Cergentis FFPE-TLC sequencing of colorectal carcinoma
In this study, formalin-fixed paraffin-embedded targeted locus capture (FFPE-TLC) sequencing is used as a novel technology for targeted detection of tumor-specific genomic structural variants (SVs) in the primary tumor of 29 colorectal cancer patients with metastatic disease. The tumor region was macrodissected and sequenced for 29 patients, and the "normal" region of the same slide was macrodissected and sequenced for 8 of these patients. SVs were found in the common fragile site (CFS)-associated genes MACROD2, PRKN, FHIT and WWOX as well as SVs caused by three LINE transposable elements. Tumor-specificity of selected SVs was independently verified by droplet digital PCR of tumor tissue DNA and their applicability as plasma circulating tumor DNA biomarkers was demonstrated. This dataset contains the hg19 reference alignment of the FFPE-TLC sequences for all 29 colorectal cancers and 8 adjacent normals.
- 24/07/2024
- 37 samples
- DAC: EGAC00001001051
- Technology: Illumina NovaSeq 6000
Data Access Policy of NKI-AvL TGO
Data Access Policy of NKI-AvL TGO To request access to this specific dataset, and in order to comply with local and (inter)national regulations, please follow the steps described below: 1. Please fill in the information requested on the website: ega.nki.nl 2. Once you’ve submitted this information, the Data Access Committee (DAC) and the NKI-AVL Internal Review Board (IRB) will review your planned study and its goals and judge whether it is competing with our interests. The DAC and IRB can approve or decline your request or request a modification. 3. Upon approval by the IRB, you will receive a Data Transfer Agreement (DTA) that needs to be filled in and signed by the legal representative of your institute / company. 4. Upon acceptance of a signed DTA by our Knowledge Transfer & Contracting Office (KT&C), your party will receive a copy signed by our legal representative, and you will need to submit your access request via the EGA website
Studies are experimental investigations of a particular phenomenon, e.g., case-control studies on a particular trait or cancer research projects reporting matching cancer normal genomes from patients.
| Study ID | Study Title | Study Type |
|---|---|---|
| EGAS50000000427 | Resequencing |
This table displays only public information pertaining to the files in the dataset. If you wish to access this dataset, please submit a request. If you already have access to these data files, please consult the download documentation.
| ID | File Type | Size | Located in | |
|---|---|---|---|---|
| EGAF50000142715 | bai | 3.1 MB | ||
| EGAF50000142716 | bam | 2.8 GB | ||
| EGAF50000142717 | bai | 3.3 MB | ||
| EGAF50000142718 | bam | 2.9 GB | ||
| EGAF50000142719 | bai | 3.5 MB | ||
| EGAF50000142720 | bam | 2.6 GB | ||
| EGAF50000142721 | bai | 3.5 MB | ||
| EGAF50000142722 | bam | 2.5 GB | ||
| EGAF50000142723 | bam | 2.9 GB | ||
| EGAF50000142724 | bai | 3.7 MB | ||
| EGAF50000142725 | bam | 1.4 GB | ||
| EGAF50000142726 | bai | 3.7 MB | ||
| EGAF50000142727 | bam | 2.4 GB | ||
| EGAF50000142728 | bai | 3.8 MB | ||
| EGAF50000142729 | bam | 2.0 GB | ||
| EGAF50000142730 | bai | 4.2 MB | ||
| EGAF50000142731 | bam | 1.6 GB | ||
| EGAF50000142732 | bai | 3.4 MB | ||
| EGAF50000142733 | bam | 2.4 GB | ||
| EGAF50000142734 | bai | 3.5 MB | ||
| EGAF50000142735 | bam | 2.8 GB | ||
| EGAF50000142736 | bai | 3.2 MB | ||
| EGAF50000142737 | bam | 2.7 GB | ||
| EGAF50000142738 | bai | 3.5 MB | ||
| EGAF50000142739 | bam | 2.1 GB | ||
| EGAF50000142740 | bai | 3.1 MB | ||
| EGAF50000142741 | bam | 3.5 GB | ||
| EGAF50000142742 | bai | 3.4 MB | ||
| EGAF50000142743 | bam | 2.4 GB | ||
| EGAF50000142744 | bai | 4.0 MB | ||
| EGAF50000142745 | bam | 2.3 GB | ||
| EGAF50000142746 | bai | 3.4 MB | ||
| EGAF50000142747 | bam | 2.5 GB | ||
| EGAF50000142748 | bai | 3.8 MB | ||
| EGAF50000142749 | bam | 2.5 GB | ||
| EGAF50000142750 | bai | 3.7 MB | ||
| EGAF50000142751 | bam | 2.2 GB | ||
| EGAF50000142752 | bai | 3.9 MB | ||
| EGAF50000142753 | bam | 1.9 GB | ||
| EGAF50000142754 | bai | 3.4 MB | ||
| EGAF50000142755 | bam | 2.9 GB | ||
| EGAF50000142756 | bai | 3.2 MB | ||
| EGAF50000142757 | bam | 4.0 GB | ||
| EGAF50000142758 | bai | 3.5 MB | ||
| EGAF50000142759 | bam | 2.7 GB | ||
| EGAF50000142760 | bai | 3.1 MB | ||
| EGAF50000142761 | bam | 3.8 GB | ||
| EGAF50000142762 | bai | 2.8 MB | ||
| EGAF50000142763 | bam | 7.3 GB | ||
| EGAF50000142764 | bai | 2.8 MB | ||
| EGAF50000142765 | bam | 6.4 GB | ||
| EGAF50000142766 | bai | 3.2 MB | ||
| EGAF50000142767 | bam | 4.0 GB | ||
| EGAF50000142768 | bai | 3.0 MB | ||
| EGAF50000142769 | bam | 5.5 GB | ||
| EGAF50000142770 | bai | 2.9 MB | ||
| EGAF50000142771 | bam | 6.7 GB | ||
| EGAF50000142772 | bai | 3.2 MB | ||
| EGAF50000145192 | bai | 4.2 MB | ||
| EGAF50000145193 | bam | 2.3 GB | ||
| EGAF50000145194 | bai | 4.5 MB | ||
| EGAF50000145195 | bam | 1.8 GB | ||
| EGAF50000145196 | bai | 4.0 MB | ||
| EGAF50000145197 | bam | 2.7 GB | ||
| EGAF50000145198 | bai | 4.0 MB | ||
| EGAF50000145199 | bam | 2.4 GB | ||
| EGAF50000145200 | bai | 3.9 MB | ||
| EGAF50000145201 | bam | 3.0 GB | ||
| EGAF50000145202 | bai | 4.7 MB | ||
| EGAF50000145203 | bam | 844.8 MB | ||
| EGAF50000145204 | bai | 4.1 MB | ||
| EGAF50000145205 | bam | 2.3 GB | ||
| EGAF50000145206 | bai | 3.7 MB | ||
| EGAF50000145207 | bam | 2.7 GB | ||
| 74 Files (109.9 GB) | ||||