Tricky question indeed!))) STR profile of HCT-116 provided by ATCC matches DNA profile of a patient - donor. Strictly the concordance should be 99,9999%. However the cells gain new mutations within long cultivations. This may influence the allele dropout. In fact what have you obseved: allele dropout or some new alleles?

As you will see from the Cellosaurus entry:

http://web.expasy.org/cellosaurus/CVCL_0291

There is quite a lot of variability in the STR profile of HCT-116 mostly due (as the previous answer propose) to allelle dropout.

This is the case for: Amelogenin, CSF1PO, D16S539, D18S51, TH01, TPOX and vWA.

In particular the DSMZ profile of their HCT-116 is quite different from that of ATCC. So it all depend where your cells comes from! 

Best

Amos Bairoch

http://web.expasy.org/cellosaurus/CVCL_0291

good luck