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Circulating plasma mitochondrial DNA (mt-DNA) were assessed by measuring copy number of the NADH dehydrogenase 1 gene using quantitative real-time PCR.
Accurate and precise methods for measuring copy number are essential when investigating subtle changes in copy number distribution between patients and healthy controls, which may reflect an effect of beta-defensin copy number on susceptibility to the disease under study.
Array comparative genomic hybridization (CGH) technology is frequently used for measuring copy number gains or losses.
Because we analyze interval data, rather than probe data, our approach is readily applicable to microarray or high-throughput sequencing approaches for measuring copy number.
Our PRT methods for measuring copy number were of sufficient precision to detect very slight but systematic differential bias between results from case and control DNA samples in one study.
All the methods were correlated, strongly suggesting that they were all measuring copy number, with the highest correlation coefficient between PRT and the first principal component of the aCGH data.
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We used real-time PCR for measuring copy numbers in genomic DNA.
mCNVs are not routinely evaluated in array- or NGS-based genome-wide studies because these approaches have limitations in accurately measuring copy numbers greater than four.
To determine the required surface area, a test was undertaken measuring copy numbers in incremental surface areas, ranging from 10 to 10 μm.
Although recent developments have enabled experiments to measure copy number on a genome scale with high genomic resolution, individual point measurements are still noisy, making the crucial separation of signal from noise difficult.
However, multiplex PCR cannot quantitatively measure copy number of genomic DNA.
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