The (very rough) process with next-gen sequencing is as follows:

  1. one or more samples are taken from the patient (tumor/normal, peripheral blood, bone marrow, etc.)
  2. the samples are sequenced, this can take different forms, involve different processes, but basically, specific sections of the genome are extracted, amplified, then turned into digital data
  3. the data is aligned to a reference genome
  4. the aligned data is scanned for variants (mutations), often in specific genes, and even specific sites of certain genes. This again involves different methods often used in combination
  5. the variants are partially filtered out automatically (poor quality, bad reads, spurious, synonymous, etc.)
  6. the remaining variants are then reviewed manually, relying on academic papers and historical data
  7. what remains is reviewed again, taking the patient's history into account, and potential targeted treatments are inferred
  8. the patient and his/her doctor make the final decision

So from what I understand, even in an optimal scenario, Watson would be taking care of steps 6 and 7, which represent maybe 15% of the overall time. I believe the article presented here is rather misleading in this regard, as it seems to suggest that Watson would be taking care of the actual sequencing too.

Additionally, I imagine that in most cases some humans would still need to review Watson's data.

What the article doesn't mention either is access to the actual patient data, which in itself is a political and operational problem, not so much a technical one.

Finally, I imagine Watson would infer the individual variant diagnoses from papers, which again, is far easier said than done (though I do believe that would be the point where Watson shines most). Parsing papers reliably for usable data is really, really hard, in no small part because the academic system is antiquated, as are paper formats. Even if you manage that, you still have to figure out whether the papers in question, or their authors, are actually reliable sources. And even then, you will likely end up with conflicting interpretations which will need to be sorted out.

So while a nice fluff piece for IBM, I have serious doubts about the actually meaningful benefits Watson supposedly brings to the table.

To be clear, I do believe that AI/ML can and do really help, and contrarily to what the article might want you to believe, people are already working with/on it. However making Watson look like it will solve all the current problems with cancer care is disingenuous at best.