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Recent Pharmacogenomics-Related Patents, November 2006

US Patent 7,135,286. Pharmaceutical and diagnostic business systems and methods. Inventors: Bradley Margus, David Cox, Stephen Fodor. Assignee: Perlegen Sciences.
Protects “improved pharmaceutical and diagnostic business systems and methods,” according to the patent abstract, in which “one or more genomes are scanned for single nucleotide polymorphisms. The polymorphisms are assigned to haplotype blocks, and representative SNPs from the haplotype blocks are used in association studies for pharmaceutical and diagnostic development.”

US Patent 7,132,238. Method of determining a chemotherapeutic regimen based on ERCC1 expression. Inventor: Kathleen Danenberg. Assignee: Response Genetics.
Protects prognostic methods for cancer chemotherapy based on a method for assessing ERCC1 expression levels in fixed or fixed and paraffin embedded tissues. The method is used to determine a platinum-based chemotherapy “by examination of the amount of ERCC1 mRNA in a patient's tumor cells and comparing it to a predetermined threshold expression level,” according to the patent abstract.

US Patent 7,127,355. Methods for genetic analysis. Inventors: David Cox, Mark McCamish. Assignee: Perlegen Sciences.
Protects methods for assessing an individual's likelihood of developing or exhibiting a multifactorial trait. The methods include “determining a plurality of genotypes for the individual at a plurality of biallelic polymorphic loci, using the genotypes to compute a score for the individual, and comparing the score to at least one threshold value,” according to the patent abstract.

US Patent 7,125,662. Method of identifying putative antibiotic resistance genes. Inventors: Barry Hall, Miriam Barlow. Assignee: University of Rochester.
Relates to methods of identifying putative antibiotic resistance genes. According to one embodiment, “this is carried out by first isolating a microbial DNA molecule or cDNA which encodes a putative antibiotic resistance protein or polypeptide and then determining whether the microbial DNA molecule or cDNA confers resistance against an antibiotic agent,” the patent abstract states.

US Patent 7,122,652. Polymorphisms in the human hPXR gene and their use in diagnostic and therapeutic applications. Inventors: Leszek Wojnowski, Elisabeth Hustert. Assignee: None.
Protects variations of the hPXR gene that are associated with insufficient metabolism or drug sensitivity. The patent also covers methods “for identifying and obtaining inhibitors for therapy of disorders related to the malfunction of the hPXR gene as well as methods of diagnosing the status of such disorders,” according to the abstract, as well as compositions for diagnosing and treating various diseases with drugs that are substrates, inhibitors, or modulators of the hPXR gene product.

US Patent 7,122,311. Methods for determining the risk of developing asthma characterized by bronchial hyperresponsiveness. Inventors: Paul Andrew Whittaker, Deborah Alexis Meyers, Dirkje Sjoukje Postma, Eugene Roland Bleecker. Assignees: Novartis, Wake Forest University Health Sciences, Rijksuniversiteit Groningen.
Covers the use of an asthma-associated gene, designated AAGA, as well as the protein molecule encoded by AAGA and related molecules in diagnostic and prognostic screening of patient populations. The patent also protects polymorphisms in AAGA and the use of the protein encoded by AAGA or a variant thereof as a therapeutic target.

US Patent 7,118,869. Genomic sequence of the 5-Lipoxygenase-activating protein (FLAP), polymorphic markers thereof and methods for detection of asthma. Inventors: Marta Blumenfeld, Ilya Chumakov, Lydie Bougueleret. Assignee: Serono Genetics Institute.
Protects biallelic markers of the FLAP gene and the association established between these markers and diseases involving the leukotriene pathway, such as asthma. The invention “provides means to determine the predisposition of individuals to diseases involving the leukotriene pathway as well as means for the diagnosis of such diseases and for the prognosis/detection of an eventual treatment response to agents acting on the leukotriene pathway,” according to the patent abstract.

US Patent 7,118,853. Methods of classifying, diagnosing, stratifying and treating cancer patients and their tumors. Inventors: David Botstein, Patrick Brown, Charles Perou, Brian Ring, Douglas Ross, Rob Seitz, Jan Matthijs van de Rijn. Assignee: Applied Genomics, Board of Trustees of Leland Stanford Junior University.
Protects reagents for use in the diagnosis and management of breast cancer. According to the patent abstract, the invention uses cDNA microarray technology to identify genes whose expression profile across a large group of tumor samples correlates with cytokeratin 5 and cytokeratin 17, markers for basal cells of the normal mammary lactation gland. The invention “demonstrates that tumors that express cytokeratin 5/6 and/or 17 have a poor prognosis relative to tumors overall,” and provides basal marker genes and their expression products and uses of these genes for diagnosis of breast cancer and for identification of therapies for breast cancer.

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The Scan

Study Examines Insights Gained by Adjunct Trio RNA Sequencing in Complex Pediatric Disease Cases

Researchers in AJHG explore the diagnostic utility of adding parent-child RNA-seq to genome sequencing in dozens of families with complex, undiagnosed genetic disease.

Clinical Genomic Lab Survey Looks at Workforce Needs

Investigators use a survey approach in Genetics in Medicine Open to assess technologist applications, retention, and workforce gaps at molecular genetics and clinical cytogenetics labs in the US.

Study Considers Gene Regulatory Features Available by Sequence-Based Modeling

Investigators in Genome Biology set sequence-based models against observational and perturbation assay data, finding distal enhancer models lag behind promoter predictions.

Genetic Testing Approach Explores Origins of Blastocyst Aneuploidy

Investigators in AJHG distinguish between aneuploidy events related to meiotic missegregation in haploid cells and those involving post-zygotic mitotic errors and mosaicism.