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| Status |
Public on Feb 21, 2024 |
| Title |
Genomic Landscape of Diploid and Aneuploid Microsatellite Stable Early Onset Colorectal Cancer |
| Organism |
Homo sapiens |
| Experiment type |
Genome variation profiling by genome tiling array
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| Summary |
We applied DNA content based flow cytometry methods to interrogate the genomes of clinical samples from 21 patients with early onset colorectal carcinoma (EOCRC). These included a fresh frozen sample obtained from a surgical resection and 20 archived formalin fixed paraffin embedded (FFPE) samples from a Mayo Clinic tissue bank. Our flow sorting methods are compatible with analyses of biopsies of interest including FFPE samples and frozen biopsies. Notably for this study we distinguished and sorted diploid and aneuploid tumors. We then profiled the exomes of tumor normal pairs for all 21 cases, the whole genome copy number for a subset of 6 samples, and telomere length in diploid and aneuploid nuclei from 9 cases. Additionally, we screened the 20 FFPE cases for EGFR expression with an established IHC assay.
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| Overall design |
We applied DNA content based flow sorting to isolate the nuclei of clonal populations from early onset colorectal carcinoma biopsies. We coupled this strategy with oligonucleotide array CGH (aCGH) thereby obtaining high definition genomic profiles of clonal populations from each tumor. Whole exome sequencing of each flow sorted sample identified somatic pathogenic variants.
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| Contributor(s) |
Zhou Y, Chen X, Chen J, Kendrick CD, Ramanathan RK, Graham RP, Kossick KF, Boardman LA, Barrett MT |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Aug 08, 2023 |
| Last update date |
Feb 22, 2024 |
| Contact name |
Michael Thomas Barrett |
| E-mail(s) |
barrett.michael@mayo.edu
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| Phone |
480-301-6736
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| Organization name |
Mayo Clinic Arizona
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| Department |
Molecular Pharmacology and Experimental Therapeutics
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| Street address |
13400 East Shea Boulevard
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| City |
Scottsdale |
| State/province |
AZ |
| ZIP/Postal code |
85259 |
| Country |
USA |
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| Platforms (1) |
| GPL19387 |
Agilent-021850 SurePrint G3 Human CGH Microarray (Probe Name version) |
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| Samples (7)
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| Relations |
| BioProject |
PRJNA1003404 |
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