Sunday, July 17, 2011

0.1.116 - It's a Family Affair

Russell: I just ran the newly released Promethease 0.1.116, it's getting better and better. It has me nailed pretty well.

me: I notice your report isn't clear on your ancestry and we now do a better job of that for some reports so in time I'd like to see what I can do to polish up that side of your data. SNPedia has you and your mother publicly, but since you have so many family members privately, take a look at these images from another family which shows where the chromosomes agree between family members. promethease_corpas_family_comparison_newfamily.html

me: Looking at you and your mother genome_Russell_Letkeman_20081023161035_newfamily.html I notice a region of similarity on chromosome 2 with a run of
similarity, and a little red spot on chromosome 11 where you and your mother are quite distinct.

Russell: I'm an identical twin, are they sensitive enough to distinguish us?

me: yes, I think you'll find this article about twins very interesting.

Russell: Wow, if they can distinguish identical twins, that's deep medicine. What about the epigenome? Is any of it sampled?

me: a new sequencer from PacBio exists, it fundamentally sees the epigenome as well as the usual ATCGs

Russell: I read somewhere if the coverage was deep enough you could estimate CNV. Does v3 detect any CNVs?

me: Generally, no. 23andMe does not provide CNV information. we have one CNV which is currently replicable with a SNP gs217 but it's just a test case. We don't yet have any interesting literature except for some horribly obvious birth defects which you don't have. Standard naming is still new.

me: if you want CNVs Complete Genomics will a full genome do for $5k. They have released 57 full genomes and about 7 of those are one large multi-generation family tree. If you can find anything interesting in there then you're ready for $5k per family member for your own.

Russell: You've cover 6k+ snps on my v2 sample. What human mind could learn something that big? And it's just a start. It's going to get weird from here on, my twin became a licensed GP in 2005 and genetics was hardly covered and personal not at all. So the data is coming in faster than the medical profession can keep up with.

me: is the first class anywhere to expose pre-meds to their own genomes. I think it defines the '1st wave of doctors' with genuine exposure to the topic. More will follow every year, but every doctor practicing today, will someday describe themself as 'PRE-' in some way. And if your 6k seems like a lot, consider David Ewing Duncan is now over 20k annotated snps thanks to mixing his 23andMe v2 with Complete Genomics.

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