Although the number of non-germline variants found per individual is a very small fraction of the total number of variants per individual (~0.03% for the CEU child and ~0.02% for the YRI child), these variants will not be shared between samples. Assuming that the number of non-germline mutations in these two trios is representative of all cell line DNA we analysed, we estimate that non-germline mutations might constitute 0.36% and 2.4% of all variants, and 0.61% and 3.1% of functional variants, in the low coverage and exon pilots respectively. In larger samples of thousands the overall false positive rates from cell line mutations would become significant, and confound interpretation, suggesting that large scale studies should use DNA from primary tissue such as blood where possible.
