Hi I want to check the mutations from one disease cell line, that sequenced by exome seq. I don't have other normal control sample. Is that possible to figure out the disease related mutations? Thanks!
If these are human cell lines, you can compare to 1000genomes, dbSNP, and the NHLBI exome variant server as controls. Depending on your analysis pipeline for variant annotation, you can (and should) incorporate all of these datasets. You would align your sequence data to hg19.
EDIT: Although, the usefulness of these data as controls will really depend on what your research question is, and whether or not your technique of inducing a cell line might also induce mutations and genomic rearrangements -- you may need to include exomes of other cell lines developed under the same protocol too. Also (again depending on what you are looking for) parental samples may also be very helpful in evaluating the variants you do find.
To add to the above it depends on the nature of the disease. Is this a complex disease that may have multiple variants associated? If so then n=1 really tells you nothing. It will be virtually impossible to associate which of the private/rare variants are disease related, let alone the more common ones that may be involved. If, on the other hand, you are dealing with a rare, mendelian, recessive disorder the number of homozygous and compound heterozygous variants unique to the individual with low minor allele frequencies may be quite small.
Speaking from personal experience however, this may not always be the case. Keep in mind that you will also not sequence all targeted exons due to capture failure and GC content. Some will have zero coverage, others will have low enough coverage (< 5x) in some regions that no variants will be called.
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What species are you working in? If these are human cell lines, there are publicly available control data.
Yes. they are human patient
Do you mean I can use hg19 genomic reference?
Just a comment and not terribly constructive, but an n=1 experiment is likely to be quite challenging to use to define "disease related mutations." Despite any databases of normal variants, there will still likely be many variants that are unaccounted for and having a strategy for following up on those will be important.