Knowing More about What We Don’t Know: John McPherson on Cancer Genomics


John McPherson, Genome Technologies Director, Ontario Institute for Cancer Research (OICR)

Chapters:

Listen (1:48) How good are new shortcuts to long reads?

Listen (6:21) Structural variations in cancers under appreciated

Listen (3:21) Why is single molecule sequencing important?

Listen (2:08) How do you decide how much to spend on sequencing to answer a specific question?

Listen (3:35) We know less than we did 5 years ago

Listen (3:00) Clinical genomics in Canada

More than with any other major disease, the understanding and treatment of cancer is being transformed by genomics. And these are early days.

John McPherson has been involved in sequencing since the original Human Genome Project. He now directs the Genome Technologies Program at the Ontario Institute for Cancer Research. John chaired a panel on cancer genomics at the recent AGBT, or Advances in Genome Biology and Technology conference, and shares his thoughts on this year's meeting.

Like many others, John is excited about the new possibilities gained by long read sequencing, particularly in showing structural variations of various cancers.

We ask John which platforms he likes, and most importantly--in this day with increasing sequencing instrument options--how he decides how much to spend on sequencing to answer a specific question.

"Our goal is to be as accurate as we can," he says. "For single nucleotide variants (SNPs), we see about a 93-95% verification rate. And we’re pretty happy with that. The question becomes how many samples you do, and not what you do to a sample. Depending what question you’re asking, the number of samples affects your power overall.”

John works in Ontario. We ask him about the state of clinical genomics in Canada, a country with a single payer system.



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