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Series GSE75284 Query DataSets for GSE75284
Status Public on Jan 30, 2017
Title SNP profiles of 50 HB tumors
Organism Homo sapiens
Experiment type SNP genotyping by SNP array
Summary Hepatoblastoma (HB) is the most common liver cancer in children, but few pre-treatment tumors have been molecularly profiled. Consequently, there are no validated prognostic or therapeutic biomarkers for HB patients. We report on molecular analysis of 88 clinically-annotated HB tumors. This analysis pointed to three risk-stratifying molecular subtypes—low, intermediate and high risk—that are characterized by differential activation of hepatic progenitor cell markers and metabolic pathways. High-risk tumors are characterized by high NFE2L2 activity and LIN28B, HMGA2, SALL4 and AFP expression, low let-7 expression and HNF1A activity, and high coordinated expression of oncofetal proteins and stem cell markers. Tests on a 35 HB validation set supported these genes as prognostic biomarkers.
Overall design 88 clinically-annotated frozen pre-clinical HB specimens with corresponding surgical pathology reports were included in the study (Table S1) following histological review. Specimens and clinical annotation were obtained from the COG Tumor Biospecimen Bank in Columbus, Ohio, the Pediatric Oncology Group Hepatoblastoma Biology Study P9346, and Texas-based institutions, under IRB-approved protocols. Whole exome sequencing (WES) was performed on 35 tumors for which matching normal DNA – either a blood sample or tumor-adjacent normal liver – was available (Table S2). Targeted sequencing of the CTNNB1 and NFE2L2 genes and the TERT promoter was completed on all 88 tumors. DNA from 47 HBs, including all 35 samples subjected to WES, was also analyzed by SNP array. RNA and miRNA expression profiling were performed on 50 and 57 tumors, respectively.
Contributor(s) Sumazin P, Chen Y, Treviño LR, Sarabia SF, Hampton OA, Patel K, Mistretta T, Zorman B, Thompson P, Heczey A, Comerford S, Wheeler DA, Chintagumpala M, Meyers R, Rakheja D, Finegold MJ, Tomlinson G, Parsons DW, López-Terrada D
Citation(s) 27775819
Submission date Nov 21, 2015
Last update date Nov 27, 2018
Contact name Toni-Ann Mistretta
Organization name Baylor College of Medicine
Department Pathology
Lab TCH Pathology\TCMC
Street address 1 Baylor Plaza, BCM 315
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
Platforms (1)
GPL6801 [GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array
Samples (80)
GSM1948821 SNP_TLT-D-001-LV
GSM1948822 SNP_TLT-D-001-TT
GSM1948823 SNP_TLT-P-003-LV
This SubSeries is part of SuperSeries:
GSE75285 mRNA, miRNA and SNP profiles of 50 HB tumors
BioProject PRJNA303089

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
GSE75284_RAW.tar 2.1 Gb (http)(custom) TAR (of CEL)
GSE75284_allele_intensity.txt.gz 9.1 Mb (ftp)(http) TXT
Processed data are available on Series record

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