Family-based pedigree studies have also suggested tentative loci linked to increased cancer risk, often characterized by pedigree-specificity.
As GATK UnifiedGenotyper does not fully handle multiple VCF loci overlapping on the reference, each chain of overlapping tentative loci was merged (with a custom script, as GATK CombineVariants was found insufficient) into a single variant locus (growing the extent involved on the reference and adjusting alleles appropriately in response).
Amino acid sequence identity within tentative locus ranged from 85 to 93% across species while identity between all salmonid class II alpha sequences ranged from 39 to 61% both across loci and species.
However, one SNP close to the RPS12P4 locus in chromosome 2 reached a p value of 2 × 10 and this locus can thus be considered as a tentative candidate locus for ACPA-negative RA.
On the molecular genetic level, linkage and candidate gene studies have been used for the genetic analysis of PD, and several potential linkage loci and tentative associations with candidate genes have been found [ 7].
Additionally, using opsin intergenic sequences and cross-species comparisons to other teleosts, we identified potential distal gene regulatory elements including a tentative teleost LWS opsin Locus Control Region (LCR), analogous to LCRs previously described for mammalian and other teleost opsin loci.
This analysis confirms linkage to microsatellite marker z10441, and further defines a tentative interval for the enz locus distal to z6819 and z55887 and proximal to z8252 and z10441.
In the HmYb locus, the only gene with tentative evidence for positive selection was HM00021.
One must acknowledge, however, that so few female progeny could also reflect instability in male function or seed contaminants, so the inferred genotypes at the LG x are more tentative than those at the LG4 and LG6 loci.
A tentative gene-gene interaction between the two major AMD-associated loci, LOC387715 and CFH, was found in this study using a multiplicative (logistic regression) model, a synergy index (departure-from-additivity model) and the mutual information method (MI), suggesting that a common causative pathway may exist for these genes.
While this conclusion is tentative because we cannot necessarily extrapolate from assays of only four loci, it nonetheless suggests the possibility that the spermatogenesis pathway in these sterile hybrids may be disrupted sometime after the expression of the early meiotic arrest genes.
