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Series GSE63420 Query DataSets for GSE63420
Status Public on Jan 22, 2015
Title Massive parallel sequencing uncovers actionable FGFR2-PPHLN1 fusion and ARAF mutations in intrahepatic cholangiocarcinoma
Organism Homo sapiens
Experiment type Genome variation profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary Intrahepatic cholangiocarcinoma (iCCA) is a fatal bile duct cancer with dismal prognosis and limited therapeutic options. By performing RNA- and exome sequencing analyses we have discovered a novel fusion event, FGFR2-PPHLN1 (16%), and damaging mutations in the ARAF oncogene (11%).
Overall design Methods: mRNA and gDNA were exctracted from fresh frozen tumor tissues and corresponding normal tissue (n=8 pairs) from patients with iCCA who underwent surgical resection. RNA-seq was performed using Illumina HiSeq 2500 System with 100 nucleotide single-end reads. One sample and its paired non-tumoral tissue were eliminated from the subsequent analysis because of bad RNa quality. The same 8 paired tumors were also analyzed by whole-exome seq.
*** Submitter confirms there are no patient privacy concerns with these data. ***
Contributor(s) Losic B, Sia D
Citation(s) 25608663
Submission date Nov 18, 2014
Last update date May 15, 2019
Contact name Daniela Sia
Organization name Icahn school of Medicine at Mount Sinai
Department Liver Diseases
Street address 1425 Madison Avenue
City New York
ZIP/Postal code 10029
Country USA
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (30)
GSM1548437 ICC6 (Exome-seq)
GSM1548438 ICC8 (Exome-seq)
GSM1548439 ICC9 (Exome-seq)
BioProject PRJNA267702
SRA SRP050003

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