Testing for genetic differences that lead to well characterized diseases are better done methods other than sequencing. Methods such as real time PCR and microarray analysis costs large amounts of money to set up and validate but are much cheaper once they are up and running. This is why places like 32andme are $400 and not $1000s.
The power of next gen sequencing like ion torrent is that you can go fishing for things you don't know about. Deep sequencing is a good example. Many cancers result from spontaneous mutations or chromosomal rearrangements. Catching them early requires identifying sequence differences in a very rare cells. Because Ion torrent and many of the other next gen sequencers are capable of massively parallel sequencing they can sequence regions of DNA prone to rearrangement or oncogenes over and over, finding that one in a 1000 cells, or one in 100,000 cells that is the beginning of cancer.
They can also be used to sequence novel genomes, such as newly emerging strains of pathogenic E. coli, and find what changes have led to the change.