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| Status |
Public on Apr 17, 2018 |
| Title |
Circulating-cell free DNA pooled samples for epigenome-wide discovery of methylation biomarkers for colorectal cancer screening |
| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by genome tiling array
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| Summary |
We explored the differential methylation patterns found in cfDNA between healthy controls (individuals with no colorectal findings, NCF) and patients with advanced neoplasia (advanced adenomas and colorectal cancer, AA andCRC) using pooled samples, to determine if pooled serum cfDNA samples can be used to search for non-invasive methylation biomarkers, as an affordable and efficient alternative to tissue biopsy. cfDNA was extracted from serum samples and methylation measurements were assessed with the Infinium MethylationEPIC BeadChip. Data was mainly preprocessed and analyzed with R/Bioconductor packages.
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| Overall design |
Two independent pooled samples were constructed for each pathological group (NCF, AA and CRC) using equal amounts of cfDNA from 5 men and 5 women per pool. Genome-wide DNA methylation in the six pooled samples was analyzed with the Infinium MethylationEPIC BeadChip microarray, covering over 850,000 CpG sites across the genome. Two independent pooled samples were constructed for each pathological group (NCF, AA and CRC) using equal amounts of ccfDNA from 5 men and 5 women per pool. Genome-wide DNA methylation in the six pooled samples was analyzed with the Infinium MethylationEPIC BeadChip microarray, covering over 850,000 CpG sites across the genome.
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| Contributor(s) |
Gallardo-Gómez M, De Chiara L |
| Citation(s) |
29686738 |
| Submission date |
Feb 06, 2018 |
| Last update date |
Jan 20, 2019 |
| Contact name |
Sebastian Moran |
| Organization name |
IDIBELL
|
| Department |
PEBC
|
| Street address |
Av. Gran Via de l'Hospitalet, 199-203
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| City |
L'Hospitalet del Llobregat |
| State/province |
Barcelona |
| ZIP/Postal code |
08908 |
| Country |
Spain |
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| Platforms (1) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA433091 |
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