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There were no cases of this ∼1.2 Mb distal 7q11.23 deletion copy number variant identified in over 20,000 control samples surveyed.
single copy deletion (copy number < 1.5), double copy deletion (copy number < 0.5), gain of copy number (copy number > 2.5), amplification (copy number > 3.5).
Currently our model only considers deletion, copy neutral, single copy or multiple copies.
Four classes of abnormal segments were considered based on their estimated copy number [ 16]: single copy deletion (copy number < 1.5), double copy deletion (copy number < 0.5), gain of copy number (copy number > 2.5), amplification (copy number > 3.5).
Finally, we generated a multi-source compendium of 63 OR loci harboring deletion Copy Number Variations (CNVs).
Further colony PCR revealed about 50% of 33 colonies had the deletion copy of SO1377 gene in place of the wild-type copy.
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The 'truth' is a panel of regions whose DNA copy number status in the cell line (normal, gain, hemizygous deletion, copy-neutral loss of heterozygosity (LOH) …) is known.
For instance, in DELs normal copy-two is analogous to homozygosity for the major allele of a SNP, a single copy-one deletion is analogous to heterozygosity and a double deletion copy-zero is analogous to homozygosity for the minor allele.
Next, a four component Gaussian mixture model (one component for each of the following copy number states: deletion, copy-neutral, 1 and 2 additional copies) was fitted to the smoothed copy number ratios with a constraint on the differences between the mixture means.
breakpoints: given a signal length n, draw K breakpoint positions uniformly out of the n − 1 possible intervals between successive data points (vertical lines in Figure 3); region labels: draw K + 1 region labels from a predefined set of copy-number state labels, such as normal, gain of one copy, hemizygous deletion, homozygous deletion, copy-neutral LOH (labels on top of each plot in Figure 3).
Many of our significant regions appear to be large differentiated duplications and deletions (copy number variants, or CNVs).
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