Going Beyond the $1,000 Genome with Mark Gerstein


Mark Gerstein, Co-director of the Yale Computational Biology and Bioinformatics program

Chapters:

Listen 0:00 What is the $1,000 genome missing? (5:47)

Listen 5:47 Pseudogenes and the non coding portion of the genome (2:19)

Listen 8:07 Which sequencing platform, when? (6:08)

Listen 11:48 How best to query big genomics data? (3:58)

Listen 15:46 Privacy the big issue for genomics and society (9:15)

Listen 25:01 The importance of genomics to big data science in general (1:45)

Listen 26:47 A Mars colonizer? (2:10)

Though recent guests at Mendelspod say we're not quite to the $1,000 genome, we're close enough to use that benchmark in genomics discussions. But what are we getting for that almost $1,000?

Mark Gerstein is the co-director of the Yale Computational Biology and Bioinformatics program where he focuses on better annotation of the human genome and better ways to mine big genomics data. He has played a big role in some of the large genomics initiatives since the first human genome project, including ENCODE and the 1,000 Genomes Project.

“I’m very enthusiastic, of course, about the thousand dollar genome, but I don’t think that a true human genome has arrived for a thousand dollars,” Mark says at the outset of today’s interview. "The great excitement of next generation sequencing—which is deserved—has also obscured that there are a lot of very deep technical questions in terms of really assembling the tricky parts of the genome and really being able to conceptualize the more complex bits of human genetic variation that need to be tackled.”

So what are those tricky remaining parts? Mark shares his interest into the importance of structural variation, and says there is much more to learn from the overlooked non-coding portion of the genome. He’s particularly interested in pseudogenes.

We took some audience questions for Mark which lead us into a discussion of how best to query and mine big genomics data. As with several other leading bioinformaticians on the show, Mark agrees that privacy is the big issue for genomics and for society at large.



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