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SNP array analysis validated copy-number aberrations and revealed that RB1 and WRN were altered by recurrent copy-neutral loss of heterozygosity.
One additional locus showed validated copy number changes in the autosomes.
In addition to the known and validated copy-number variations, a large number of additional copy-number variations was detected but not validated.
The known and validated copy-number changes were previously identified on the 32k BAC microarray platform, and ranged in sizes from 230 kb to 8.9 Mb.
We selected samples from 13 patients in which we have previously identified and validated copy-number variations using our in-house produced tiling-resolution 32k BAC arrays.
The HMM algorithm correctly detected 10 out of 11 previously identified and validated copy-number variations on the Affymetrix 250k SNP microarray.
In contrast, two of the previously identified and validated copy-number variations out of the 13 tested were not automatically detected on the Affymetrix 100k SNP array platform.
To generate a database of polymorphic deletion sites and validated copy number-informative probe sets, we used SCIMM-Search to analyze data generated by the Illumina 1M-DuoV3 array for 269 HapMap samples.
Samples from 10 patients were tested on the 385k NimbleGen oligonucleotide microarray platform, and all of the previously identified and validated copy-number variations were detected by the automated HMM algorithm.
The normalized ratios were analyzed for loss and gain of regions by a standard Hidden Markov Model (HMM), which was optimized for each of the microarray platforms in order to maximize the detection of the known validated copy-number aberrations, while minimizing the false-positive rate, as described before.
They were then subjected to the following steps to validate copies.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com