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This was expected because the aCGH reference was a sample of genomic DNA of another goat of the same breed.
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Considering that we estimated the CN of selected individuals with respect to reference genome which cannot be used for the aCGH reference sample, we calculated the predicted log2 CN ratios for the 11 test samples against RJF to make the CN values comparable with the aCGH results, which was designated as digital aCGH approach [ 12, 38].
aCGH reference DNA was isolated from peripheral blood lymphocytes from six apparently healthy female individuals.
This may be because the aCGH data is not sensitive to detect small copy number difference between test sample and reference sample due to the impact of noise signals, especially in highly duplicated regions.
Third, quantitative PCR (qPCR) was perfomed using Taqman assays on 10 canids (included the Boxer used in the aCGH experiments as a reference) to further validate 3 CNV regions (see Methods).
FRAH1H was excluded because the bibliographic reference was incorrect.
This is because the cell reference is relative.
The genome of a female Chinese Dehong chicken, which was undomesticated in south of China was used as the reference for the aCGH experiment.
DNA from the NA10851 cell line was used as a reference for the aCGH to extract signal intensity ratio with hg18/NCBI build 36.
All goats that were shown to have multiple copies of the ASIP and AHCY genes with different methods [ 22] reported evidence of gain in the aCGH experiment, compared to the reference Camosciata delle Alpi genomic DNA.
Furthermore, they were present in a BCL sample (Case 199) when DNA from the patient's CP was used as reference for the aCGH analysis, thus proving their secondary origin.
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