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Bioarray Solutions, Affymetrix

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Bioarray Solutions of Warren, NJ, has received US Patent No. 6,958,245, "Array cytometry." The patent claims a set of operations that enable interactive control over the creation and placement of planar arrays of several types of particles and biomolecules and permit the manipulation of array shape and size. The patent also claims an invention that enables sample preparation and handling for diagnostic assays and biochemical analysis in an array format, and the functional integration of these operations. Additionally, a procedure for the creation of material surfaces with desired properties and for the fabrication of surface-mounted optical components is claimed as is a method and apparatus to direct the lateral motion and induce the assembly of planar arrays of cells on semiconductor surfaces in response to electric fields and projected patterns of illumination.


Affymetrix of Santa Clara, Calif., has received US Patent No. 6,957,149, "Computer-aided probability base calling for arrays of nucleic acid probes on chips." The patent claims a computer-aided system for calling unknown bases in sample nucleic acid sequences from multiple nucleic acid probe intensities. According to the patent's summary, the system can identify an unknown base in a sample nucleic acid sequence by the steps of 1) inputting a plurality of hybridization probe intensities; 2) determining a probability that the corresponding nucleic acid probe best hybridizes with the sample nucleic acid sequence; and 3) calling the unknown base according to the nucleic acid probe with the highest associated probability.


Affymetrix has also received US Patent No. 6,958,225, "Complexity management of Genomic DNA." The patent claims methods and kits for reducing the complexity of a nucleic acid sample by providing non-gel-based methods for amplification of a subset of the sequences in a sample. The patent also claims that the amplification of a subset can be accomplished by digesting a sample with two or more restriction enzymes and ligating adaptors to the fragments so that only a subset of the fragments can be amplified. The patent also claims a method for analyzing an amplified sample by hybridization to an array, which may be specifically designed to interrogate the desired fragments for particular characteristics such as the presence or absence of a polymorphis

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.