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| Status |
Public on Feb 06, 2013 |
| Title |
Genome-wide SNP analysis of cutaneous squamous cell carcinomas and actinic keratoses from organ transplant recipients |
| Organism |
Homo sapiens |
| Experiment type |
Genome variation profiling by SNP array
SNP genotyping by SNP array
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| Summary |
The risk of developing cutaneous squamous cell carcinoma (SCC) is markedly increased in organ transplant recipients (OTRs) compared to the normal population. Next to sun exposure, the immunosuppressive regimen is an important risk factor for SCC development in OTRs. Various gene mutations (e.g. TP53) and genetic alterations (e.g. CDKN2A loss, RAS amplification) have been found in SCCs. The aim of this study was to identify genomic alterations that are consistently involved in the formation of SCCs and their precursor lesions, actinic keratoses (AKs). To perform the analysis in an isogenic background, DNA was isolated from SCC and AK from each of 13 OTRs. Tumor samples and their matching normal control (peripheral blood) were analyzed on the Illumina HumanHap550V3_duo genotyping beadchips. In contrast to previous studies, genome-wide SNP analysis showed very few copy number variations in AKs and SCCs, and these variations had no apparent relationship with observed changes in mRNA expression profiles (GSE32628). Other molecular mechanisms, such as DNA methylation or miRNA alterations, may affect gene expression in SCCs of OTRs.
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| Overall design |
Patients were selected from the group of OTRs that are regularly seen at the dermatology clinic of the Leiden University Medical Center. Patients with clinically suspected SCC were informed on the study and after informed consent was obtained, fresh frozen samples were obtained from SCCs (n=15, including 2 repeats) and AKs (n=11). Peripheral blood was taken as normal control. DNA was isolated and SNP profiles were obtained using HumanHap550V3_duo Genotyping BeadChips (Illumina). Both the log R ratio and the B allele frequency (BAF) were investigated to identify copy number alterations and loss of heterozygosity (LOH)
The tumor DNA samples are from the same tumor samples as the RNA samples in GSE32628.
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| Contributor(s) |
Hameetman L, Commandeur S, Bouwes Bavinck JN, Wisgerhof HC, de Gruijl FR, Willemze R, Mullenders L, Tensen CP, Vrieling H |
| Citation(s) |
23379751 |
| |
| Submission date |
Oct 13, 2011 |
| Last update date |
Sep 04, 2015 |
| Contact name |
Harry Vrieling |
| E-mail(s) |
[email protected]
|
| Organization name |
Leiden University Medical Center
|
| Department |
Toxicogenetics, S4-P
|
| Lab |
room T4-34
|
| Street address |
Einthovenweg 20
|
| City |
Leiden |
| ZIP/Postal code |
2333 ZC |
| Country |
Netherlands |
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| Platforms (2) |
| GPL6102 |
Illumina human-6 v2.0 expression beadchip |
| GPL6982 |
Illumina HumanHap550-Duov3 Genotyping BeadChip (HumanHap550-2v3_B) |
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| Samples (94)
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| This SubSeries is part of SuperSeries: |
| GSE32979 |
Cutaneous squamous cell carcinomas and actinic keratoses from organ transplant recipients |
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| Relations |
| BioProject |
PRJNA154405 |
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