Can ExAC database be used to filter out variant with MAF >1%?

Question

[ShahiRB]

Hi there,

Some input needed:

1. Can ExAC database be used to filter out variant with MAF >1% as we do with1000G, ESP, CG etc?
2. 7,601 exomes from TCGA were also included in ExAC data-set. Do they mean exomes of healthy samples/individuals from TCGA study?

Thanks!

Answer 1

[SteveL]

1. I don't see why not - while there will be a few rare variants that may be enriched due to the datasets incorporated, they should still be very rare within the whole dataset.
2. I am not sure about this one, but I would guess they were the germ-line (i.e. non-cancer) samples, and can thus be regarded as healthy, unless there were any hereditary cancers in there - but again any rare variants that are enriched should still be swamped within the whole dataset. IMHO.