SKAT test output explaination

Question

[maroulaki]

I am running on Plinkseq a SKAT test but I cannot find the output explanation on the documentation.

LOCUS   POS     ALIAS   NVAR    TEST    P       I       DESC
NM_000014       chr12:9220678..9268288  2,A2M   25      SKAT    0.636024        .       1/0(12);1/1(3);10/0(1);2/0(3);3/1(1);3/2(1);3/3(1);6/0(1);6/1(1);9/0(1)

The main question is for the DESC column which is different from simple Burden test

Could you pleas help on that?

Thanks a lot

Answer 1

[luca.bello]

It seems to be describing the allelic configuration of 25 individuals with rare variants... 12 individuals are heterozygous for variant 1, 3 are homozygous for variant 1, and so forth...

[maroulaki]

Thanks a lot for the answer

I estimate that 25 refers to NVAR(number of variations) at this area. But I still cannot understand what these genotypes mean 10/0(1);2/0(3);3/1(1);3/2(1);3/3(1);6/0(1);6/1(1);9/0(1) ?

Thanks a lot

Answer 2

[vikas115]

I would interpret the DESC column to be a summary of the allele counts for the 25 variants used in the burden test:

• 1/0(12): 12 variants have 1 carrier in one group and 0 in another
• 1/1(3) : 3 variants have 1 carrier each in cases and controls
• 10/0: 1 variant has 10 carriers in one group and 0 in another

and so on. I don't think that the counts are directional (1/0 vs 0/1) but the output for a large number of tests should make this clear.