Most of the SNPs identified in the present work are not classified in the group of SNPs computationally characterized by Kharabian (2010) and present in OryzaSNP (http://oryzasnp.plantbiology.msu.edu/cgi-bin/gbrowse/osa_snp_tigr/) and dbSNP (http://www.ncbi.nlm.nih.gov/sites/entrez?db=snp&TAbCmd=Limits) databases.
No other group of SNPs was significant.
One group of SNPs tags the HLA-B*44:02 allele.
rs35285258, belonging to the other independent group of SNPs associated with T1D [13] showed the maximal association in this study.
This group of SNPs, however, shows relatively low LD with the two flanking SNPs (rs665780 and rs1567871).
The downside of studying a group of SNPs is that the method sometimes identifies too many markers as CNNLOH, which affects specificity negatively (see Fig. 5B).
However, the rs35285258, belonging to another independent group of SNPs associated with T1D, showed the maximal association in this study but different risk allele.
Within this group of SNPs, those with domain-altering properties are even more likely to be associated with a disease state.
The test for overall association was significant for the breast cancer associated group of SNPs identified by genome wide association studies (P-het. = 0.0003, P-trend = 0.0028; adjusted P-trend = 0.0059).
These random SNPs were chosen based on major allele frequency and the number of SNPs assayed per gene in order to select a group of SNPs similar to those assayed for the selection-candidate genes.
In order to select a group of SNPs comparable to those assayed for the selection-candidate genes, SNPs were selected based on major allele frequency and the number of SNPs assayed per gene.
