Does anybody have experience with (or know of anybody) performing whole genome sequencing (WGS) of genetically matched (i.e., from the same individual) peripheral blood leukocyte vs lymphoblastoid cell line samples as constitutive tissue controls for tumors WGS? Unfortunately, we are in a position where we do not have matching PBL for all tumor samples, but (fortunate to?) have immortalized LBCLs. How good of a surrogate are the LBCLs for such studies if no PBL Is available? In addition to SNVs I am particularly concerned about possible differences in CNVs.
For analyzing the data, a lymphoblastoid cell line would not be a useful control for WGS; you wouldn't be able to subtract out all the unimportant SNVs in the patient's germline DNA. If you can get any other tissue from the patient to use as germline, that would work -- it doesn't need to be the same tissue if you're not doing a gene expression study.
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