The merge analysis of the three QTLs suggested several candidate causal genes with significant merge SNPs nearby.
The merge analysis for Kprl1, 2 and 3 are shown in Figure 6A, B and C respectively.
The list of all potential causal variants identified by the merge analysis is presented in Additional file 2: Table S3.
By merge analysis, sunitinib and Lysotracker were found to highly colocalise in the majority of cells (yellow, Figure 5A), demonstrating a lysosomal sequestration of sunitinib.
This method is similar in spirit to merge analysis (Yalcin et al. 2005), which also uses genetic similarity to narrow QTL regions in multi-founder crosses.
Consistent with our earlier findings with Aspergillosis [ 10], the most significant merge analysis variants involved one wild-derived strain vs the other 7 strains.
We used the merge analysis [ 17] to test which variants under a QTL peak were compatible with the pattern of action at the QTL.
In the merge analysis the eight founder strains are partitioned and merged according to the strain distribution pattern (SDP) of the alleles at the quantitative trait nucleotides (QTN) within a given QTL (formerly obtained by the initial mapping).
Using the full genome sequence data of the eight founders of the CC [ 7], with the advantage of the merge analysis [ 17], it possible to refine the QTL map interval to small genomic regions and identify strong candidate genes.
The way imputation (merge analysis) is performed in the CC is to compute the dosage of a SNP allele in a CC line by adding together the probabilities for those founders carrying that allele in the variant catalogue.
