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| Status |
Public on Jun 15, 2007 |
| Title |
Comparative whole genome profiling of post-transplant lymphoproliferative disorders and diffuse large B-cell lymphomas. |
| Organism |
Homo sapiens |
| Experiment type |
Genome variation profiling by SNP array
SNP genotyping by SNP array
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| Summary |
Post-transplant lymphoproliferative disorders (PTLD) are a major complication of solid organ transplantation and represent a cause of severe morbidity and mortality among transplanted patients. Apart from EBV infection, knowledge of the pathogenesis of monoclonal PTLD is limited. Powerful analysis techniques, such as whole genomic DNA profiling (arrayCGH), can improve our understanding of PTLD pathogenesis. Toward this aim, we obtained the whole genome profiling using the Affymetrix GeneChip Human Mapping 10k 2.0 from 20 cases of PTLD and we compared them with those assessed in 25 cases of DLBCL from immunocompetent patients, as a control group. Recurrent lesions were detected among all the samples. Chromosome 18q, 7q, 3q and 12 were the most common gains in DLBCL of immunocompetent hosts. Chromosomes 5p and 11p were commonly gained in PTLD-DLBCL. The latter had frequent losses of 6q, 17p, 1p, and 9p. Chromosome 12p was the most frequent target of deletions among PTLD-DLBCL. The LOH pattern was characterized by involvement of chromosomes 13q and 17p in DLBCL and 10, 1q, 9p and 11q among PTLD-DLBCL. Interestingly, LOH did not always match the DNA loss. In particular, chromosome 10 seemes to be targeted by uniparental disomy in PTLD. Small deletions and gains, involving both known (BCL2 and PAX5) and unknown genes (ZDHHC14), have been identified. Our data suggest that PTLD share, at a lower frequency, common genetic aberrations with DLBCL from immunocompetent patients. The demonstration of 9p13 amplification indicates the importance of PAX5 in PTLD. The combination of DNA copy number and LOH assessment lead to the hypothesis that uniparental disomy may be a potential mechanism in B-cell lymphomagenesis. Twenty specimens of monoclonal B-cell PTLD, collected from 20 solid organ transplant recipients.
Keywords: Genomic DNA on Affymetrix 10K SNP array
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| Overall design |
20 PTLD samples. No technical replications.
25 DLBCL samples (20 patient + 5 cell lines). No technical replications.
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| Contributor(s) |
Rinaldi A, Bertoni F, Kwee I |
| Citation(s) |
16803564 |
| Submission date |
Jun 14, 2007 |
| Last update date |
Sep 20, 2012 |
| Contact name |
Francesco Bertoni |
| E-mail(s) |
francesco.bertoni@ior.usi.ch
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| Phone |
+41 91 820 0367
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| Organization name |
IOR
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| Department |
Lymphoma & Genomics Research Program
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| Street address |
Via V. Vela 6
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| City |
Bellinzona |
| State/province |
Ticino |
| ZIP/Postal code |
6500 |
| Country |
Switzerland |
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| Platforms (1) |
| GPL2641 |
[Mapping10K_Xba142] Affymetrix Human Mapping 10K 2.0 Array |
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| Samples (45)
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| Relations |
| BioProject |
PRJNA101001 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE8123_RAW.tar |
64.2 Mb |
(http)(custom) |
TAR (of CEL) |
| Processed data included within Sample table |
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