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Thus, an optimal CGH profile has a low variance to give a better estimate of the copy number level, a high dynamic range to give the best resolution of copy numbers and a low average standard deviation for reproducibility.
Matrix-based CGH or array CGH overcomes this problem increasing the sensitivity for the detection of DNA copy number changes at specific loci, through the use of well defined genomic DNA fragments whose mapping location is known, arrayed onto a solid surface [ 21- 23], thereby achieving a resolution of copy number imbalances up to the single gene level.
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A novel method of gene resolution analysis of copy number variation (graCNV) yields high-resolution maps of DNA copy number changes and is applicable to a broad range of organisms for which commercial oligonucleotide expression microarrays are available.
The present study describes a novel method of gene resolution analysis of copy number variation (graCNV) yielding high-resolution maps of DNA copy number changes and applicable to a broad range of organisms for which commercial oligonucleotide expression microarrays are available.
For a subset of the samples (n = 41) a high resolution dataset of copy number changes obtained by array comparative genome hybridization data (aCGH) was available (Roche NimbleGen, 385 000 oligo probe array) [30].
Here we present gene resolution analysis of copy number variation (graCNV), a method utilizing the most frequently used expression microarray platform for aCGH.
A 32 k aCGH platform was used for high resolution mapping of copy number changes in 30 stage I-IV ESCC.
Our results provide a significant replenishment for the high resolution map of copy number variation in the bovine genome and valuable information for investigation of genomic structural variation underlying traits of interest in cattle.
This study reports the highest resolution map of copy number variation in the cattle genome, with 304 CNV regions (CNVRs) being identified among the genomes of 20 bovine samples from 4 dairy and beef breeds.
In the present study, we have increased the resolution of the copy number analysis over 20-fold to more accurately visualize the breakpoints of the copy number alterations.
This step resulted in the refinement of 99 breakpoints, effectively increasing the mean resolution of those copy number boundaries to 3.396 kbp, which is far lower than the 25.3 kbp resolution possible through the use of bins.
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