WES and RNAseq data were obtained from FFPE patient samples. Raw data, including WES (paired BAM) and RNAseq (FASTQ) files, were transferred in batches on a quarterly basis.
Data Processing
- WES Data: Processed using either the CGL pipeline (Jianhua Zhang Lab, MD Anderson) or the Consensus Calling pipeline (Wenyi Wang Lab).
- RNAseq Data: Processed by Ganiraju Manyam.
Data Storage
- WES Data:
- Batch1–Batch5: /rsrch5/home/gi_med_onc/GIMO_CRC_CentralizedDataStorage/Natera/
- CGL Results: /rsrch5/home/gi_med_onc/GIMO_CRC_CentralizedDataStorage/ngs_runs/
- Batch6 and beyond: /rsrch9/home/gi_med_onc/GIMO_CRC_CentralizedDataStorage/Natera_DNA/
- CGL Results: /rsrch9/home/gi_med_onc/GIMO_CRC_CentralizedDataStorage/ngs_runs/
- RNAseq Data:
- /rsrch9/home/gi_med_onc/GIMO_CRC_CentralizedDataStorage/Natera_RNA/
Data Access
Results, along with clinical mapping, are available on Foundry under:
/MDACC/Colorectal Cancer: LAB09-0373/09-Projects_with_Multiple_Tumor_Locations/Signatera/WES_RNA
For access requests, please contact Kangyu Lin and cc Scott Kopetz.
Statistics
WES:
| Batch | Patient_number | MRN_Number (mapped) | CGL pipeline status | Consensus Calling pipeline status | CGL results on Foundry | Consensus results on Foundry |
| Batch1_11Nov2022 | 809 | 800 | Finish | Finish | YES | NO |
| Batch2_02Jun2023 | 475 | 473 | Finish | Finish | YES | NO |
| Batch3_19Oct23 | 290 | 289 | Finish | YES | ||
| Batch4_02Feb2024 | 251 | 251 | Finish | YES | ||
| Batch5_24May2024 | 225 | 225 | Finish | YES | ||
| Batch6_15OCT2024 | 209 | 209 | Finish | YES | ||
| Total | 2259 | 2250 |
RNAseq:
| Batch | Patient_number | MRN_Number (mapped) | Expression calling status | Results on Foundry |
| Batch1_07OCT2024 | 998 | 991 | YES | YES |
| Batch2_28OCT2024 | 476 | 476 | YES | YES |
| Total | 1474 | 1467 |
Total number of samples with WES and RNAseq:
| Patient_number | MRN_Number (mapped) |
| 1227 | 1223 |
Last Updated: 3/14/2025