Difference between capture and WXS

Question

[solo7773]

Hi everyone,

I am currently using R bioconductor package "SomaticCancerAlterations". The info shows sequence sources are either WXS of capture.

Example data is as follows

Cancer_Type Center NCBI_Build Sequence_Source Sequencing_Phase Sequencer

gbm_tcga GBM broad.mit.edu 37 WXS Phase_I Illumina GAIIx

hnsc_tcga HNSC broad.mit.edu 37 Capture Phase_I Illumina GAIIx

kirc_tcga KIRC broad.mit.edu 37 Capture Phase_I Illumina GAIIx

luad_tcga LUAD broad.mit.edu 37 WXS Phase_I Illumina GAIIx

lusc_tcga LUSC broad.mit.edu 37 WXS Phase_I Illumina GAIIx

Could anyone tell my what is "Capture"?

Is "Capture" a subgroup of WXS or WES?

What's the difference and similarity between "Capture" and "WES"?

Thanks in advance.

[WouterDeCoster]

Hello solo7773!

It appears that your post has been cross-posted to another site: https://support.bioconductor.org/p/91391/

This is typically not recommended as it runs the risk of annoying people in both communities.

[solo7773]

Thanks Wouter. I just delete the one in bioconductor

Answer 1

[Brian Bushnell]

Text fields can hold anything, and biologists who enter data into computers are notoriously bad about observing things like "standards" or "schemae". It's likely that WXS, WES, and Capture all mean "Exon Capture", but who knows? Basically, you have to hunt down the person who submitted the data and ask them, if the answer is important. Looks like they're all Broad; possibly, they differentiate between "Capture" and "WXS". I recommend calling and asking, then reporting the result here and accepting it as the answer.

[solo7773]

Dear Brian, thanks a lot. I emailed the author of the R package. Hope he will reply me. I will post and update this once I find out.

[solo7773]

Hi Brian, I've found ways to download the WXS I need from the TCGA GDC. I won't use data from the R package. Thus, my doubt was solved in another way.

Answer 2

[Eric T.]

It looks like the rows you showed here indicate TCGA studies. You can read how their sequencing centers work here. It says that in 2009 some of their centers used target capture panels that did not cover the whole exome, and the whole-exome protocols went into production in 2010. The papers on each of the TCGA studies describe the methods in more detail and should list the captured genes somewhere, if you need that. In any case, I'd take "Capture" to mean a sub-exome panel, and WXS as a synonym for WES, but look for supporting evidence of that assumption.

See a similar question here.

[solo7773]

Dear Etal. Thanks for providing so much details. Indeed it is data from TCGA. According to the R package, they were sequenced by broad. I can find some info from the broad firehose but cannot go further. I Googled capture sequencing. I prefer to agree with you, taking 'capture' as an incomplete exome sequencing.