::  Posts  ::  RSS  ::  ◂◂RSS  ::  Contact

Interpreting genetic testing

December 15th, 2018
genetics  [html]
Several years ago I participated in a study where my DNA was sequenced, and while I ended up not getting the sequence data [1] I did get a file of 23andme-style SNP variant calls. I loaded it into Promethease, and excluded mutations with magnitude below 2 ("looks interesting enough to be worth reading"). I saw 139 mutations marked as "bad," 41 as "good," and 26 as "not set."

Initially I interpreted this to mean that I should be more pessimistic about my health than I was before getting the report, since more of the mutations are bad (2x risk of something) than good (0.5x risk of something else). To figure out how your beliefs should change, though, you need to know how many bad vs good mutations people typically have. For example, if someone might normally have 200 bad mutations and 10 good ones then my report is good news, but if instead normal is 100 bad mutations and 70 good ones then my report is bad news.

In general, I would expect most people to have more negative mutations than positive ones, simply because most mutations with an effect are negative. Randomly changing something is much more likely to break things than make them better.

This also applies when determining total risk of something. For example, lets say I have SNPs that individually give me 3x, 1.5x, 2x, and 0.5x risk for heart disease. I could naively multiply them together, ignoring that they don't stack perfectly, [2] and conclude that I had 4.5x the risk of the general population. But most people will probably have some mutations that increase their risk of heart disease. I think the proper way to handle this is for each case where you have the normal value of a variant you count that as slightly improving your risk, and when you consider all of these tiny improvements you get back to the average person having the average risk. Alternatively, and probably more accurately, you could just naively compute each person's risk, and then normalize.

Is this just a Promethease problem? Do other places that give health reports handle this better? Or do places just avoid giving consumer health information because this is both really hard to do well and highly regulated?

(It's also definitely possible I'm misinterpreting Promethease, or not thinking well about how the stats work here.)


[1] This was really frustrating. They confirmed receipt of my sample in September 2012, and in March 2015 they said they had the full 26GB sequence data available for me to transfer. Unfortunately they only ever uploaded the first few 200MB chunks, and then stopped responding to my emails in mid-April. I wrote to them a few more times, and eventually gave up about a year later.

[2] This caveat about stacking is pretty serious, though. Imagine mutations A and B both give you a 3x risk of some condition. If they act completely independently then a "stacked" 9x risk from having both A and B is reasonable. But if instead A and B act exactly the same way, breaking something that has multiple ways to be rendered fully inoperable, then having them both is no worse than having just one. I don't know which end of this is closer to how things usually work.

Comment via: facebook, lesswrong

Recent posts on blogs I like:

Fare Evasion

There’s a moralistic discourse in the United States about fare evasion on public transport that makes it about every issue other than public transport or fares. It’s a proxy for lawlessness, for police racism, for public safety, for poverty. In lieu of tr…

via Pedestrian Observations November 14, 2019

Pieces of time

My friend used to have two ‘days’ each day, with a nap between—in the afternoon, he would get up and plan his day with optimism, whatever happened a few hours before washed away. Another friend recently suggested to me thinking … Continue reading →

via Meteuphoric November 11, 2019

Wild animal welfare in Hans Christian Andersen

Continuing the theme of wild animal suffering in children’s lit… Hans Christian Andersen’s stories involve a lot of suffering of both human and animal varieties. “The Ugly Duckling” takes a brief detour from describing the duckling’s repeated social humil…

via The whole sky November 7, 2019

more     (via openring)

More Posts:


  ::  Posts  ::  RSS  ::  ◂◂RSS  ::  Contact