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Our high-speed congenic system uses immature males as founders at each generation.
It is also possible that an unknown and therefore untested sequence variant (for example an indel or CNV) that is not tagged by a known SNP could be responsible, although this is unlikely since most indels have similar SDP to a neighbouring SNP, and only a limited number of distinct strain distribution patterns are ever observed in the founders at each locus [ 18].
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The most likely founder at each position is assigned using a hidden Markov model (HMM) similar to the one used in GAIN, a genotype call-based method designed for pedigrees with inbreeding such as the CC (Liu et al. 2010).
When we estimate the effect of each founder at each marker along Chromosome 6, we see that CAST/EiJ alleles are associated with greater expression of the short isoform, whereas A/J alleles are associated with greater expression of the long isoform.
The company was incorporated as a California C corporation owned by its principal founders, at 25% ownership each.
The feedback the founders get at each stage can take months to incorporate.
King, Macdonald et al. (2012) describe the implementation of a hidden Markov model incorporating dense genotype data for the RILs and the founder genome sequences to infer the founder haplotype at each position in each RIL.
These data were recoded as 0, 1, and 0.5 for each of eight founder alleles at each marker, where 0 refers to nonfounder haplotype; 1, homozygous founder haplotype; and 0.5, heterozygous founder haplotype.
TRD spans at least a 100-Mb region (35 135 Mb) that includes the center of chr X. Estimation of TRD significance was based on assuming equal contribution of each founder rather than the actual contribution dictated by the frequency at which each founder was at each position in the funnel (funnel order, see Materials and Methods and Figure 1).
Founder ancestry at each marker is defined as the probability that each of (8 2 ) = 28 possible pairs of founders (e.g., C57BL/6J and CAST/EiJ) are the two founders from which the two alleles at that marker are inherited.
We estimated the effects of each founder genotype at each QTL separately for each population (pA and pB).
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