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Recent Patents in Bioinformatics, June — July, 2008

US Patent 7,400,982. Automated generation of multi-dimensional structure activity and structure property relationships. Inventors: Holger Fischer, Manfred Kansy. Assignee: F. Hoffman-La Roche.
Protects a method for automatically generating multi-dimensional structure activity and structure property relationships. The method first provides data about at least one set of chemical structures and about one biological descriptor, and then calculates the physico-chemical properties of each chemical structure and associates those properties with the biological descriptor data in order to obtain a data matrix. The method next analyzes the data in the matrix “with a view on the effect of each physico-chemical property of each chemical structure on said biological descriptor,” and then generates new molecules with favorable multi-dimensional profiles, according to the patent description.

US Patent 7,400,981. Systems, methods, and computer program product for analyzing microarray data. Inventor: David Roth Rigney.
Protects systems, methods, and computer program products for analyzing gene expression data, “especially data that have been acquired using microarray technologies,” according to the patent abstract. In particular, the invention relates to “methods for analyzing a set of genes that have been partitioned into disjoint subsets known as clusters,” and describes methods for quantitatively evaluating the quality of gene clustering, based on the extent to which the “similarity of documents associated with genes in a cluster collectively distinguish that cluster from all the other clusters, as well as the extent to which words and phrases, present in documents associated with genes in the cluster, collectively distinguish that cluster from all the other clusters.”

US Patent 7,398,171. Automated quality control method and system for genetic analysis. Inventors: David Woo, Yerramalli Subramaniam. Assignee: Applera (now called Applied Biosystems).
Protects an automated quality control method for gene expression data based on a computer-based device that receives gene expression data associated with a spectral species and genetic sample in each well of a plate. The device identifies gene expression data determined to have “anomalous characteristics according to a set of one or more quality control metrics and may conditionally flag one or more wells of the plate affected by the anomalous characteristics,” according to the patent abstract. Filters can then be selectively applied to temporarily or permanently remove the flagged data from subsequent gene expression studies.

US Patent 7,396,646. Alien sequences. Inventors: Sean Quinlan, Temple Smith, Prashanth Vishwanath. Assignee: Modular Genetics, Trustees of Boston University.
Protects methods for creating sequences and reagents for use as internal hybridization controls on microarrays. The method first provides a naturally occurring sequence, then determines one or more “natural sequence statistics” of the naturally-occurring sequence, according to the patent description. The method next applies a hidden Markov model algorithm to one or more natural sequence statistics of the naturally-occurring sequence to generate an “alien sequence” that “comprises intermittent highly improbable sequence patterns or subsequences throughout its length.”

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The Scan

Researchers Compare WGS, Exome Sequencing-Based Mendelian Disease Diagnosis

Investigators find a diagnostic edge for whole-genome sequencing, while highlighting the cost advantages and improving diagnostic rate of exome sequencing in EJHG.

Researchers Retrace Key Mutations in Reassorted H1N1 Swine Flu Virus With Avian-Like Features

Mutations in the acidic polymerase-coding gene boost the pathogenicity and transmissibility of Eurasian avian-like H1N1 swine influenza viruses, a PNAS paper finds.

Genome Sequences Reveal Evolutionary History of South America's Canids

An analysis in PNAS of South American canid species' genomes offers a look at their evolutionary history, as well as their relationships and adaptations.

Lung Cancer Response to Checkpoint Inhibitors Reflected in Circulating Tumor DNA

In non-small cell lung cancer patients, researchers find in JCO Precision Oncology that survival benefits after immune checkpoint blockade coincide with a dip in ctDNA levels.