HTAN Datasets to Curate

[ritikakundra]

Listed are the HTAN manuscripts we should curate for cBioPortal:

• [x] -An omic and multidimensional spatial atlas from serial biopsies of an evolving metastatic breast cancer (https://pubmed.ncbi.nlm.nih.gov/35243422/)
• [ ] - Signatures of plasticity, metastasis, and immunosuppression in an atlas of human small cell lung cancer (https://pubmed.ncbi.nlm.nih.gov/34653364/)

[rmadupuri]

SCLC HTAN study from MSK:

@ritikakundra @inodb @sbabyanusha, briefly looking through the second paper in the list, the paper focusses on single cell RNA-sequencing of the tumors.

For data availability,

• There's currently only clinical/some treatment data available in the supplemental files.
• For scRNA-seq, the data is of the format cell * gene (they say 155,098 cells by 23,628 genes - SCLC, LUAD tumors combined). There's no bulk RNA-seq/DNA level data (no MAF, CNA..).
• The level4 scRNA-seq data seems to be available HERE. But could not properly parse the .h5ad files.

Question: Can this study be added to the portal? Should we reach out to the authors for data?

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STATUS: The RU ID to DMP ID mappings provided were not accurate. True mappings were not available unf.

From the author (06/16/22) - I can confirm that multiple HTAN IDs map to the same DMP ID, the reason being is that these samples were not necessarily sent for MSK IMPACT (a prior sample might have been sent). I map the scRNA-seq samples to the closest DMP ID to time of collection. I’m not sure though which samples actually have true matching of MSK IMPACT to the same sample vs MSK IMPACT in a different sample from the same patient. If it helps, I can get the time of collection for all these samples and it can then be cross-referenced with the time of collection of the DMP ID.

Not sure the time of collection would be helpful here unless the sample collection and IMPACT sequencing were done in parallel. Waiting for confirmation from author.

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