In contrast, the proportion of amplifications in regions prone to random chromosomal event was not significantly predictive of outcome.
Protein coding genes were found in a higher proportion of amplifications (88.8%% of amplification calls overlapped a protein coding gene region) than deletions (55.6 %).
Pseudogenes were also found to overlap a higher proportion of amplifications (18.0 %) than deletions (13.9 %), as were RNAs (18.2 % vs 7.1%%) and antisense gene regions (5.1 % vs 2.6%%).
SINE elements, as expected, are enriched in all CNV calls, with a higher proportion of amplifications overlapping these regions (86.2%% of deletions, 95.0 % of amplifications) (Additional file 1: Figure S5).
A high proportion of successful amplification was achieved for all species within the Bovinae subfamily from primers designed using the Bos taurus genome despite divergence times of 8 14 MY (Taurotragus oryx).
The reliability of PCR amplifications may be assessed by using a statistical test to compare the proportion of successful amplifications in sample and control PCR, in order to determine whether the sample PCR success rate is significantly different from amplification rate due to contaminants.
The high proportion of shared amplifications in the Indonesian DD2 sample is mainly due to the strong signal derived from the PfMDR1 locus.
Likewise in the above comparison, the high proportion of shared amplifications in DD2 laboratory strain also results from hits in the PfMDR1 locus.
The most important factors influencing the proportion of successful amplifications are the number of index species mismatches, GC-richness of the target amplimer, and the relatedness of the target species to the index species, at least under the single PCR condition used.
Amplification and overexpression of MDM2 is a recognised mechanism of p53 inactivation, but although one study detected MDM2 amplification in a small proportion of cases [ 26], amplification of MDM2 is an infrequent event in breast cancer [ 27].
