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These observations suggested CNV at the AMY2A reference locus.
The CpG islands of SNURF were selected as a reference locus.
Subsequent calculations of raw CNs are the ratios of areas from target locus amplicon and reference locus amplicon assuming a CN of two for the reference locus (CN = 2 × target/reference).
Both PRT and qPCR compare the signal generated at a variable locus to that at a reference locus.
Smith Waterman alignments (EMBOSS Water) were performed for each sample reads against the corresponding 53 nucleotide reference locus.
F-tests were performed to determine whether copy numbers detected with qPCR have the same variance between the reference locus and CNV loci.
Similar(27)
The copy number of the test locus in each case was defined as 2T−ΔΔC where ΔCT is the difference in threshold cycle number for the test and reference loci.
A selection hypothesis could also be further examined by detailed population genetic studies that compare PGI and PGM to a greater number of reference loci that are likely to be selectively neutral.
Consider R reference loci in addition to the focal locus.
For homozygous reference loci, allele frequency must be 100%%.
The tumor sample will be compared only to reference loci in the normal sample and the output will contain all non-reference loci in the tumor sample.
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