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Series GSE50973

Query DataSets for GSE50973

Status

Public on Jan 17, 2014

Title

Analysis of the coding exome of follicular lymphoma

Organism

Homo sapiens

Experiment type

SNP genotyping by SNP array
Genome variation profiling by SNP array

Summary

Follicular lymphoma (FL) constitutes the second most common non-Hodgkin lymphoma in the Western world. FL carries characteristic recurrent structural genomic aberrations. However, information regarding the coding genome in FL is still evolving. Here, we describe the results of massively parallel exome sequencing and high-resolution SNP 6.0 array profiling of 12 highly purified FL cases and validation of mutations in an expansion cohort of 45 cases. In addition to confirming high-frequency mutations in MLL2, CREBBP and BCL2, we report identification of 18 recurrently mutated genes in FL. These include novel mutations in MCL1, IRF8 and POU2FA/OCT2, and high-frequency mutations in various components of the linker histone HIST1H1. Further, multiple novel mutated genes located within regions of acquired uniparental disomy (aUPD) are identified, providing candidate genes for this common lesion type in FL. In aggregate, these data substantially broaden our understanding of the types and frequency of recurrently mutated genes and pathways in FL

Overall design

Twelve paired normal and tumor follicular lymphoma cases were profiled by SNP array for this study. However, in addition the data from 125 CEL files derived from the DNA of flow-sorted CD3+ cells from 125 CLL patients (122 CEL files from GSE30777) were used to firmly establish a normal copy number baseline for the dChip software to compute all subsequent normal and tumor DNA copy number values.

Contributor(s)

Kaminski MS, Li Y, Li H, Ouillette PD, Jones S, Fox HM, Jacobi KM, Saiya-Cork K, Bixby DL, Lebovic D, Shedden KA, Sabel MS, Marentette LJ, Cimmino VM, Chang AE, Malek SN

Citation(s)

24435047

Submission date

Sep 18, 2013

Last update date

Nov 27, 2018

Contact name

Sami N Malek

E-mail(s)

smalek@med.umich.edu, pouillet@med.umich.edu

Phone

734-763-1222

Organization name

University of Michigan

Department

Internal Medicine, Hematology-Oncology

Street address

4410 Cancer Center; 1500 E Medical Center Dr

City

Ann Arbor

State/province

ZIP/Postal code

48109

Country

USA

Platforms (1)

GPL6801

[GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array

Samples (27)

More...

GSM1233508	ML002N_CD3
GSM1233509	ML002T_kappa_CD20
GSM1233510	ML013N_CD3

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BioProject

Download family	Format
SOFT formatted family file(s)	SOFT
MINiML formatted family file(s)	MINiML
Series Matrix File(s)	TXT

Supplementary file	Size	Download	File type/resource
GSE50973_RAW.tar	817.5 Mb	(http)(custom)	TAR (of CEL, TXT)
Processed data included within Sample table
Processed data provided as supplementary file