<p>Dear everyone,</p>

<p>I have been asked to comment on an experiment design that involves WES or WGS of cancer cell lines which lack matched normal.</p>

<p>I know that this design is far from ideal, but I was wondering if there are people who have already stream-lined it (to the extent possible of course). I can think of a couple of common variation filters to keep out the germline variants, but I am not sure how to go beyond.</p>

<p>I am sorry if this is a duplicate question; I couldn&#39;t find a related hit.</p>

<p>Thank you,</p>

<p>Noushin</p>

Since you are asking about cell lines, maybe these have already been sequenced. There are bigger studies I'm aware of:

1. Cancer Cell Line Encyclopedia (CCLE), see http://www.ncbi.nlm.nih.gov/pubmed/22460905  
   Browse and download the data: http://www.broadinstitute.org/ccle/home
2. NCI-60 cell line, see e.g. here: http://www.cbioportal.org/public-portal/study.do?cancer_study_id=cellline_nci60

Then I would check against COSMIC for known somatic mutations. And maybe the cell line in question even has data in COSMIC, see By Sample at http://cancer.sanger.ac.uk/cancergenome/projects/cosmic/