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Affymetrix, Agilent Technologies, Roche NimbleGen

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Affymetrix has received US Patent No. 7,424,368, “Methods for identifying DNA copy number changes.” The patent describes methods of estimating genomic DNA copy number, where amplified genomic DNA is hybridized to an array of allele specific SNP probes to generate a hybridization pattern. A value, S, is calculated for individual SNPs in the experimental sample, where S is the log of the arithmetic average of the intensities of the perfect match probes for the SNP. S is calculated for the SNP in reference samples that are matched to the experimental sample in genotype. The mean and standard deviation for the S values of the reference samples are calculated and a log intensity difference is calculated by subtracting the mean values for the reference and experimental samples. The copy number of the SNP region is then estimated using the difference between the mean for the SNP in the reference samples and the S value for the SNP in the experimental sample in a log-log linear model.
 

 
Affymetrix has also received US Patent No. 7,423,143, “Nucleic acid labeling compounds.” The patent claims nucleic acid labeling compounds containing heterocyclic derivatives. The heterocyclic-derivative containing compounds are synthesized by condensing a heterocyclic derivative with a cyclic group, such as a ribofuranose derivative. The described labeling compounds are suitable for enzymatic attachment to a nucleic acid, either terminally or internally, to provide a mechanism of nucleic acid detection.
 

 
Agilent Technologies has received US Patent No. 7,422,911, “Composite flexible array substrate having flexible support.” The patent claims a flexible array substrate that includes: a) a flexible support, where the flexible support provides a surface for handling the flexible array substrate; b) a flexible base; and c) a reflective layer. The reflective layer includes a stack of dielectric layer units, where each dielectric layer unit is between about 40 nanometers and about 400 nanometers thick. Each dielectric layer unit is monolithic and the stack of layers also includes a monolithic transparent layer comprised of silicon dioxide, titania, or alumina.
 

 
Roche NimbleGen has received US Patent No. 7,422,851, “Correction for illumination non-uniformity during the synthesis of arrays of oligomers.” The patent provides an apparatus and a method for the synthesis of arrays of oligomers that have tight illumination intensity requirement. The apparatus and the method contain a mechanism to correct for illumination non-uniformity during the oligomer array synthesis process. To correct for illumination non-uniformity, the illumination intensity of different oligomer synthesis positions across an area in which oligomers are synthesized are determined first. Then, the difference in illumination intensity among the positions is evaluated mathematically. Next, any non-uniformity in illumination intensity is corrected by either reducing the intensity of the light for the brighter positions before the light reaches the illumination area or reducing the illumination time of the brighter positions during one protection group deprotection period.

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