To determine whether this result was caused by linkage disequilibrium (LD) between SNPs or by multiple causative genes within this region, we reconstructed haplotypes corresponding to these significant SNPs in the Sutai pigs.
It is manifested by compromised ventricular contraction and prolonged relaxation attributable to multiple causative factors including oxidative stress.
Further validation study needs to explore candidate causative SNPs from the PBA-identified pathways, by annotating the SNPs of the genes involved in pathways based on genomic features including protein coding features and non-coding features.
They are either part of a larger number of putatively causative SNPs not yet discovered or mere additional markers for unknown causative variants.
The two SNPs, rs3077 in HLA-DPA1 and rs9277535 in HLA-DPB1, could be independently considered to be possible causative SNPs for this disease.
All causative SNPs are removed from the genotypes before analysis.
In addition, gene-associated SNPs could themselves be causative SNPs for traits.
We classified significant SNPs <50 Mb from causative SNPs as true positives and excluded SNPs >50 Mb when calculating FDR.
They might represent either auxiliary regulatory sites or SNPs that are in LD with undetected causative SNPs.
These causative SNPs were also outside of human-mouse conserved regions.
