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IP Roundup: Mar 17, 2009


Agilent Technologies has received US Patent No. 7,504,072, "Biopolymeric array scanning devices that focus on the far side of an array and methods for using the same." The patent describes array-scanning methods that focus on the far side of an array and devices configured for such use. According to the methods, an array is placed in a reading position of a scanning device so that the nominal focal plane of the scanning device is present within the array substrate at a predetermined fixed substrate thickness fraction distance from the far side of the array. The scanner is configured to hold an array substrate in a reading position where its nominal focal plane is present within the array substrate, according to the patent.

Agilent has also received US Patent No. 7,504,213, "Methods and apparatus for preparing arrays comprising features having degenerate biopolymers." The patent claims methods for synthesizing biopolymers at predetermined feature locations on a surface of a substrate. One or more of the feature locations includes degenerate biopolymers. Biopolymer subunit precursors are added, in multiple rounds of subunit additions, at each of multiple feature locations on the surface to form the plurality of biopolymers on the surface. For each feature location comprising degenerate biopolymers, the biopolymer subunit precursors include a mixture of biopolymer subunit precursors for forming the degenerate biopolymers at the feature location.

PamGene of Den Bosch, the Netherlands, has received US Patent No. 7,504,209, "Method and device for integrated nucleic acid integrity assessment and analysis." The patent describes methods for integrated ribonucleic acid integrity assessment and analysis by: a) providing a support containing a set of detector probes and a set of at least two control probes; b) contacting the support with analyte ribonucleic acids derived from a sample, under conditions allowing the hybridization of complementary analyte ribonucleic acids and immobilized probes to form analyte ribonucleic acid-probe complexes; c) detecting signals generated by the complexes; d) determining the ratio of signals generated by the probe complexes; e) assessing the integrity of the sample; and f) evaluating microarray analysis results in view of the integrity assessment.

Ribonomics of Durham, NC, has received US Patent No. 7,504,210, "Methods for isolating and characterizing endogenous mRNA-protein (mRNP) complexes." The patent claims a method in which cellular mRNA-protein complexes are partitioned in vivo by contacting a biological sample with at least one ligand that specifically binds at least one component of a mRNP complex. The mRNP complex is separated by binding the ligand with a binding molecule specific for the ligand, where the binding molecule is attached to a solid support. The mRNP complex is collected by removing the mRNP complex from the solid support. After collecting the mRNP complex, the mRNA bound within the complex may be characterized and identified. Subsets of the total mRNA population of a cell may accordingly be characterized, and a gene expression profile of the cell obtained, the patent states.

Affymetrix has received US Patent No. 7,504,215, "Nucleic acid labeling methods." The patent claims a method of detecting the presence of an RNA of interest in a sample by: a) providing the sample; b) treating the sample with a fragmenting reagent to provide RNA fragments; c) removing phosphate groups from the fragments to provide fragments with free 3' OH groups; d) ligating the fragment with a labeling reagent according to the instant invention; e) providing a nucleic acid array having probes directed to the RNA of interest; f) hybridizing the labeled nucleic acid fragments to the nucleic acid array; and g) determining the extent of hybridization to the probes to determine the presence of the RNA of interest.

Receptors of Chaska, Minn., has received US Patent No. 7,504,364, "Methods of making arrays and artificial receptors." The patent claims artificial receptors and arrays or microarrays of artificial receptors or candidate artificial receptors. Each member of the array includes building block compounds, typically immobilized in a spot on a support. The patent also includes the building blocks, combinations of building blocks, arrays of building blocks, and receptors constructed of these building blocks together with a support. The patent also includes methods of making and using these arrays and receptors.

The Scan

Breast Cancer Risk Related to Pathogenic BRCA1 Mutation May Be Modified by Repeats

Several variable number tandem repeats appear to impact breast cancer risk and age at diagnosis in almost 350 individuals carrying a risky Ashkenazi Jewish BRCA1 founder mutation.

Study Explores Animated Digital Message Approach to Communicate Genetic Test Results to Family Members

In the Journal of Genetic Counseling, the approach showed promise in participants presented with a hypothetical scenario related to a familial hereditary breast and ovarian cancer syndrome diagnosis.

Computational Tool Predicts Mammalian Messenger RNA Degradation Rates

A tool called Saluki, trained with mouse and human messenger RNA data, appears to improve mRNA half-life predictions by taking RNA and genetic features into account, a Genome Biology paper reports.

UK Pilot Study Suggests Digital Pathway May Expand BRCA Testing in Breast Cancer

A randomized pilot study in the Journal of Medical Genetics points to similar outcomes for breast cancer patients receiving germline BRCA testing through fully digital or partially digital testing pathways.