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IP Update: Jul 16, 2010

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Recent Patents in Bioinformatics, June — July 2010

US Patent No. 7,756,646. Method for predicting peptide detection in mass spectrometry. Inventors: Lars Kangas, Richard Smith, Konstantinos Petritis. Battelle Memorial Institute.

Describes a method of predicting whether a peptide present in a biological sample will be detected via analysis with a mass spectrometer. The method first uses a mass spectrometer to analyze a sample containing peptides from proteins with known amino acids and then generates a data set of peptides contained within the sample. It then calculates the probability that a specific peptide in the data set was detected in the repeated analysis as well as a set of multidimensional vectors, in which each dimension represents a property of one or more of the amino acids present in each peptide and adjacent peptides in the data set. "Using these vectors, the method then generates an algorithm from the plurality of vectors and the calculated probabilities that specific peptides in the data set were detected in the repeated analysis," the patent abstract states.


US Patent No. 7,756,645. Methods of storing, aligning, and retrieving haplotype data. Inventors: Yun-sun Nam, Tae-jin Ahn. Assignee: Samsung Electronics.

Protects methods of storing, aligning, and retrieving haplotype data. In particular, the patent describes a method for storing haplotype data that includes determining the order of alleles in each SNP position of the haplotype data, aligning the haplotype data according to the order, and storing the aligned haplotype data in a predetermined data structure.


US Patent Nos. 7,751,986 and 7,747,391. Methods, systems, and software for identifying functional biomolecules. Inventors: Claes Gustafsson, Sridhar Govindarajan, Robin Emig, Richard John Fox, Ajoy Roy, Jeremy Minshull, Christopher Davis, Anthony Cox, Phillip Patten, Linda Castle, Daniel Siehl, Rebecca Lynne Gorton, Teddy Chen. Assignee: Maxygen.

Covers methods of searching biologically related data space in order to identify biomolecules with desired properties from complex biomolecule libraries. The invention also provides methods of modeling sequence-activity relationships and digital systems and software for performing these methods.


US Patent No. 7,751,981. Articles of manufacture and methods for modeling Saccharomyces cerevisiae metabolism. Inventors: Imandokht Famili, Jochen Forster, Pengcheng Fu, Jens Nielsen, Bernhard Palsson. Assignee: The Regents of the University of California.

Describes an in silico model for determining a physiological function of Saccharomyces cerevisiae. The model includes a data structure that relates several S. cerevisiae reactants to several S. cerevisiae reactions; a constraint set for the S. cerevisiae reactions; and commands for determining a distribution of flux through the reactions that is predictive of a S. cerevisiaephysiological function.


US Patent No. 7,749,984. Computer-based model for identification and characterization of non-competitive inhibitors of nicotinic acetylcholine receptors and related ligand-gated ion channel receptors. Inventors: Irving Wainer, Krzysztof Jozwiak, Ruin Moaddel, Sarangan Ravichandran, Jack Collins. Assignee: US Department of Health and Human Services.

Describes a computer-readable molecular model of a ligand-gated ion channel receptor and/or a computer system for modeling such a receptor. The molecular model can be used to design novel compounds having activity as non-competitive inhibitors of the ion channel, according to the patent abstract.


US Patent No. 7,747,394. Information processing system using base sequence relevant information. Inventors: Takamasa Katoh, Takeo Morimoto. Assignee: Hitachi.

Covers a system for processing information for an individual organism "via effective utilization of differences in nucleotide sequence information among individual [organisms]." The method first receives requested information for an object and/or service and then obtains positional information "representing a position in a nucleotide sequence memorized therein." The method then obtains semantic information "implied by the received nucleotide sequence-related information and/or information associated with the semantic information," and transmits the semantic information in association with the positional information.


US Patent No. 7,747,393. Methods, systems, and software for identifying functional biomolecules. Inventor: Richard Fox. Assignee: Maxygen

Covers methods of searching biologically related data space in order to identify biomolecules with desired properties from complex biomolecule libraries. The invention also provides methods of modeling sequence-activity relationships and digital systems and software for performing these methods.


US Patent No. 7,747,392. Physiogenomic method for predicting clinical outcomes of treatments in patients. Inventors: Gualberto Ruano, Andreas Windemuth. Assignee: Genomas.

Provides a method for predicting an individual's response to an environmental stimulus. The method is based on producing and recording a physiogenomic model. The model is produced by first selecting genetic markers and then identifying "significant covariates among demographic data to produce correlated markers for use as a covariate in an unadjusted association test," according to the patent abstract. The method then performs an unadjusted association test for each genetic marker and uses permutation testing to select several model-building markers. It next identifies one or more genes that are not associated with a particular outcome in the individual in order to serve as a physiogenomic control, and then displays the individual's predicted physiological response. "One can then compare the genetic markers of the individual to the physiogenomic database and convey to the individual an appropriate treatment intervention," the patent abstract states.


US Patent No. 7,747,389. Scoring system for the prediction of cancer recurrence. Inventors: Masaaki Oka, Yoshihiko Hamamoto, Hisafumi Okabe. Assignee: F. Hoffmann-La Roche.

Covers a scoring system for the prediction of cancer recurrence based on first measuring the expression of genes or proteins of human tumor tissues, and then comparing their patterns with those of the gene or protein expression of human primary tumors from patients who have cancer recurrence and those who do not have cancer recurrence.


US Patent No. 7,747,049. Method of analyzing a representation of a separation pattern. Inventors: Ian Morns, Anna Kapferer, David Bramwell. Assignee: BioSignatures.

Protects a method for statistical analysis of protein separation patterns. "The invention solves the problems associated with producing models which are predictive of classification using unreduced data," according to the patent abstract. The method analyzes a representation of a separation pattern, which includes a "neighborhood" representing a region of the separation pattern that includes a plurality of data points. The method augments this data by "representing the entire region using each data point of the neighborhood, and building a classification model using some or all of the data points."


US Patent No. 7,747,048. Method of analyzing separation patterns. Inventors: Ian Morns, Anna Kapferer, David Bramwell. Assignee: BioSignatures.

Protects a method for statistical analysis of protein separation patterns. The method includes separating protein samples to produce several separation patterns; forming a representation of each separation pattern; building an "importance map" by iteratively recording performance values of classification models against locations in the map that correspond to locations in representations of separation patterns of data points used to build the classification models; and then processing the importance map to identify important areas. "Parts of the map [that] include high performance values indicate regions of the separation pattern [that] are statistically important in predicting a classification of the pattern," the patent abstract states.

The Scan

US Booster Eligibility Decision

The US CDC director recommends that people at high risk of developing COVID-19 due to their jobs also be eligible for COVID-19 boosters, in addition to those 65 years old and older or with underlying medical conditions.

Arizona Bill Before Judge

The Arizona Daily Star reports that a judge weighing whether a new Arizona law restricting abortion due to genetic conditions is a ban or a restriction.

Additional Genes

Wales is rolling out new genetic testing service for cancer patients, according to BBC News.

Science Papers Examine State of Human Genomic Research, Single-Cell Protein Quantification

In Science this week: a number of editorials and policy reports discuss advances in human genomic research, and more.