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We observed a copy number variant in the course of genotyping the HLA-B*44:02 proxy SNP rs2256583C <img src="http://journals.plos.org/plosone/article/asset?id=info?doi/10.1371/journal.pone.0013454.e069.PNG" class= inline-graphic"/> T in the replication dataset.
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In 3.6% of the segregants (n = 26), we observed an extra copy of a chromosome (including two with partial chromosome duplication).
In our hands, when comparing gene expression levels with gene copy number of a set of differentially expressed genes located at chromosomes 1p36 and 17q13-q21, we observed a concordance between copy number and mean expression values in all those analyzed genes that displayed in the microarray analysis higher expression levels in near-triploid NBTs.
Besides the variable number of phospholipase D genes, we also observed a third full copy of the cytotoxin gene (toxC) in the PZ of the porcine L71 genome.
Hence, in this case we likely observed a true case of copy number alterations interacting with SNV-impaired genes.
Some studies (Aiken et al., 2008; Cree et al., 2008) have observed a depletion of mtDNA copy number during the bottleneck to minima around several hundred; other studies (Cao et al., 2007, 2009) have observed that mtDNA copy number remains >10.
Campbell and colleagues observed a decrease of mtDNA copy number and an increase of lesions such as ss nicks in mtDNA in cell clones that constitutively expressed antisense RNA against DNA ligase III mRNA [22] or catalytically inactive DNA ligase III mutants [23].
Interestingly, we observed a strong correlation between copying events resulting in preferential transmission of both the gene-drive cassette and the preferred non-cleavable allele.
For common variants (frequency >10%), we observed a distinct bias against copy-number losses, suggesting that deletions are subject to purifying selection.
We observed an excess of copy losses (28) and five gains and two regions where both gains and losses were found (Additional file 1: Table S3).
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CEO of Professional Science Editing for Scientists @ prosciediting.com