Different types of imagery data available in TCGA

Question

[kountaydwivedi]

Hey to everyone,

I was exploring the GDC portal in order to download certain whole slide images for training a deep network for BRCA classification. However, I came across multiple images corresponding to an individual patient. For instance: Case id: TCGA-AN-A046 comprise 3 slide images -- TCGA-AN-A046-01Z-00-DX1, TCGA-AN-A046-01A-02-BS2, TCGA-AN-A046-01A-01-BS1.

My question is -

1. What is the significance of these different images?
2. Which image is utilised for histopathological classification?
3. How are these images different from one another?

Thank you.

Answer 1

[Zhenyu Zhang]

If you have used the GDC portal to query for these images, it's clearly labelled as different "Experimental Strategy" in the repository. Some are tissue slides and some are diagnosis slides.

From the file names, DX are likely diagnosis and BS are tissue slides. But this is only TCGA convention, and I suggest you follow the GDC "Experimental Strategy"

As to the question of why there are multiple tissue slides? because often multiple were taken

[kountaydwivedi]

Thank you so much for your answer.