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| Status |
Public on Dec 23, 2013 |
| Title |
Affymetrix SNP array data for recurrent deletion in 19p in DLBCLs and BLs |
| Organism |
Homo sapiens |
| Experiment type |
Genome variation profiling by SNP array
SNP genotyping by SNP array
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| Summary |
A single nucleotide polymorphism (SNP)-chip analysis of 98 cases of aggressive B-cell lymphomas revealed a recurrent deletion at 19p13 in 9 of the cases. Six further cases with deletions encompassing this region were found in array-comparative genomic hybridization data of 295 aggressive B-cell lymphomas from a previous study. Three cases even showed a homozygous deletion, suggesting a tumor suppressor gene in the deleted region. Two genes encoding members of the tumor necrosis factor superfamily were located in the minimally deleted region, i.e. TNFSF7 and TNFSF9. As no mutations were found within the coding exons of the remaining alleles in the lymphomas with heterozygous deletions, we speculate that the deletions may mostly function through a haploinsufficiency mechanism. The cases with deletions encompassed both diffuse large B-cell lymphomas and Burkitt lymphomas, and a deletion was also found in a Hodgkin lymphoma cell line. Thus, TNFSF7 and TNFSF9 deletions are recurrent genetic lesions in multiple types of human lymphomas.
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| Overall design |
Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from whole tissue. Copy number and LOH analysis of 500K SNP/250K SNP arrays was performed on 9 cases of aggressive B-cell lymphoma harboring the described deletion. Genotyping was performed using the BRLMM-algorithm. 20 normal references (10 of those hybridized to nsp-chips) extracted from healthy blood donors, used as normals in the analysis in addition to the HapMap references provided by Affymetrix, are included in the set.
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| Contributor(s) |
Scholtysik R |
| Citation(s) |
22213068 |
| |
| Submission date |
Nov 29, 2011 |
| Last update date |
May 17, 2017 |
| Contact name |
Rene Scholtysik |
| E-mail(s) |
rene.scholtysik@uni-due.de
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| Organization name |
University Hospital Essen
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| Department |
IFZ
|
| Street address |
Virchowstrasse 173
|
| City |
Essen |
| ZIP/Postal code |
45127 |
| Country |
Germany |
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| Platforms (2) |
| GPL3718 |
[Mapping250K_Nsp] Affymetrix Mapping 250K Nsp SNP Array |
| GPL3720 |
[Mapping250K_Sty] Affymetrix Mapping 250K Sty2 SNP Array |
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| Samples (42)
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| Relations |
| BioProject |
PRJNA150583 |
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