The largest number of SNP selected for the BovineSNP50 assay came from the RRL source (Table 1).
The serum samples used in this assay came from a cohort which has previously been described [11], [21].
Because the available porcine genome sequence (build 7) only covered 70% of the genome, 70% of the SNPs selected to be included on the assay came from those for which position on genome build 7 was known.
Further validation of this assay came from analyzing RNA samples that had previously been labeled and hybridized, but provided poor quality expression data.
Nonetheless, the finding that SIVcpz, SIVgor, and HIV-1 group O Vpus were active in this assay came as a surprise, since these viruses use Nef instead of Vpu to antagonize tetherin in their respective hosts (Sauter et al., 2009; Kluge et al., 2014).
It has also become apparent that the most important prognostic and predictive component of these first generation assays comes from their ability to measure proliferation reproducibly and quantitatively [ 6].
Primers and probes for TaqMan assays come from the Applied Biosystems bank (Assays ID: rpl13: Dr03119261_m1; klf4: Dr03080183_m1; Dio3: custom assay AJ20SMU).
Moreover, sequencing-based assays come with new challenges for data processing and storage.
Data for the hypodermal and head cell expression assays come from two and three independent experiments, respectively.
