Evaluation of various approaches and datasets in identifying selected regions is particularly important, because it provides an independent verification of regions found by a combination of different methodologies and databases.
We obtained partial verification of reassortments found by Holmes et al., who performed a phylogenetic analysis of 156 Human H3N2 New York flu strains from 1999 2004 [ 8].
Verification of newly found associations would be greatly aided by the deposition of genotypes and detailed phenotype data in public databases such as dbGaP [ 13] for use in (disease sub-type-specific) meta-analyses.
FluReF corroborated two new reassortments identified by visual analysis of 75 Human H3N2 New York flu strains from 2005 2008 and gave partial verification of reassortments found using another bioinformatics method.
The gene set including all inactivating and leaky variants (regardless of verification status) was found in 5 of 7 of the same pathways in A431 (additionally, a variant was found in the semaphorin interaction pathway), 8 of 12 of the same pathways in U2OS and 0 of 11 pathways in U251.
Two populations were included in this study; population I was the primary study population of interest and population II was a smaller population used for verification of the results found in population I. Population I consisted of 56 healthy men and women who participated in a controlled feeding trial [13].
This procedure was used for verification of transcriptional differences found by RNA-seq.
This procedure was applied to each candidate gene and was also used for verification of transcriptional differences found by RNA-seq.
Using in silico analysis coupled with PCR verification, we found no convincing evidence of breakpoints between the wAnaITG and D. ananassae nuclear unique sequence from the euchromatic chromosomes X, 2, and 3.
A more detailed explanation of this theoretical proposition, as well as an empirical verification, can be found in Maitra (2017).
This systematic approach allows the identification of key spoilage problems, corrective actions that will be undertaken if a problem is found, verification of the impact of the corrective action, and documentation of the whole process.
