Our model is also consistent with inheritance of phase precession in CA1 from upstream circuits in CA3 and entorhinal cortex (Jaramillo et al., 2014).
The amino acid tree does have class 1 copies as monophyletic and classes 2 to 5 copies as sister clade to them, which is consistent with inheritance of multiple copies from a common ancestor.
We investigated conversion performance of the variants on the array with respect to (i) genotype call rates, cluster separation, and reproducibility, (ii) polymorphism in the panel under study, and (iii) consistent Mendelian inheritance from parents to off-spring in trios.
It turned out that ovarian and some other cancers also traveled in these families, in a pattern consistent with inheritance of a single mutated gene increasing risk of both ovarian and breast cancers.
The elevated frequency of CD44hi cells trait, which occurred at a frequency consistent with inheritance of a recessive gene variant, was used to map the mutation in an F2 intercross to an interval between 114 and 121.2 Mb on chromosome 2. 10.7554/eLiFigure20.003 Figure 1.
Consistent co-inheritance of the marker with the disease in families means that they are 'linked' and indicates that the actual disease gene is in close proximity.
Any SNP with a success rate of <80% or any SNP that showed consistent bad inheritances (>10 errors after data clean-up) within each independent cohort were removed from the association analyses.
These included SNPs with a genotype rate of <80%, a minor-allele frequency of <2.5%, SNPs with unusual Beadstudio cluster patterns (Illumina) or atypical peaks in MassArray TyperAnalyser (Sequenom), SNPs with a GenTrain score of <0.5 (Illumina), and markers that showed consistent bad inheritances (>10 errors after data clean up).
Progeny clones were consistent with Mendelian inheritance, but triploids were also recovered; divergent trait inheritance was observed among the progeny.
Despite this recent duplication, whether by allo- or auto-tetraploidy, our map is consistent with disomic inheritance in Miscanthus, in contrast to the polysomic inheritance found in the closely related polyploid sugarcane.
