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Affymetrix: Oct 3, 2006

Affymetrix has received the following US patents:
No. 7,117,097, “Methods, computer software products and systems for correlating gene lists.” The patent claims methods, computer software products, and systems for comparing two or more lists of genes. The genes are ranked according to certain criteria, such as the statistical significance of their expression change and the magnitude of expression change. The Spearman correlation is then calculated for the common genes in the lists. A higher Spearman correlation indicates the similarity between the lists. According to the patent, the methods can be used to analyze the similarity between gene-expression data sets obtained from different laboratories.

No. 7,117,095, “Methods for selecting nucleic acid probes.” The patent claims a computer implemented method for selecting nucleic acid probes. The methods include steps of inputting quality scores and locations for a plurality of candidate probes and selecting a number of probes from the candidate probes, where the selected probes have a maximum aggregate adjusted quality score. The adjusted quality score is then based upon the quality score and the overlapping of the selected probes.


No. 7,116,809, “Computer software system, method, and product for scanned image alignment.” The patent claims an image alignment tool for adjusting the alignment of a grid with an image. According to the patent, an initial grid aligner determines an approximately aligned position of the grid. An intensity scorer then determines a set of intensity scores for each of a plurality of test grid elements of the plurality of grid elements. Each member of the set is based, at least in part, on intensities of pixels of one or more image features within the test grid element in one of the initial or additional positions. A combined-rank-score generator then combines, for each of the initial and additional grid positions, members of sets of rank scores corresponding to the grid position in order to generate a combined rank score for the grid position. To complete the process, a grid alignment adjuster adjusts the alignment of the grid based on a comparison among the combined rank scores.

The Scan

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.

Team Presents Cattle Genotype-Tissue Expression Atlas

Using RNA sequences representing thousands of cattle samples, researchers looked at relationships between cattle genotype and tissue expression in Nature Genetics.

Researchers Map Recombination in Khoe-San Population

With whole-genome sequences for dozens of individuals from the Nama population, researchers saw in Genome Biology fine-scale recombination patterns that clustered outside of other populations.

Myotonic Dystrophy Repeat Detected in Family Genome Sequencing Analysis

While sequencing individuals from a multi-generation family, researchers identified a myotonic dystrophy type 2-related short tandem repeat in the European Journal of Human Genetics.