The PennCNV algorithm allowed us to detect four abnormal copy number states other than the normal diploid state: deletion by one or two copies and duplication by one or two copies (Figure 1A).
Also, their Birdsuite recovery rate was inflated since no agreement on CNV state (deletion or duplication) was required by Korn et al. just after the development of Birdsuite; we found that only 70% of CNVs containing 20 or more markers were recovered by Birdsuite with an agreement on CNV state.
The non-diploid state deletion and amplification indicate either disease susceptibility or resistance; thus, copy number variation explains not only genetic variation but also certain types of diseases.
Previous reports do not list an integer copy number state, so it is possible that the reported deletions in these gene regions are one-copy-state deletions.
Generally this question is formulated as a cluster problem, in which each of the gene locus in classified into one of the clusters B1, B2 and B3 represent the three states deletion, normal and amplification.
Next, a four component Gaussian mixture model (one component for each of the following copy number states: deletion, copy-neutral, 1 and 2 additional copies) was fitted to the smoothed copy number ratios with a constraint on the differences between the mixture means.
The different salmonid species are currently in the process of reverting to a stable diploid state through deletions and rearrangements [ 17, 32- 34].
Copy-state-zero deletions are significantly smaller than copy-state-one deletions (P < 2.2 × 10−16, Mann Whitney test), where copy-state-zero deletions have a median length of 13,766 bp compared to copy-state-one deletions at 26,980 bp.
3) The authors state that deletion of Pak2 at the DN2 stage blocks positive selection.
The genotype calls for SNP markers are expected to be homozygous if they fall within a detected deletion CNV (both zero- and one-state-copy deletions).
Thus, our assay is able to account for gain or loss of steady-state temporal deletions as well as clonal expansions.
