Genetic alterations associated with multiple primary malignancies
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ABSTRACT:
PROVIDER: PRJNA693811 | ENA |
REPOSITORIES: ENA
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Project description:Affymetrix OncoScan arrays were used to identify potential driver DNA copy number alterations and somatic mutations that promote the development of multiple primary malignancies in 26 breast cancer patients.
2021-07-14 | GSE165240 | GEO
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Project description:Immuno-Transcriptomic Profiling Identifies Actionable Alterations in Pediatric Solid Malignancies
2021-12-07 | PXD017130 | Pride
Project description:To test the long-term effects of lack of Dnmt3a on mouse HSCs, we established a cohort of lethally irradiated mice transplanted with Dnmt3a-KO or WT HSC control cells. Dnmt3a deletion in purified HSCs transplanted alone leads to an array of hematologic disorders that models the spectrum of disorders seen in human malignancies. We investigated DNA methylation alterations in disease and control mice by RRBS. We generated an average of 23.81 million reads per sample (18.97 - 31.67 million) of which an average of 18.07 million could be mapped to the mm9 genome (2.78 - 26.42 million). We achieved an average CpG coverage depth of 31.79-fold (8.09 - 47.44-fold) and average bisulfite conversion efficiency of 99.91% (99.87 - 99.95%). Reduced representation bisulfite sequencing of cells using Illumina HiSeq 2000 and 2500
2014-12-08 | E-GEOD-60264 | biostudies-arrayexpress
Project description:To test the long-term effects of lack of Dnmt3a on mouse HSCs, we established a cohort of lethally irradiated mice transplanted with Dnmt3a-KO or WT HSC control cells. Dnmt3a deletion in purified HSCs transplanted alone leads to an array of hematologic disorders that models the spectrum of disorders seen in human malignancies. We investigated DNA methylation alterations in disease and control mice by RRBS. We generated an average of 23.81 million reads per sample (18.97 - 31.67 million) of which an average of 18.07 million could be mapped to the mm9 genome (2.78 - 26.42 million). We achieved an average CpG coverage depth of 31.79-fold (8.09 - 47.44-fold) and average bisulfite conversion efficiency of 99.91% (99.87 - 99.95%).
2014-12-08 | GSE60264 | GEO
Project description:Background: Hodgkin lymphoma (HL) and testicular cancer (TC) survivors have an increased risk of developing second primary bowel malignancies (both colorectal cancer (CRC) and small bowel adenocarcinoma (SBA)). We aimed to determine differences in genetic characteristics of second primary bowel malignancies and primary bowel malignancies.
Methods: Copy number aberrations (CNAs) generated by low-coverage whole-genome sequencing (WGS) were collected from previous studies of second primary CRC (HL survivors, n=39), primary CRC (n=90) and primary SBA (n=14). In addition, seven new samples of second primary SBA from HL (n=3) or TC (n=5) survivors, identified in the Dutch national pathology registry (PALGA), were available for low-coverage WGS.
Results: Overall, CNA patterns observed in second primary bowel malignancies were similar to those in primary bowel malignancies. Losses of 21q22.2 were observed more frequently (p=0.057) in second primary CRC compared with primary CRC, while in second primary SBA gains of 10p15.3-15.1 and losses of 18q12.1-23 were significantly more frequent detected compared with primary SBA.
Conclusions: Second primary CRC and SBA show comparable genome wide CNAs to those in primary CRC and SBA, respectively. This suggests that part of the pathogenesis of second primary tumours in these cancer survivors is similar to those of primary CRC and SBA in general, despite the exposure to DNA damaging treatments received for earlier HL and TC.
| EGAS00001005940 | EGA
Project description:This SuperSeries is composed of the following subset Series: GSE39380: Genome-wide analysis of primary plasma cell leukemia identifies recurrent imbalances associated with transcriptional Profile alterations (Copy number) GSE39381: Genome-wide analysis of primary plasma cell leukemia identifies recurrent imbalances associated with transcriptional Profile alterations (Expression) Refer to individual Series
2012-10-12 | E-GEOD-39383 | biostudies-arrayexpress
Project description:Germ cell tumor and associated hematologic malignancies
| PRJNA660496 | ENA
Project description:Germ cell tumor and associated hematologic malignancies
| PRJNA660497 | ENA
Project description:BACKGROUND: Promoter hypermethylation coupled with loss of heterozygosity at the same locus results in loss of gene function in many tumor cells. The "rules" governing which genes are methylated during the pathogenesis of individual cancers, how specific methylation profiles are initially established, or what determines tumor type-specific methylation are unknown. However, DNA methylation markers that are highly specific and sensitive for common tumors would be useful for the early detection of cancer, and those required for the malignant phenotype would identify pathways important as therapeutic targets. METHODS AND FINDINGS: In an effort to identify new cancer-specific methylation markers, we employed a high-throughput global expression profiling approach in lung cancer cells. We identified 132 genes that have 5' CpG islands, are induced from undetectable levels by 5-aza-2'-deoxycytidine in multiple non-small cell lung cancer cell lines, and are expressed in immortalized human bronchial epithelial cells. As expected, these genes were also expressed in normal lung, but often not in companion primary lung cancers. Methylation analysis of a subset (45/132) of these promoter regions in primary lung cancer (n = 20) and adjacent nonmalignant tissue (n = 20) showed that 31 genes had acquired methylation in the tumors, but did not show methylation in normal lung or peripheral blood cells. We studied the eight most frequently and specifically methylated genes from our lung cancer dataset in breast cancer (n = 37), colon cancer (n = 24), and prostate cancer (n = 24) along with counterpart nonmalignant tissues. We found that seven loci were frequently methylated in both breast and lung cancers, with four showing extensive methylation in all four epithelial tumors. CONCLUSIONS: By using a systematic biological screen we identified multiple genes that are methylated with high penetrance in primary lung, breast, colon, and prostate cancers. The cross-tumor methylation pattern we observed for these novel markers suggests that we have identified a partial promoter hypermethylation signature for these common malignancies. These data suggest that while tumors in different tissues vary substantially with respect to gene expression, there may be commonalities in their promoter methylation profiles that represent targets for early detection screening or therapeutic intervention. Experiment Overall Design: We compared the gene expression changes HBEC and NSCLC cells before and after treatment with 5-aza-2'deoxycytidine.
2008-06-15 | E-GEOD-6695 | biostudies-arrayexpress