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Genome-wide copy number analyses reveal genomic abnormalities involved in transformation of follicular lymphoma

ABSTRACT: We studied 277 lymphoma samples (198 FL and 79 transformed FL [tFL]) using a single-nucleotide polymorphism array to identify the secondary chromosomal abnormalities that drive the development of FL and its transformation to diffuse large B-cell lymphoma. Affymetrix 250K NspI SNP arrays were performed according to the manufacturer's directions on DNA extracted from frozen follicular lymphoma or transformed follicular lymphoma tumor specimens

ORGANISM(S): Homo sapiens

SUBMITTER: Wing Chan

PROVIDER: E-GEOD-67385 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Genome-wide copy-number analyses reveal genomic abnormalities involved in transformation of follicular lymphoma.

Bouska Alyssa A McKeithan Timothy W TW Deffenbacher Karen E KE Lachel Cynthia C Wright George W GW Iqbal Javeed J Smith Lynette M LM Zhang Weiwei W Kucuk Can C Rinaldi Andrea A Bertoni Francesco F Fitzgibbon Jude J Fu Kai K Weisenburger Dennis D DD Greiner Timothy C TC Dave Bhavana J BJ Gascoyne Randy D RD Rosenwald Andreas A Ott German G Campo Elias E Rimsza Lisa M LM Delabie Jan J Jaffe Elaine S ES Braziel Rita M RM Connors Joseph M JM Staudt Louis M LM Chan Wing-Chung WC

Blood 20130913 11

Follicular lymphoma (FL), the second most common type of non-Hodgkin lymphoma in the western world, is characterized by the t(14;18) translocation, which is present in up to 90% of cases. We studied 277 lymphoma samples (198 FL and 79 transformed FL [tFL]) using a single-nucleotide polymorphism array to identify the secondary chromosomal abnormalities that drive the development of FL and its transformation to diffuse large B-cell lymphoma. Common recurrent chromosomal abnormalities in FL include ...[more]

PMID: 24037725

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Affymetrix SNP array data for follicular lymphoma (FL) and transformed follicular lymphoma (tFL) samples

Project description:Follicular lymphoma is the most common indolent non-Hodgkin's lymphoma involving germinal centre B cells, with a subset of patients undergoing transformation to a diffuse large B-cell lymphoma (DLBCL) morphology for which the clinical outcomes are poor. To elucidate the differences in copy number profiles between FL and tFL groups, we performed Affymetrix SNP 6.0 Array analysis on 31 paired FL-tFL cases. We wanted to identify and compare recurrent somatic copy number alterations (CNAs) between the two groups (FL vs. tFL). In addition, the concordance and discordance in the copy neutral loss of heterozygosity (cnLOH) between the two groups were also investigated to identify recurrent target gene regions. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from follicular lymphoma (FL), transformed follicular lymphoma (tFL) and matching germline (GL) sample (if available). Copy number analysis of Affymetrix SNP 6.0 Array were performed on 91 DNA samples, consisting of 31 patients. Among the 31 patients, 19 had matching germline samples, while 12 had no germline samples. The Log R Ratio (LRR) values and the B Allele Frequency (BAF) values were subsequently calculated to search for copy number aberrations and copy neutral (CN)-LOH in the FL and tFL samples. Paired and unpaired analyses were performed accordingly.

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Homo sapiens

Project description:Affymetrix SNP array data for follicular lymphoma (FL) and transformed follicular lymphoma (tFL) samples

| PRJNA182209 | ENA