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Series GSE132929 Query DataSets for GSE132929
Status Public on Jun 19, 2019
Title Pathognomonic and epistatic genetic alterations in B-cell non-Hodgkin lymphoma
Organism Homo sapiens
Experiment type Expression profiling by array
Summary B-cell non-Hodgkin lymphoma (B-NHL) encompasses multiple clinically and phenotypically distinct subtypes of malignancy with unique molecular etiologies. Common subtypes of B-NHL such as diffuse large B-cell lymphoma (DLBCL) have been comprehensively interrogated at the genomic level, but other less common subtypes such as mantle cell lymphoma (MCL) remain sparsely characterized. Furthermore, multiple B-NHL subtypes have thus far not been comprehensively compared to identify conserved or subtype-specific patterns of genomic alterations. Here, we employed a large targeted hybrid-capture sequencing approach encompassing 380 genes to interrogate the genomic landscapes of 755 B-NHL tumors at high depth; primarily including DLBCL, MCL, follicular lymphoma (FL), and Burkitt lymphoma (BL). We identified conserved hallmarks of B-NHL that were deregulated across major subtypes, such as the frequent genetic deregulation of the ubiquitin proteasome system (UPS). In addition, we identified subtype-specific patterns of genetic alterations, including clusters of co-occurring mutations that are pathognomonic. The cumulative burden of mutations within a single cluster were more significantly discriminatory of B-NHL subtypes than individual mutations, implicating likely patterns of genetic epistasis that contribute to disease etiology. We therefore provide a framework of co-occurring mutations that deregulate genetic hallmarks and likely cooperate in lymphomagenesis of B-NHL subtypes.
 
Overall design RNA was extracted frin fresh/frozen tumor specimens and interrogated by Affymetrix U133 plus 2.0 microarray.
 
Contributor(s) Green MR
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Submission date Jun 18, 2019
Last update date Jun 22, 2019
Contact name Michael R Green
E-mail(s) mgreen5@mdanderson.org
Organization name MD Anderson Cancer Center
Department Lymphoma/Myeloma
Street address 1515 Holcombe Blvd, Unit 903
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
 
Platforms (1)
GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array
Samples (290)
GSM3896454 Follicular Lymphoma patient FL_001
GSM3896455 Follicular Lymphoma patient FL_002
GSM3896456 Follicular Lymphoma patient FL_003
Relations
BioProject PRJNA549483

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE132929_RAW.tar 1.2 Gb (http)(custom) TAR (of CEL)
Raw data provided as supplementary file
Processed data included within Sample table

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