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Recent guidance issued by the American College of Medical Genetics emphasizes that the strongest form of evidence supporting causality of a mutation is whether it results in a truncation of the protein (nonsense, frameshift or canonical splice-site mutations), specifically for genes where loss-of-function mutations are known to cause disease (Richards et al., 2015).
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"There may be other factors in the tissue that determine whether the mutation is retained" and whether it triggers a malignancy.
DOI: http://dx.doi.org/10.7554/eLife.00631.001 During evolution, the effect of one mutation on a protein can depend on whether another mutation is also present.
There is an on-going debate regarding whether the CFTR mutation is itself pro-inflammatory or whether the excessive inflammation is secondary to bacterial infection.
Second, whether a mutation is beneficial always — but always — depends on the environment it happens in.
It is unclear whether this mutation is in the 3'UTR or outside the gene since the two annotations we used differed on exactly where exon 15 ends.
Knockout of some of the genes can lead to increase in this ratio that differentiates whether the mutation is bacteriostatic or bactericidal.
Whether this mutation is laboratory derived or is a lineage specific event remains to be determined.
To date it remains unknown whether the mutation is restricted to glial tumor cells.
It will be useful and interesting in the future to explore whether PIK3CA mutation is correlated with tumor grade status.
Further work is required to determine whether this mutation is specifically associated with risk of developing renal cancer.
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CEO of Professional Science Editing for Scientists @ prosciediting.com