inconsistency in the kinship formula ?

Questions about GenABEL (aka *ABEL) suite of packages
Forum rules
Please remember not to post any sensitive data on this public forum.
The first few posts of newly registered users will be moderated in order to filter out any spammers.

When get a solution to the problem you posted, please change the topic name (e.g. from "how to ..." to "[SOLVED] how to ..."). This will make it easier for the community to follow the posts yet to be attended.
Mueller
Posts: 4
Joined: Mon Mar 21, 2011 3:13 pm

inconsistency in the kinship formula ?

Postby Mueller » Wed Sep 07, 2011 10:37 am

Hi,
in my opinion there is an inconsistency in the formula for the calculation of the kinship between two individuals on the base of IBS. According to the Paper "A genomic background based method ...by Amin et al (2007) and the help(ibs) information the formula for kinship calculation contains pk as the frequency of the major allele. In this way the rare genotype AA leads to smaller kinship coefficients between the two individuals i and j then the GT BB (A= minor allele B=major allele). But sharing rare allele should add more to the kinship compared to sharing common allele. Maybe my calculations are wrong. If not, then using the frequency of the minor allele gives more plausible results (table 2,3). In table 3 I only used the formula part F*(1-sqrtF) instead of F*(1-F). In my opinion this table shows better differentiated results. I am interested in the view of the Able community.
Best regards
Uwe

table 1
col 2and 3=genotype ind i, col 4 and 5 = genotype ind j, col 6=freq, col 7= calculated kinship coefficient

genotype Ind i genotype ind j pk kin
SNP1 AA 1.00 AA 1.00 0.51 0.10
SNP2 AA 1.00 AA 1.00 0.90 0.01
SNP3 BB 0.00 BB 0.00 0.51 0.10
SNP4 BB 0.00 BB 0.00 0.90 0.90
SNP5 AB 0.50 BB 0.00 0.51 0.00
SNP6 AB 0.50 BB 0.00 0.90 0.40
SNP7 AB 0.50 AB 0.50 0.51 0.00
SNP8 AB 0.50 AB 0.50 0.90 0.18
SNP9 AA 1.00 BB 0.00 0.51 -0.10
SNP10 AA 1.00 BB 0.00 0.90 -0.10

table 2 pk=freq minor allele
SNP1 AA 1.00 AA 1.00 0.49 0.10
SNP2 AA 1.00 AA 1.00 0.10 0.90
SNP3 BB 0.00 BB 0.00 0.49 0.10
SNP4 BB 0.00 BB 0.00 0.10 0.01
SNP5 AB 0.50 BB 0.00 0.49 0.00
SNP6 AB 0.50 BB 0.00 0.10 -0.04
SNP7 AB 0.50 AB 0.50 0.49 0.00
SNP8 AB 0.50 AB 0.50 0.10 0.18
SNP9 AA 1.00 BB 0.00 0.49 -0.10
SNP10 AA 1.00 BB 0.00 0.10 -0.10

table 3
SNP1 AA 1.00 AA 1.00 0.49 0.18
SNP2 AA 1.00 AA 1.00 0.10 1.18
SNP3 BB 0.00 BB 0.00 0.49 0.16
SNP4 BB 0.00 BB 0.00 0.10 0.01
SNP5 AB 0.50 BB 0.00 0.49 0.00
SNP6 AB 0.50 BB 0.00 0.10 -0.06
SNP7 AB 0.50 AB 0.50 0.49 0.00
SNP8 AB 0.50 AB 0.50 0.10 0.23
SNP9 AA 1.00 BB 0.00 0.49 -0.17
SNP10 AA 1.00 BB 0.00 0.10 -0.13

Return to “GenABEL”

Who is online

Users browsing this forum: No registered users and 1 guest