Question: Matching TCGA Aliquot ID to UUID or Barcode
0
gravatar for Dario Strbenac
5 months ago by
Dario Strbenac1.5k
Australia
Dario Strbenac1.5k wrote:

Genomic Data Commons hosts a gene-wise copy number summary for each cancer, which has genes as rows and samples as columns. The column headings are aliquot UUIDs. How may these be matched to other data types, such as a MAF file of SNVs which contains TCGA barcodes as the sample identifier?

ADD COMMENTlink modified 4 months ago by Marcel Ramos ♦♦ 410 • written 5 months ago by Dario Strbenac1.5k
Answer: Matching TCGA Aliquot ID to UUID or Barcode
3
gravatar for Marcel Ramos
4 months ago by
Marcel Ramos ♦♦ 410
United States
Marcel Ramos ♦♦ 410 wrote:

Hi Dario, Thanks for your question. I've added support for this in TCGAutils 1.5.5.

library(TCGAutils)
UUIDtoBarcode("d85d8a17-8aea-49d3-8a03-8f13141c163b", "aliquot_ids")
#>            analytes.aliquots.aliquot_id analytes.aliquots.submitter_id
#> 13 d85d8a17-8aea-49d3-8a03-8f13141c163b   TCGA-CV-5443-01A-01D-1510-01

Created on 2019-07-17 by the reprex package (v0.3.0)

ADD COMMENTlink written 4 months ago by Marcel Ramos ♦♦ 410

Hi, thank you very much for this library.

I seem to have noticed a mismatch on some UUID when converting from file_id. For example, '56467ebd-af89-4413-84b5-1e00699a2744' returns 'TCGA-2L-AAQM-01A-11D-A396-01' but the GDC portal returns 'TCGA-IB-A5SO' instead. I am converting the masked copy number segment data and I noticed that a number of these mismatch comes from those cases with multiple aliquots. Could you confirm this or perhaps I have done something wrong?

My code is simply: UUIDtoBarcode('56467ebd-af89-4413-84b5-1e00699a2744', fromtype = "fileid")

Thank you in advance.

ADD REPLYlink written 7 weeks ago by e03382720

Hi e0338272, Thank you for your report. I will look into this today. It seems like the function should be returning multiple identifiers. I'll check the package's tests. Follow this issue for updates: https://github.com/waldronlab/TCGAutils/issues/24 Best, Marcel

ADD REPLYlink written 7 weeks ago by Marcel Ramos ♦♦ 410

It seems the UUID you have '56467ebd-af89-4413-84b5-1e00699a2744' is the file ID that contains multiple Barcodes (https://imgshare.io/image/vYlHe)

ADD REPLYlink modified 7 weeks ago • written 7 weeks ago by Tiago Chedraoui Silva240

Thanks this has been fixed.
-Marcel

ADD REPLYlink written 7 weeks ago by Marcel Ramos ♦♦ 410
Answer: Matching TCGA Aliquot ID to UUID or Barcode
1
gravatar for Tiago Chedraoui Silva
5 months ago by
Brazil - University of São Paulo/ Los Angeles - Cedars-Sinai Medical Center
Tiago Chedraoui Silva240 wrote:

In TCGAbiolinks, when reading the copy number data we use the GDC API to map the aliquot id to barcode: https://github.com/BioinformaticsFMRP/TCGAbiolinks/blob/master/R/prepare.R#L1182-L1211

ADD COMMENTlink written 5 months ago by Tiago Chedraoui Silva240
1

It looks like the function takes a barcode as input and returns the aliquot ID. What about converting an aliquot ID to a barcode?

ADD REPLYlink written 5 months ago by Dario Strbenac1.5k

Hi Dario, I just tested Marcel code and it is working fine. I think that is the easiest way would be using TCGAutils.

From my code you would need to change the filter from barcode to aliquot ID.

https://github.com/BioinformaticsFMRP/TCGAbiolinks/blob/master/R/prepare.R#L1190 -> cases.submitterid to samples.portions.analytes.aliquots.aliquotid. But this would give you all aliquots/barcodes to a patient.

So, Marcel code is a better solution.

ADD REPLYlink written 4 months ago by tiagochst150

Hi Dario, I just tested Marcel code and it is working fine. I think that is the easiest way would be using TCGAutils.

From my code you would need to change the filter from barcode to aliquot ID.

https://github.com/BioinformaticsFMRP/TCGAbiolinks/blob/master/R/prepare.R#L1190 -> cases.submitterid to samples.portions.analytes.aliquots.aliquotid. But this would give you all aliquots/barcodes to a patient.

So, Marcel code is a better solution.

ADD REPLYlink written 4 months ago by tiagochst150

Hi Dario, I just tested Marcel code and it is working fine. I think that is the easiest way would be using TCGAutils.

From my code you would need to change the filter from barcode to aliquot ID.

https://github.com/BioinformaticsFMRP/TCGAbiolinks/blob/master/R/prepare.R#L1190 -> cases.submitterid to samples.portions.analytes.aliquots.aliquotid. But this would give you all aliquots/barcodes to a patient.

So, Marcel code is a better solution.

ADD REPLYlink written 4 months ago by tiagochst150

Hi Dario, I just tested Marcel code and it is working fine. I think that is the easiest way would be using TCGAutils.

From my code you would need to change the filter from barcode to aliquot ID.

https://github.com/BioinformaticsFMRP/TCGAbiolinks/blob/master/R/prepare.R#L1190 -> cases.submitterid to samples.portions.analytes.aliquots.aliquotid. But this would give you all aliquots/barcodes to a patient.

So, Marcel code is a better solution.

ADD REPLYlink written 4 months ago by tiagochst150
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