Sunday, May 16, 2010

Call Me Sometime

When you test with 23andMe, there are always some no-calls: locations at which the genotyping chip wasn't able to get a good reading, so no result is reported.

I tested twice with 23andMe. The first time I tested, there were 2607 no-calls, and the second time there were 3260 no-calls.

But these generally weren't the same SNPs. Most of the time, a no-call on one test was resolved by the other test. Only 459 SNPs were no-calls both times.

Merging the results from the two tests actually gives 544 no-calls, since I have to add as new no-calls the 85 SNPs that were reported differently on the two tests.

There are 578,320 SNPs that 23andMe reports on. So merging the two tests brings the no-call rate from 0.45% and 0.56% individually all the way down to 0.094% for the combo data.

By the way, it's possible that some of the 459 repeated no-calls don't represent inadequacies in the test at all but instead indicate microdeletions—short fragments of DNA that most people have but that are missing in my genome. (For the autosomes, this would require my having inherited a microdeletion from both parents, which seems unlikely.)


  1. I am curious if you received any feedback on the no-call rate. I just completed the 23andme testing on their v3 platform and had 10,216 no-calls. I am curious what their QC considers an acceptable no-call frequency.

    1. Sorry for replying so late; I just saw your comment now.

      The results published in the blog were on 23andMe's v2 platform. As for v3, your no-call rate appears to be on the high side, comparing with the ones I've seen, but that's based on a very small sample size.

      You didn't say if you are male or female, but keep in mind that 23andMe reports the entire Y chromosome as "no-calls" for females, but those shouldn't be counted as actual no-calls, of course.