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Old 03-29-2018, 07:43 AM   #1
lre1234
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Default Somatic mutation calling with out normal samples

Hi all,
I have a question, a collaborator of mine has a set of primary and metastatic tumor samples that they are interesting in doing exome or genome sequencing (not sure which one yet). The issue is that there is only the primary and mets available, and 'normal' tissue (i.e. DNA from blood). This may be a little problematic as we wouldn't necessarily know if a potential mutation is somatic or not. After some investigating, I haven't been able to find other examples (papers) that had similar examples. So my thoughts are two potential options:

1. to simply compare the primary vs the met sample and determine the changes that occurred as the tumor metastasized. Here, we would assume (?) that most variants identified would be germline and we would be interested in only those that are changing between the two samples.

2. use the TCGA as a reference. As they have blood normal samples that were used in the exome-seq, I could get those samples and use a large number of those as a set of "normals" to determine the potential somatic/germline events.

Has anyone every had an issue such as this? and/or would either of these two options be suitable?

Thanks for your advice.
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