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Series GSE63601 Query DataSets for GSE63601
Status Public on Aug 10, 2015
Title Widespread somatic L1 retrotransposition occurs early during gastrointestinal cancer evolution
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
Summary Somatic L1 retrotransposition events have been shown to occur in epithelial cancers1-8. Here, we attempted to determine how early somatic L1 insertions occurred during the development of gastrointestinal (GI) cancers. Using L1-targeted resequencing (L1-seq), we studied different stages of four colorectal cancers arising from colonic polyps, seven pancreatic carcinomas, as well as seven gastric cancers. Surprisingly, we found somatic L1 insertions not only in all cancer types and metastases, but also in colonic adenomas, well-known cancer precursors. Some insertions were also present in low quantities in normal GI tissues, occasionally caught in the act of being clonally fixed in the adjacent tumors. Insertions in adenomas and cancers numbered in the hundreds and many were present in multiple tumor sections implying clonal distribution. Our results demonstrate that extensive somatic insertional mutagenesis occurs very early during the development of GI tumors, probably before dysplastic growth.
 
Overall design Here we show Human SNP 6.0 Array experiments on DNAs from four colorectal cancer patients (1BV, 2BV, 3BV, and 4BV) with polyps and metastases. Here we characterize the samples for CNVs and compare the samples' CNV status to their respective somatic L1 retrotransposition profile.
 
Contributor(s) Ewing AD, Gacita A, Wood LD, Ma F, Xing D, Kim M, Manda SS, Abril G, Pereira G, Makohon-Moore A, Looijenga LH, Gillis AJ, Hruban RH, Romans KE, Pandey A, Iacobuzio-Donahue CA, Vogelstein B, Kinzler KW, Kazazian, HH Jr, Solyom S
Citation(s) 26260970
Submission date Nov 24, 2014
Last update date Nov 27, 2018
Contact name Szilvia Solyom
E-mail(s) ssolyom1@jhmi.edu
Organization name Johns Hopkins University School of Medicine
Department Institute for Genomic Medicine
Street address 733 North Broadway
City Baltimore
State/province MD
ZIP/Postal code 21205
Country USA
 
Platforms (1)
GPL6801 [GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array
Samples (12)
GSM1553400 patient 1BV, sample 1, normal colon
GSM1553401 patient 1BV, sample 3/1, primary colorectal cancer
GSM1553402 patient 2BV, sample 20, normal liver
Relations
BioProject PRJNA268381

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
GSE63601_Ptk-Signals.txt.gz 127.3 Mb (ftp)(http) TXT
GSE63601_RAW.tar 296.5 Mb (http)(custom) TAR (of CEL)
Processed data are available on Series record

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