Cancer Researcher at Mayo Says Illumina Platform Maxing Out, Looks to BGI/Complete


David Smith, Chairman of the Technology Assessment Committee, Mayo Clinic

Chapters:

Listen (7:21) 80% of oropharyngeal cancers are HPV positive

Listen (4:03) Using long read mate pair sequencing

Listen (4:13) Anticipating the $1,000 assembled genome

Listen (1:33) Oxford Nanopore still a very immature technology

Listen (4:44) How will your research impact treatment?

Listen (1:40) Any push back at Mayo against LDT regulation?

Today we bring you a story which you probably wouldn’t have heard at last week’s AGBT conference at Marcos Island. While PacBio and 10X Genomics were getting most of the buzz at the annual show on all things sequencing, it could be the new BGI/Complete Genomics platform that steals the show later this year, says David Smith, a cancer researcher at the Mayo Clinic.

In his research, David uses sequencing to analyze the connection between the human papillomavirus (HPV) with oropharyngeall cancer.

“A couple decades ago, the incidence of HPV in oropharyngeal cancer was less than 20%. And now at the Mayo Clinic, 80-90% of these cancers are HPV positive,” he says.

Why? A change in sexual practices, David says.

To find out just how HPV causes cancer and integrates into the genome, David is using ‘long read, mate pair’ sequencing. This is a new technology that essentially converts short reads got from such platforms as Illumina’s into long reads. David acknowledges the nice long reads coming from the PacBio machines, but says the cost is still prohibitive. He’s looking for a price that scales into the clinic, and for this, he's most excited about a product that BGI is rolling out later this year, i.e., an already assembled human genome sequencing for $1,000.

We finish the interview with a discussion about how well clinical genomics is being adopted into practice at Mayo.



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