity. Most sporadic and HBOC associated tumors had complex genetic profiles with multiple gains and losses with an average of 41% of the genome altered, whereas mismatch repair defective tumors had stable genetic profiles, with an average of 18% of the genome altered. Losses of 4q34, 13q12-q32 and 19p13 were overrepresented in the HBOC subset, gains of chromosomes 17 and 19 characterized the HNPCC tumors and gains of 20q11 were more common in the sporadic tumors. The genetic distinction between HBOC and HNPCC associated ovarian cancer suggests that genetic profiles can be applied for refined classification of hereditary cases and reflects tumor development along different genetic pathways.
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Project description:Genomic profile of 47 tumors from hereditary breast cancer cases by Array CGH, 7 of which were BRCA mutation carriers (4 in BRCA2 and 3 in BRCA1), previously analyzed for BRCA1 expression by immunohistochemistry. Our goal was to identify specific alterations for BRCA1 not expressing tumors DNA from 47 Tumors versus DNA pool from normal tissue. BRCA1 expression, Hierarchical clustering and overall survival analyses.
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Project description:This dataset contains targetted DNA sequencing data generated in the context of genetic diagnostics of hereditary cancer. Target enrichment was performed with the I2HCP, a custom hereditary cancer gene panel based in Agilent SureSelect and developed by the Germans Trias i Pujol Research Institute (IGTP, Badalona, Catalonia, Spain) and the Catalan Institute of Oncology (ICO, L'Hospitalet de Llobregat, Catalonia, Spain). After the enrichment, 108 samples were sequenced in Illumina HiSeq machines and 130 in MiSeq machines. Some of the samples were sequenced on both platforms. The dataset also includes MLPA validation data for all identified copy-number alterations, annotated with exon resolution and information about negative MLPA results.
All this data was generated in the context of routine diagnostics and compiled together with MPLA validation data for a genetic diagnostics oriented benchmark of germline CNV calling tools.
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Project description:RATIONALE: The use of intrauterine levonorgestrel may prevent atypical endometrial hyperplasia and endometrial cancer in women with hereditary non-polyposis colorectal cancer or Lynch syndrome. It is not yet known whether intrauterine levonorgestrel and observation are more effective than observation alone in preventing atypical endometrial hyperplasia and endometrial cancer in women with hereditary non-polyposis colorectal cancer or Lynch syndrome.
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