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 | ||
| Batch7_21JAN2025 | 178 | 164 | Finish | YES | ||
| Batch8_09JUNE25 | 170 | Finish | ||||
| Total | 2607 | 2411 | ||||
| Total_unique | 2575 |
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 |
| Batch3_31MAR2025 | 59 | |||
| Total | 1533 | 1467 |
Total number of samples with WES and RNAseq:
| Patient_number | MRN_Number (mapped) |
| 1278 | 1223 |
Last Updated: 07/03/2025
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Clinical Data:
Clinical information is not available for all cases.
The available clinical data fields are as follows:
- mrn (MRN) – Note: MUST include leading zero/s Validation: number Field type: text
- name_first (First Name) – Note: pulled from Epic Field type: text
- name_last (Last Name) – Note: pulled from Epic Field type: text
- dob (Date of Birth) – Note: pulled from Epic Validation: date_mdy Field type: text
- sex (Sex) – Note: pulled from Epic Choices: female, Female | male, Male Field type: radio
- ethnicity (Ethnicity) – Note: pulled from EPIC Choices
- race (Race) – Note: pulled from Epic Choices
- natera_portal_patient_id (Natera Portal Patient ID) – Note: used for WES/WGS matching Validation: integer Field type: text
- intercept_site_group (INTERCEPT Site Group) – Note: primary tumor site (programmatic metric) Choices: 1, Colon/Rectum (any variation) | 3, Anus | 4, Appendix | 5, Pancreas | 6, Small Intestine (Duodenum/Ampulla of Vater, Jejunum, Ileum) | 7, Bile Duct (Cholangiocarcinoma) | 8, Gallbladder | 9, Stomach (Gastric/Gatroesaphogeal) | 10, Unknown Primary / CUP | 77, Other | 99, Colorectal Monitoring-metastatic palliative/IO treatment Field type: dropdown
- notice_stop_data (<div class=”rich-text-field-label”><h3 style=”text-align: center;”><span style=”background-color: #f8cac6;”>Enter <span style=”text-decoration: underline; font-weight: normal;”>ONLY</span> Natera tissue and blood data.</span></h3></div>) – Field type: descriptive
- consent_date (Date Consent Signed) – Validation: date_mdy Field type: text
- oncore (OnCore Seq#) – Field type: text
- age_current (Current Age) – Note: calculated field Choices: rounddown(datediff([dob], ‘today’, ‘y’)) Field type: calc
- demo_com (Demographics Comments) – Field type: text
- diag_index_date (Date of Diagnosis/Recurrence) – Validation: date_mdy Field type: text
- diag_initial_recur (Was this the initial diagnosis or a recurrence?) – Choices: 1, Initial | 2, Recurrence Field type: radio
- site_primary (Primary CRC Site/s) – Note: select all that apply Choices: 1, Ascending colon (including cecum) | 2, Transverse colon (including hepatic and splenic flexures) | 3, Descending colon | 4, Sigmoid colon | 5, Rectum | 6, Rectosigmoid junction | 7, Overlapping or multiple sites Field type: checkbox
- diag_secondary (Is there a secondary malignancy diagnosis?) – Field type: yesno
- diag_secondary_date (Date of Secondary Malignancy Diagnosis) – Validation: date_mdy Field type: text
- site_secondary (Secondary Malignancy Site/s) – Note: select all that apply Choices: 1, Colon (any variation) | 2, Rectum | 3, Anus | 4, Appendix | 5, Pancreas | 6, Small Intestine (Duodenum, Jejunum, Ileum) | 7, Bile Duct | 8, Gallbladder | 9, Stomach | 99, Other Field type: dropdown
- notice_staging (<div class=”rich-text-field-label”><h3><span style=”background-color: #f8cac6;”><span style=”text-decoration: underline;”>DO NOT </span>enter <span style=”font-weight: normal;”>pathologic staging</span> from pathology reports.</span></h3></div>) – Field type: descriptive
- clin_t (Clinical Staging – T) – Note: only for rectal patients Choices: 10, T0 No evidence of primary tumor | 11, Tis Carcinoma in situ, intramucosal carcinoma (involvement of lamina propria with no extension through muscularis mucosae) | 12, T1 Tumor invades the submucosa (through the muscularis mucosa but not into the muscularis propria) | 13, T2 Tumor invades the muscularis propria | 14, T3 Tumor invades through the muscularis propria into pericolorectal tissues | 18, T3a < 1 mm extension (rectal) | 19, T3b 1-5 mm extension (rectal) | 20, T3c 5-15 MM extension (rectal) | 21, T3d > 15 mm extension (rectal) | 15, T4 Tumor invades the visceral peritoneum, or invades or adheres to adjacent organs or structures | 16, T4a Tumor invades through the visceral peritoneum (including gross perforation of the bowel through tumor and continuous invasion of tumor through areas of inflammation to the surface of the visceral peritoneum) | 17, T4b Tumor directly invades or adheres to adjacent organs or structures | 9, TX Primary tumor cannot be assessed / T unknown | 99, Metastatic only (T and N stages not applicable) Field type: radio
- clin_n (Clinical Staging – N) – Note: only for rectal patients Choices: 3, N0 No regional lymph node metastasis | 4, N1 One to three regional lymph nodes are positive (tumor in lymph nodes measuring ≥0.2 mm), or any number of tumor deposits are present and all identifiable lymph nodes are negative | 5, N1a One regional lymph node is positive | 6, N1b Two or three regional lymph nodes are positive | 7, N1c No regional lymph nodes are positive, but there are tumor deposits | 11, N2 Four or more regional nodes are positive | 12, N2a Four to six regional lymph nodes are positive | 13, N2b Seven or more regional lymph nodes are positive | 15, N+ (at least one lymph node is positive, but total number is unknown) | 2, NX Regional lymph nodes cannot be assessed / N unknown | 99, Metastatic only (T and N stages not applicable) Field type: radio
- clin_m (Clinical Staging – M) – Choices: 14, M0 (Stage I-III, non-metastatic) | 15, M1a-c (Stage IV, metastatic) | 19, MX / M unknown Field type: radio
- site_met (Metastatic Site/s) – Note: select all that apply Choices: 3, Liver | 4, Lung | 5, Anastamotic Site/Peritoneum/Omentum | 7, Pelvis/Abdomen | 6, Lymph Nodes | 99, Other Field type: checkbox
- site_met_other (Metastatic Site/s Other) – Field type: text
- clin_com (Clinical Factors Comments) – Field type: notes
- therapy (Was therapy administered?) – Field type: yesno
- therapy_start (Date Therapy Started) – Validation: date_mdy Field type: text
- therapy_end (Date Therapy Ended) – Note: Enter start date as end date if therapy completed same day. Validation: date_mdy Field type: text
- therapy_date_est (Are therapy start and end dates estimates?) – Field type: yesno
- therapy_type (Therapy Type) – Choices: 1, Chemotherapy | 2, Chemoradiation | 3, Radiation | 6, Ablation | 7, Immunotherapy | 4, Investigational Therapy | 5, Other Field type: radio
- therapy_type_other (Therapy Type Other) – Field type: text
- therapy_agent (Therapy Agent/Drug) – Field type: text
- rt_abl_site (Radiation/Ablation Site) – Choices: 1, Colon | 2, Rectum | 4, Liver | 5, Lung | 6, Adrenal | 7, Distant Lymph Node | 8, Brain | 9, Bone | 11, Peritoneum | 10, Other Field type: checkbox
- rt_abl_site_other (Radiation/Ablation Site Other) – Field type: text
- therapy_com (Therapy Comments) – Field type: notes
- surgery (Was surgical resection performed?) – Field type: yesno
- surg_date (Date of Surgery) – Validation: date_mdy Field type: text
- surg_type (Surgical Procedure Type) – Note: ex: abdominoperineal resection (APR) Field type: text
- surg_site (Surgical Site/s) – Note: Tumor Site Choices: 1, Colon | 2, Rectum | 4, Liver | 5, Lung | 6, Adrenal | 7, Distant Lymph Node (anything not captured by N stage, ex: lymphodectomy) | 8, Brain | 9, Bone | 11, Peritoneum | 10, Other Field type: checkbox
- surg_site_other (Surgical Site Other) – Field type: text
- surg_histology (Surgical Histology) – Note: Histologic Type and Grade Validation: autocomplete Choices: 1, Well differentiated adenocarcinoma | 2, Moderately differentiated adenocarcinoma | 3, Poorly differentiated adenocarcinoma | 7, Metastatic | 6, pCR (pathologic complete response) / no malignancy identified | 4, Mixed | 5, Other Field type: dropdown
- surg_histology_other (Surgical Histology Other) – Field type: text
- surg_lvi (Was lymphatic/vascular invasion (LVI) present?) – Choices: 0, No | 1, Yes | 2, Not Reported Field type: radio
- surg_pni (Was perineural invasion (PNI) present?) – Choices: 0, No | 1, Yes | 2, Not Reported Field type: radio
- surg_trg (Treatment Effect/Pathologic Response) – Note: Treatment Effect Score Choices: 0, score 0-complete response, no viable cancer cells | 1, score 1-near complete response, single or rare small groups | 2, score 2-partial/minimal response, residual cancer with tumor regression | 3, score 3-poor or no response, absent with residual cancer | 4, no known presurgical therapy | 5, unknown / not reported Field type: dropdown
- surg_ln_positive (Number of Regional Lymph Nodes Involved/Positive) – Note: enter 0 if none examined / not reported Validation: integer Field type: text
- surg_ln_removed (Number of Regional Lymph Nodes Examined/Removed) – Note: enter 0 if none examined / not reported Validation: integer Field type: text
- surg_t (Surgical Staging – T) – Choices: 10, T0 No evidence of primary tumor / pCR / no malignancy identified | 11, Tis Carcinoma in situ, intramucosal carcinoma (involvement of lamina propria with no extension through muscularis mucosae) | 12, T1 Tumor invades the submucosa (through the muscularis mucosa but not into the muscularis propria) | 13, T2 Tumor invades the muscularis propria | 14, T3 Tumor invades through the muscularis propria into pericolorectal tissues | 18, T3a < 1 mm extension (rectal) | 19, T3b 1-5 mm extension (rectal) | 20, T3c 5-15 MM extension (rectal) | 21, T3d > 15 mm extension (rectal) | 15, T4 Tumor invades the visceral peritoneum, or invades or adheres to adjacent organs or structures | 16, T4a Tumor invades through the visceral peritoneum (including gross perforation of the bowel through tumor and continuous invasion of tumor through areas of inflammation to the surface of the visceral peritoneum) | 17, T4b Tumor directly invades or adheres to adjacent organs or structures | 9, TX Primary tumor cannot be assessed / T unknown | 99, Metastatic resection only (T and N stages not applicable) Field type: radio
- surg_n (Surgical Staging – N ) – Choices: 3, N0 No regional lymph node metastasis / pCR / no malignancy identified | 4, N1 One to three regional lymph nodes are positive (tumor in lymph nodes measuring ≥0.2 mm), or any number of tumor deposits are present and all identifiable lymph nodes are negative | 5, N1a One regional lymph node is positive | 6, N1b Two or three regional lymph nodes are positive | 7, N1c No regional lymph nodes are positive, but there are tumor deposits | 11, N2 Four or more regional nodes are positive | 12, N2a Four to six regional lymph nodes are positive | 13, N2b Seven or more regional lymph nodes are positive | 15, N+ (at least one lymph node is positive, but total number is unknown) | 2, NX Regional lymph nodes cannot be assessed / N unknown | 99, Metastatic resection only (T and N stages not applicable) Field type: radio
- surg_m (Surgical Staging – M) – Note: select M1 if M1a-c staging is not reported Choices: 14, M0 No distant metastasis by imaging, etc, no evidence of tumor in distant sites or organs. (This category is not assigned by pathologists.) | 15, M1 Metastasis to one or more distant sites or organs, or peritoneal metastasis is identified | 16, M1a Metastasis to one site or organ is identified without peritoneal metastasis | 17, M1b Metastasis to two or more sites or organs is identified without peritoneal metastasis | 18, M1c Metastasis to the peritoneal surface is identified alone or with other site or organ metastases | 19, MX / M unknown | 20, Primary resection only (M stage not applicable) Field type: radio
- surg_tnm (Surgical Staging – TNM) – Choices: 20, Tis N0 M0 (0) / pCR / no malignancy identified | T1, T1/T2 N0 M0 (I) | 21, T3 N0 M0 (IIA) | 22, T4a N0 M0 (IIB) | 23, T4b N0 M0 (IIC) | 36, Stage II (T3-4, N0, M0) | 24, T1-T2 N1/N1c M0 (IIIA) | 25, T1 N2a M0 (IIIA) | 26, T3-T4a N1/N1c M0 (IIIB) | 27, T2-T3 N2a M0 (IIIB) | 28, T1-T2 N2b M0 (IIIB) | 29, T4a N2a M0 (IIIC) | 30, T3-T4a N2b M0 (IIIC) | 31, T4b N1-N2 M0 (IIIC) | 37, Stage III (T1-4, N1-2 / N+, M0) | 32, Any T Any N M1a (IVA) | 33, Any T Any N M1b (IVB) | 34, Any T Any N M1c (IVC) | 38, Stage IV (IVA-IVC) | 35, Stage unknown Field type: radio
- surg_pathreport (Pathology Report Upload) – Field type: file
- surg_com (Surgical Comments) – Field type: notes
- recur_date (Date of Recurrence) – Validation: date_mdy Field type: text
- recur_site (Recurrence Site/s) – Note: check all that apply Choices: 1, Anastamotic Site/Peritoneum/Omentum | 2, Lymph Nodes | 4, Lung | 5, Liver | 9, Pelvis | 10, Abdominal Wall | 11, Local (regrowth at primary site) | 8, Other Field type: checkbox
- recur_site_other (Recurrence Site Other) – Field type: text
- recur_confirm (Recurrence Method of Confirmation) – Note: check all that apply Choices: 2, Radiographic (imaging) | 3, Biopsy | 4, Surgery | 5, Other Field type: checkbox
- recur_confirm_other (Recurrence Method Other) – Field type: text
- recur_com (Recurrence Comments) – Field type: notes
- imaging_date (Imaging Date) – Validation: date_mdy Field type: text
- imaging_type (Imaging Type-modality and body structure) – Note: ex: CT Chest Abdomen Pelvis Field type: text
- imaging_interp (Imaging Interpretation) – Choices: 0, No Evidence of Disease | 1, Evidence of Disease/Stable Disease | 2, Equivocal | 88, Other Field type: radio
- imaging_interp_other (Imaging Interpretation Other) – Field type: notes
- natera_tissue_date (Date Natera Tissue Collected ) – Validation: date_mdy Field type: text
- natera_tissue_sxacc (Natera Tissue Surgical Accession Number (MDA#)) – Note: S-YY-NNNNNN, SYY-NNNNNN, or OUTSIDE Field type: text
- natera_tissue_site (Natera Tissue Site) – Note: site of tissue tested by Natera Choices: 1, Primary | 3, Liver | 4, Lung | 5, Peritoneal | 99, Other (primary or metastasis) | 101, Metastasis-will remove choice in future Field type: dropdown
- res_tissue_date (Date Research Tissue Collected) – Validation: date_mdy Field type: text
- res_tissue_sxacc (Research Tissue Surgical Accession Number) – Note: from pathology report YY-NNNNNN Field type: text
- res_tissue_site (Research Tissue Site) – Choices: 1, Colon (any variation) | 2, Rectum | 3, Liver | 4, Lung | 5, Anastamotic Site/Peritoneum/Omentum | 7, Pelvis | 6, Lymph Node | 99, Other Field type: dropdown
- res_tissue_other (Research Tissue Site Other) – Field type: text
- res_tissue_source (Research Tissue Sample Source) – Choices: 1, FFPE block collected under PA18-1171 | 2, Slides from archived tissue | 3, Tissue sample not collected Field type: checkbox
- res_tissue_blocktid (Research Tissue FFPE Block TID) – Field type: text
- res_tissue_shipbill (Research Tissue Ship/Bill) – Note: KA-for tracking and reporting Field type: text
- res_tissue_none (Research Tissue Not Collected Reason) – Choices: 1, MDA tissue not available | 2, Insufficient tumor viability (< 30%) / pCR / no malignancy | 3, Patient on Follow Up/Off Study | 4, Sufficient MDA archived tissue available by request Field type: dropdown
- tissue_com (Tissue Samples Comments) – Field type: notes
- natera_blood_date (Date Natera Blood Drawn) – Validation: date_mdy Field type: text
- natera_blood_result_desc (Signatera Result Description) – Choices: 0, Negative | 1, Positive | 2, Cancelled (tissue QNS, blood issues, other) Field type: radio
- natera_blood_result_value (Signatera Result Value (MTM)) – Validation: number_2dp Field type: text
- res_blood_date (Date Research Blood Drawn) – Validation: date_mdy Field type: text
- res_blood (Was Research Blood Collected?) – Field type: yesno
- res_blood_datediff (<div class=”rich-text-field-label”><p><span style=”color: #e67e23;”>*IGNORE*</span> Months since Research Blood Collection</p></div>) – Note: calculated field for reporting Choices: datediff (([res_blood_date]), ‘today’, ‘M’, ‘MDY’) Field type: calc
- res_blood_zcode (Z-Code/s Collected) – Choices: 1, PA181171 | 2, PA181171BANK | 3, PA181171NEOG | 4, PA181171PERS Field type: checkbox
- res_blood_tp (Research Blood Contract Timepoint) – Choices: T1, T1 | T2, T2 | T3, T3 | T4, T4 | T5, T5 | T6, T6 | T7, T7 | T8, T8 Field type: dropdown
- res_blood_shipbill (Research Blood Ship/Bill) – Note: KA-for tracking and reporting Field type: text
- res_blood_shipbill_gh (Guardant Health Blood Ship/Bill) – Note: KA-for tracking and reporting Field type: text
- res_blood_com (Research Blood Comments) – Field type: notes
- status_rev_date (Date Patient Last Reviewed) – Note: date patient record last reveiwedby team Validation: date_mdy Field type: text
- status_pt (Patient Status) – Choices: 0, On Treatment-curative | 1, On Surveillance and NED | 2, Monitoring-metastatic palliative/IO treatment | 3, Lost to Follow Up/No Recent Appointments | 4, Death Field type: radio
- status_lastappt_date (Date of Last Appointment) – Validation: date_mdy Field type: text
- status_lastimage_date (Date of Last Imaging) – Validation: date_mdy Field type: text
- status_death_date (Date of Death) – Validation: datetime_ymd Field type: text
- status_pt_com (Patient Status Comments) – Field type: notes
- res_status (PA18-1171 OnCore Status) – Note: only for Follow Up and Off Study Choices: 1, Follow Up | 0, Off Study Field type: checkbox
- res_statusfu_date (Date Moved to Follow Up) – Note: date patient moved in OnCore Validation: date_mdy Field type: text
- res_statusfu_reason (Follow Up Reason) – Choices: 0, Stage I (post-operatively without neoadjuvant) | 5, Histology (any other than adenocarcimona) | 12, Residual tumor post curative therapies (no longer curative intent) | 4, Additional cancer diagnosis (any other than CRC) | 13, Completion of 5 yrs surveillance after last curative procedure | 3, Lost To Follow Up (no sample collected in 18 months) | 8, Other | 10, Progression/Recurrence-ONLY FOR CONSENT PRIOR TO 1/19/2024 Field type: dropdown
- res_statusfu_reason_other (Follow Up Reason Other) – Field type: text
- res_statusoff_date (Date Moved to Off Study) – Note: date patient moved in OnCore Validation: date_mdy Field type: text
- res_statusoff_reason (Off Study Reason) – Choices: 6, Death | 7, Ineligible | 9, Patient no longer wanted to participate | 1, Patient withdrew consent | 2, Study Completion | 8, Other | 10, Progression/Recurrence | 0, Stage I (post-operatively without neoadjuvant) | 3, Lost To Follow Up (no sample collected in 18 months) | 4, Additional Cancer Diagnosis (any other than CRC) | 5, Histology (any other than adenocarcimona) Field type: dropdown
- res_statusoff_reason_other (Off Study Reason Other) – Field type: text
- res_status_com (Research Status Comments) – Field type: notes