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| Status |
Public on Mar 01, 2014 |
| Title |
CytoScanHD array Data for 15 normal, 15 primary colorectal carcinomas and their 15 matched liver metastases |
| Organism |
Homo sapiens |
| Experiment type |
Genome variation profiling by SNP array
Genome variation profiling by genome tiling array
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| Summary |
We performed whole exome sequencing and copy number analysis for 15 triplets, each comprising normal colorectal tissue, primary colorectal carcinoma, and its synchronous matched liver metastasis. We analyzed the similarities and differences between primary colorectal carcinoma and matched liver metastases in regards to somatic mutations and somatic copy number alterationss (SCNAs). The genomic profiling demonstrated mutations in APC(73%), KRAS (33%), ARID1A and PIK3CA (6.7%) genes between primary colorectal and metastatic liver tumors. TP53 mutation was observed in 47% of the primary samples and 67% in liver metastatic samples. The grouped pairs, in hierarchical clustering showed similar SCNA patterns, in contrast to the ungrouped pairs. Many mutations (including those of known key cancer driver genes) were shared in the grouped pairs. The ungrouped pairs exhibited distinct mutation patterns with no shared mutations in key driver genes. Four ungrouped liver metastasis samples had mutations in DNA mismatch repair genes along with hypermutations and a substantial number of copy number of alterations. Genomically, colorectal and metastatic liver tumors were very similar. However, in a subgroup of patients, there were genetic variations in liver metastases in the loss of DNA mismatch repair genes.
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| Overall design |
Copy number analysis of Affymetrix CytoScanHD arrays was performed for 15 primary colorectal carcinoma and 15 samples of their matched liver metastases. 15 normal samples prepared from each of the patient was used as the reference for the study. Nexus Copy number 6.1 software was used for somatic copy number alteration analysis.
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| Contributor(s) |
Lee W, Lee S, Haq F, Kim D, Jun C, Jo H, Ahn S |
| Citation(s) |
24599305 |
| Submission date |
Jan 03, 2014 |
| Last update date |
Jul 13, 2018 |
| Contact name |
SUN YOUNG LEE |
| E-mail(s) |
farhanhaqj@gmail.com
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| Organization name |
Asan Medical Center
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| Street address |
Olympicro
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| City |
Seoul |
| ZIP/Postal code |
138-736 |
| Country |
South Korea |
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| Platforms (1) |
| GPL16131 |
[CytoScanHD_Array] Affymetrix CytoScan HD Array |
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| Samples (45)
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| Relations |
| BioProject |
PRJNA233312 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE53799_RAW.tar |
8.3 Gb |
(http)(custom) |
TAR (of CEL, CYCHP, TXT) |
| Processed data provided as supplementary file |
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