Study
The evolutionary history of human colitis-associated colorectal cancer
Study ID | Alternative Stable ID | Type |
---|---|---|
EGAS00001003028 | Other |
Study Description
Inflammatory bowel disease confers an increased lifetime risk of developing colorectal cancer (CRC), and colitis-associated CRC (CA-CRC) is molecularly distinct from sporadic CRC (S-CRC). Here we have dissected the evolutionary history of CA-CRC using multi-region sequencing.
Exome sequencing was performed on fresh-frozen multiple regions of carcinoma, adjacent non-cancerous mucosa and blood from 12 CA-CRC patients (n=55 exomes), and key variants were validated with orthogonal methods. Genome-wide copy number profiling was performed using SNP arrays and low-pass whole genome sequencing on archival non-dysplastic mucosa (n=9), low-grade dysplasia (LGD, n=30), high-grade dysplasia (HGD, n=13), mixed LGD/HGD (n=7) and CA-CRC (n=19). Phylogenetic trees were reconstructed, and evolutionary analysis used to reveal the temporal sequence of events leading to CA-CRC.
10/12 tumors were microsatellite stable with a median mutation burden of 3.0 single nucleotide alterations (SNAs) per Mb, around 20% higher than S-CRC (2.5 SNAs/Mb), and consistent with elevated aging-associated mutational ... (Show More)
Study Datasets 4 datasets.
Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data
Dataset ID | Description | Technology | Samples |
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EGAD00001004270 |
Genome-wide copy number profiling was performed using low-pass whole genome sequencing on archival non-dysplastic mucosa (n=9), low-grade dysplasia (LGD; n=30), high-grade dysplasia (HGD; n=13), mixed LGD/HGD (n=7) and CA-CRC (n=19).
|
Illumina NovaSeq 6000 | 81 |
EGAD00001004275 |
Exome sequencing was performed on fresh-frozen multiple regions of carcinoma, adjacent non-cancerous mucosa and blood from 12 CA-CRC patients (n=55 exomes).
|
Illumina Genome Analyzer II | 64 |
EGAD00010001586 |
This data set contains an .Rdata file for all the processed segmentation profiles from 81 lpWGS samples included used in downstream analyses from Github repository Evo_history_CACRC. Lastly, there is an .Rdata object with 50 segmentations for 50 total samples from 25 sporadic SNP adenomas used in the comparison with colitis samples.
|
Low Pass Whole Genome Sequencing (LP-WGS) | 131 |
EGAD00010001587 |
This dataset contains 30 idat files each from 15 SNP array runs on patient colitis-associated colorectal cancer tumours. All phenotypes are cancer. See Baker et al. 2018 Supplementary Table 2 for patient details of 12 tumours used in the analyses in the publication.
|
SNP array | 15 |
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