digitize their DNA before it's too late: a graphical models argument for saving grandma's DNA

[gusl]

Many years ago, I argued to my parents that we should try to digitize their parents' (my grandparents') DNA before they die, because this information could potentially save our lives in the future. It was a complicated argument, and I often doubted myself, because I couldn't remember it all off the top of my head.

I've just realized that our whole argument can be formalized naturally with causal graphical models. (It's also easier to remember this way).

Here's the graph with 4 nodes and 3 edges:

grandma's DNA --> grandma's medical history
grandma's DNA --> my DNA
my DNA --> my medical history

My parents' counter-argument was basically d-separation: "if you can observe your own DNA, then you don't need to know grandma's DNA".


My response:

The real graph actually has one more node and two more edges:

facts about gene expression --> grandma's medical history
facts about gene expression --> my medical history

so "grandma's DNA" and "my medical history" are no longer d-separated given "my DNA".

It seems like an odd thing to add as a node, because these facts never change (only our knowledge of them does), but I think this is a legitimate thing to do as a Bayesian.

Let me give an example of such a possible mechanism:

It is likely that grandma and I share genes and gene-combinations that are rare in the general population. If she had an unusual disease, or an unusual response to a treatment (for which we have little data), we could use her DNA to learn something about the genetic correlates of such reactions.

If we fear that I may exhibit a similar disease/reaction in the future, we could find out if I share her genes in the relevant part of the DNA, and whether my body is likely to behave in the same way.

Comments

[flamingnerd.livejournal.com]

it still takes a long time and a lot of money to sequence a person's genome. science is working on making it cheap right now, but honestly, just get a chunk of grandma -some blood and just isolate the DNA, it'll keep in the freezer for 10 years until it's cheap to do the whole sequence.

but yes, I totally agree, grandma's genome is valuable to you.

[gustavolacerda.livejournal.com]

Can I just collect blood, seal it, and leave it frozen? I wonder if Alcor would do that for me.

[flamingnerd.livejournal.com]

have them do it :P

you have to isolate the DNA right away. heh, i could prolly get you the recipe, but you'd have to keep it in a freezer that doesn't automatically defrost, and keeping it at -80 is better. and you'd have to find a suitable tool to use instead of a centerfuge, though you could probably get access to one.

[gustavolacerda.livejournal.com]

This isolate-DNA thing hardly seems like a standard service I could find somewhere. I have friends in bio labs at CMU, who might be able to save my DNA... the bigger problem is that all my ancestors are in Brazil.

OTOH, uncles and aunts are just as good as grandparents. I have a few of those in Canada.

[gustavolacerda.livejournal.com]

According to this article, it costs about US$ 2.2 million per genome.

whoa, I had no idea it was this expensive!

[rinku.livejournal.com]

Well, the first one they did was something like 10 billion, so it's going down.

[entomologist.livejournal.com]

I don't know about Alcor, but you might be able to get something like that done by a cord blood bank -- see http://parentsguidecordblood.org/content/usa/banklists/regulations.shtml for more on this type of facility.