Clarification for TCGA data

Posted in TCGA data on the CGC by Maor Maor Thu Jul 19 2018 20:13:54 GMT+0000 (Coordinated Universal Time)·1·Viewed 2,605 times
I have trouble matching WSI slides to their grade, or TNM. For example, patient: TCGA-BC-A110 has three slide samples: Sample TCGA-BC-A110-01Z (Primary Tumor) Sample TCGA-BC-A110-01A (Primary Tumor) Sample TCGA-BC-A110-11A (Normal tissue) Question 1: Is it correct samples ending with A were all sampled together? Question 2: Can I know which were sampled first? Samples ending with A, or Z? [Pathology report exist only for A, with conclusion of Grade I. Clinical file nationwidechildrens.org_clinical.TCGA-BC-A110.xml states patient had cancer with grade I, and later a reoccurence. It means A is the first tumor event, and Z the second?] Question 3: I noticed pathology reports are never available for Z samples, and only for A. Is there a reason?
July 25, 2018

Hello,

Based on our understanding of the method that TCGA used for collecting these samples (see reference paper here[url=https://onlinelibrary.wiley.com/doi/full/10.1002/path.5028]), two types of slides generally were generated: diagnostic slides and tumor analysis slides. One diagnostic slide contains a tumor sample for histologic diagnosis. The same tumor then is sectioned, and the top and bottom sections are used to make top and bottom tissue slides for the purpose of determining the ratio of tumor to necrotic cells to confirm that there is enough genetic material for tumor analysis. The middle section is used for molecular analysis. Matched tumor normal samples also were collected.

Regarding your questions about these specific files, the following is our understanding of their origin:

  1. TCGA-BC-A110-01Z and TCGA-BC-A110-01A are samples taken from the same tumor tissue.
  2. TCGA-BC-A110-01Z was used to make a diagnostic slide (TCGA-BC-A110-01Z-00-DX1), so no molecular analysis was performed on this sample.
  3. TCGA-BC-A110-01A was used to make top and bottom tissue slides (TCGA-BC-A110-01A-01-TS1 and TCGA-BC-A110-01A-01-BS1) and to generate the middle section used for all analysis of the tumor.
  4. There also is a top slide (TCGA-BC-A110-11A-01-TS1) for the matched normal tissue (TCGA-BC-A110-11A) for tumor sample TCGA-BC-A110-01A.

We hope this information is helpful. If you have further questions regarding how TCGA samples were prepared or how they are annotated, the GDC Help Desk ([email protected]) or the authors of the relevant TCGA pathology studies may be able to provide further information.

Best,
Marija

  
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