We obtain better localization of the boundaries of structural variants, distinguish genetic from putative somatic structural variants in cancer genomes, and integrate aCGH and paired-end sequencing measurements of structural variants.
The precise localization of the boundaries of structural variants provided by the GASV is helpful for distinguishing simple variants shared across multiple individuals from more complex variants resulting from repeated rearrangements at the same locus.
Even though not explicitly investigated, fine tuning of the significance threshold of the candidate CNV detection loci can be used to query complex CNVs [31] by comparing boundaries of overlapping variants.
On the other hand, our results are consistent with the observations made by others [36], [41] in the sense that the boundaries of many variants reported so far are not precisely defined, because different MLPA probes located within the same theoretical CNV did not behave uniformly (Figure S1).
The method used to derive the reported boundaries of the variants in Kidd et al. (2008) is mysterious.
This is especially important for indels, because the exact boundaries of indel variants are often called imprecisely.
In the discovery cohort (n=186), a total of 206 different sequence alterations were recorded in the exons and intron exon boundaries of USH2A; 88 variants were missense, coding insertions/deletions or splice site changes.
There are no standard methods for identifying the boundaries of structural variants in paired-end mapping studies and different heuristics have been used (Kidd et al., 2008; Korbel et al., 2007).
The boundaries of the variant detected in the majority of the animals (163) were considered to be the true boundaries of the CNV (53,481,069-53,719,948 bp in terms of map positions on bovine chromosome 6 on BTAU4 [ 11]).
Veronese's shadings are variants of the hues they inflect, and his contours aren't so much boundaries of form as sinuous frontiers where paint changes color.
