Frequently Asked Questions

1. Is patient follow-up a one-time occurrence or repeated? 

• • Routine follow-up is conducted for patients and involves multiple contacts. Patients are periodically contacted, typically every 6-12 months, through phone calls or scheduled clinic visits. In the event of a patient passing away during this follow-up period, data may be obtained from their family to ensure comprehensive medical record-keeping. 

2. Why is the follow-up period for survival set at 59 months (5 years)?

• • The statement implies that the 59-month (5-year) endpoint is intentionally selected for conducting survival follow-up assessments. This particular time point is significant as it serves as a standard reference for evaluating patient survival outcomes within the dataset. By focusing on the 5-year mark, researchers can assess the long-term survival rates of patients and analyze any trends or patterns that may emerge over this period.

3. Does a 59-month survival time with a deceased marker indicate uncertainty about the exact survival duration?  

• Yes. In such cases, while we know the patient passed away, the precise time of death is undetermined. The 59-month mark signifies they survived at least 5 years, but the actual survival time may differ. 

4. Why do multiple patients share a 59-month survival time? 

• In the dataset, multiple patients share a 59-month survival time due to the nature of the 5-year endpoint. Some patients are marked as having survived 59 months, signifying they were alive at the 5-year mark. It's recommended to reclassify categories to differentiate between "alive at a 5-year time point," "dead before a 5-year time point," and "dead after a 5-year time point" to avoid confusion.

5. Do patients with a 59-month survival time live longer than 5 years? 

• Yes, a 59-month survival time indicates a patient lived at least 5 years. It's possible they survived even longer.   For example, some patients may have survived beyond the 5-year follow-up period, but we weren't able to track them for the entire duration.

6.  Does the follow-up data include information on recurrence within the first 5 years after surgery, and if so, when is this data available?  

• •  Recurrence-free 5-year survival data is available upon request, though some curation is required. The "metachronous/synchronous CRC" column provides details on "local" recurrences. Refer to the dataset documentation for specific criteria regarding these classifications. 

7. Is the classification of metachronous-synchronous based on standardized criteria within the cohort?

• Yes, the classification is based on specific criteria:

  • Metachronous CRC: Two or more CRC tumors diagnosed > 12 months apart.

  • Synchronous CRC: Two or more CRC tumors diagnosed < 12 months apart.

• The starting point for this decision is consistent and does not significantly change from case to case. It is based on when patients present to the clinic/hospital.

8.  Does Metachronous CRC only provide information on local recurrences?

• Yes, the "Metachronous CRC" column in the dataset primarily focuses on local or locoregional recurrences of colorectal cancer (CRC). These are tumors that reappear in the same area or nearby lymph nodes after initial treatment.

• However, we do collect data on distant metastasis as well. This information can be found in a separate table called the "Metastasis Details Table" included within the recently uploaded "MCO data dictionary."  The data dictionary provides additional details about the various data points within our dataset.

9. Can we access the "Metastasis Details Table" to learn about distant metastasis information? 

• Yes, the "Metastasis Details Table" contains information on distant metastasis. However, it's important to note that the information is considered unreliable. Ongoing evaluation of biospecimens is conducted to identify recurrent traits, and ethical considerations apply to the access and use of this information. Some columns related to metastasis details may be removed in the future to prevent potential misunderstandings.

10. Is detailed information on recurrence timing available (e.g., after surgery, after therapy)? 

• Yes, detailed information on recurrences is available, but it is considered unreliable. Frequent evaluation of biospecimens is conducted to identify recurrent traits. Ethical considerations apply to the use of this information, and there's a possibility of removing these columns in the future to avoid potential misunderstandings.

11. Why isn't recurrence risk explicitly considered in the data? 

• There are two main reasons why recurrence risk isn't explicitly factored into the data we present:

  • Missing Data: In some cases, information about recurrence may be missing from patient records. This "blank" data indicates that the recurrence status is unknown for those patients.

  • Evolving Landscape: The group of patients experiencing recurrence is generally considered high-risk. Treatment guidelines and recommendations for this group have changed more significantly over time compared to lower-risk groups. These changes in treatment plans can affect how recurrence is reported and tracked, making it challenging to present a fully reliable picture of recurrence risk across the entire dataset.

12. Does "probable recurrence within 5 years" mean the cancer is likely a recurrence of colorectal cancer? 

• The term "probable recurrence within 5 years" indicates a likelihood that the tumor is a recurrence of previously diagnosed colorectal cancer. However, distinguishing between a true recurrence and an independent new tumor is challenging, especially in hereditary cases. Consideration should be given to excluding cases marked as "probable recurrence: NO" from recurrence analysis, especially if there's a possibility of a hereditary link .

13. Can you determine if a death classified as "Vital Status - Dead" was caused by colorectal cancer?

• Yes. The file named "Curated_demographics_birth_death_data_Survival_merged.xlsx" contains information on the cause of death, reported by either a relative or a clinician. While confirmation through death index data is not available, attempts were made to gather this information. 

14. Can we explore details on cancer deaths and their causes to exclude patients who died from unrelated causes? 

• Yes. The file named "Curated_demographics_birth_death_data_Survival_merged.xlsx" allows examination of this information to potentially exclude patients whose deaths were unrelated to cancer.  

15. Does the sample data include the actual results of tests like CIMP, BRAF, KRAS, and MSI? 

• The "z_JJ_MCO_Experimental_Full_Raw_2021" file contains the results for these molecular tests in the "Result" column. An empty field indicates that the test result is not available. 

16. Can there be multiple specimens from the same patient, and do they originate from different tumors? 

•  Yes, there may be multiple specimens from a single patient. The origin of these specimens can be determined by examining the clinical data, which details tumor characteristics. The distinction between "TestSpecimen as MCO Number" and "TestSpecimen as see individual assays" may be clarified by referring to the original and the corrected versions of the table. Rows with "FinalCall" typically signify finalized results. 

17. Was the dataset compiled with a focus on hereditary cancer, particularly Lynch Syndrome? How are MSI and MSS tumors distributed within the data? 

• There was indeed a focus on hereditary cancer, at least for a period. It is advisable to assess whether this might introduce a temporary bias within the dataset. A comprehensive understanding of hereditary cancer cases necessitates examining the distribution of MSI (Microsatellite Instability) and MSS (Microsatellite Stable) tumors. 

18. Were APC mutations assessed, and what is the extent of their presence in the dataset?

• APC mutation analysis was conducted, but it was limited to only 8 samples in the dataset.

19. How do we determine which treatment a patient received, considering the presence of "Cancer Treatment Type,"                        "Therapy Intent," and "Therapeutic Dose Given"? 

• "Cancer Treatment Type" indicates the type of therapy initiated, but it's possible that the treatment was discontinued prematurely, particularly for chemotherapy. "Therapeutic Dose Given: NO" signifies early termination of chemo- or radiotherapy. Patients assigned "surgery only" might have refused chemotherapy, potentially impacting their risk of recurrence.  Treatment guidelines also evolve over time, which can influence the therapy chosen for a specific patient/tumor. 

20. Is there a systematic difference between "unknown" and "not applicable"?

• Yes. "Not applicable" indicates that the information was purposefully not collected, whereas "unknown" implies that the information should have been collected but could not be documented.  In most cases, an "empty" field is equivalent to "not applicable." There are rare instances where empty values could represent either "unknown" or "not applicable," such as in recurrence data. 

21. Are microscopic slides exclusively prepared from entire tumors, or can they also originate from biopsy specimens? 

• Samples used to create slides can be collected before treatment commences. These samples may include diagnostic biopsies, biopsies obtained during surgery, or whole tumor samples removed during surgery. Notably, in instances where neoadjuvant therapy is administered, the slide will be derived from a biopsy specimen. 

22. Does the "MSI" column represent the result of the assessment of all analyzed individual genomic loci?

• Yes. The "MSI" column provides a comprehensive summary of the evaluation conducted on individual marker repeats. Results displayed in columns like "MLH1" and "MSH2" represent immunohistochemistry (IHC) stains or the outcomes of gene analyses.

  23. For certain Patient IDs, there appear to be conflicting results for "MSI Stable" and "MSI Unstable."  Is there a                                  definitive outcome for these cases? 

• In such scenarios, where a Patient ID has results for both "MSI Stable" and "MSI Unstable," the patient should be classified as "MSI Unstable" provided the "MSI final call status" is marked as "YES.".

24. If a Patient ID has multiple corresponding images, can the MSI status be applied to all the available images? 

• Yes. The MSI status can be confidently mapped to all the images available for a particular Patient ID. 

25. Why is there no corresponding image data for 62 patients with reported MSI status? 

• The image data for these specific patients has been excluded due to poor quality. 

26. Which scanner was used to capture MCO-CRC case images?

• Aperio XT scanners, presently owned by Leica, were used to scan the MCO-CRC images. Further details can be found by visiting the Analytical Light Microscopy Facility.

     27. Is it mandatory to obtain ethics approval before being granted access to the data? If so, what is the typical timeframe for acquiring such approval? 

•  Yes, securing ethics approval is a mandatory requirement for data access. The approval process typically takes 2-3 weeks, although it is possible to obtain approval in a shorter timeframe depending on the specifics of the project.  For comprehensive information, please refer to the SREDH Consortium Governance documentation.