Method and system for determining phenotype from genotype

Data processing: structural design – modeling – simulation – and em – Electrical analog simulator

Reexamination Certificate

Rate now

  [ 0.00 ] – not rated yet Voters 0   Comments 0

Details

C703S011000

Reexamination Certificate

active

07324928

ABSTRACT:
A method and system for deriving an outcome predictor for a data set in which a number of complex variables affect outcome. A two step model is applied that includes application of 1) a flexible nonparametric tool for modeling complex data, and 2) a recursive partitioning (e.g., classification and regression trees) methodology. In one variation, a determination is made as to whether the data set used is representative of a population of interest; if not, underrepresented data is replicated so as to produce a representative data set. In one variation, a holdout sample of the data is also used with the two step model and the determined outcome predictor to verify the predictor produced.

REFERENCES:
patent: 6936476 (2005-08-01), Anderson et al.
patent: 2003/0033194 (2003-02-01), Ferguson et al.
Danter et al., “Molecular Data Mining Tool: Advances In HIV Research”, p. 31, Sep./Oct. (2000).
“Cross Validation”, J. Schneider (1997); [retrieved Aug. 2006] Retreived from the Internet <URL:http://www.cs.cmu.edu/˜schneide/tut5
ode42.html>.
Danter, et al., “Molecular Data Mining Tool: Advances in HIV Research Salford Systems”, p. 31, Sep./Oct. (2000).
Kitchen, et al., “Initial Virological and Immunologic Response to Highly Active Antiretroviral Therapy Predicts Long-Term Clinical Outcome”, Clinical Infectious Diseases, 33:466-472, Aug. (2001).
Miller, V., “Resistance to Protease Inhibitors”, Journal of Acquired Immune Deficiency Syndromes, 26, S34-S50 (2001).
Loveday, C., “Nucleoside Reverse Transcriptase Inhibitor Resistance”, Journal of Acquired Immune Deficiency Syndromes, 26, S10-S24 (2001).
Deeks, S., “Nonnucleoside Reverse Transcriptase Inhibitor Resistance”, Journal of Acquired Immune Deficiency Syndromes, 26, S25-S33 (2001).
Volberding, “Introduction”, Journal of Acquired Immune Deficiency Syndromes, 26, S1-S2 (2001).
Demeter, et al., “Phenotypic and Genotypic Resistance Assays: Methodology, Reliability, and Interpretations”, Journal of Acquired Immune Deficiency Syndromes, 26, S3-S9 (2001).
Haubrich, et al., “Clinical Utility of Resistance Testing: Retrospective and Prospective Data Supporting Use and Current Recommendations”, Journal of Acquired Immune Deficiency Syndromes, 26, S51-S59 (2001).
Arens, M., “Clinically Relevant Sequence-Based Genotyping of HBV, HCV, CMV, and HIV”, Journal of Clinical Virology, 22, 11-29 (2001).
García-Lerma, et al., “Resistance of Human Immunodeficiency Virus Type 1 to Reverse Transcriptase and Protease Inhibitors: Genotypic and Phenotypic Testing”, Journal of Clinical Virology, 21, 197-212 (2001).
Understanding Phenotypic Drug Resistance Testing—People Living With HIV: PhenoSense.com—“Phenotyping”, p. 1-2, http:// www.phenosense.com/people/331.html, printed Feb. 12, 2003.
Understanding Genotypic Drug Resistance Testing—People Living with HIV: PhenoSense.com—“Genotyping”, p. 1-2, http:// www.phenosense.com/people/332.html, printed Feb. 12, 2003.
Using Both Phenotyping and Genotyping Together—People Living With HIV: PhenoSense.com—“Pheno+Geno”, p. 1, http:// www.phenosense.com/people/333.html, printed Feb. 12, 2003.
Pheno Geno With PhenoSense GT—People Living With HIV: PhenoSense.com—“Pheno+Geno with PhenoSense GT”, p. 1, http:// www.phenosense.com/people/313.html, printed Feb. 12, 2003.
Pheno Geno With PhenoSense GT—People Living With HIV: PhenoSense.com—“A Review of HIV”, p. 1-5, http:// www.phenosense.com/people/321.html, www.phenosense.com/people/322.html, www.phenosense.com/people/323.html, www.phenosense.com/people/330.html, www.phenosense.com/people/334.html printed Feb. 12, 2003.
Horn, T., “A No-Nonsense Guide To HIV Drug Resistance Testing”, pp. 1-23, (Jul. 2002).
Friedman, J., “Multivariate Adaptive Regression Splines (MARS)”, Stanford Linear Accelerator Center (SLAC) PUB-4960 Rev., Tech Report 102 Rev., Aug. 1990.
Breiman, et al., “Classification and Regression Trees” Chapman and Hall/CRC New York (1993).
Http://www.salford-systems.com, “Data Mining, Web Mining, and Business Intelligence & Solutions From Salford Systems”, MARS Webcast, p. 1, printed Aug. 22, 2003.
Http://www.r-project.org, “The R Project for Statistical Computing”, p. 1, printed Aug. 22, 2003.
Http://www.ncbi.nlm.nih.gov, National Center for Biotechnology Information/National Library of Medicine, National Institutes of Health, NCBI HomePage, p. 1-2, printed Aug. 22, 2003.
Shafer, et al., “Human Immunodeficiency Virus reverse Transcriptase and Protease Sequence Database”, Nucleic Acids Research, vol. 27, No. 1, 348-352 (1999).
Http://hivdb.stanford.edu/cgi-bin/PR—Phenotype.cgi, Phenotype Query, Stanford HIV Drug Resistance Database, website, p. 1, printed Aug. 22, 2003.
Qari, et al., “Comparative Analysis of Two Commercial Phenotypic Assays for Drug Susceptibility Testing of Human Immunodeficiency Virus Type 1”, Journal of Clinical Microbiology, vol. 40, No. 1, p. 31-35 (2002).
Rhee, et al., “Human Immunodeficiency Virus Reverse Transcriptase and Protease Sequence Database”, Nucleic Acids Research, vol. 31, No. 1, p. 298-303 (2003).
Http://www.ncbi.nlm.nih.gov, Entreaz-Nucleotide, Human Genome, website, p. 1, printed Aug. 22, 2003.
Http://omni.ac.uk/browse/mesh/detail/C0376565L0496597.html, Anti-HIV Agents, p. 1-3, printed Feb. 12, 2003.

LandOfFree

Say what you really think

Search LandOfFree.com for the USA inventors and patents. Rate them and share your experience with other people.

Rating

Method and system for determining phenotype from genotype does not yet have a rating. At this time, there are no reviews or comments for this patent.

If you have personal experience with Method and system for determining phenotype from genotype, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and Method and system for determining phenotype from genotype will most certainly appreciate the feedback.

Rate now

     

Profile ID: LFUS-PAI-O-2815512

  Search
All data on this website is collected from public sources. Our data reflects the most accurate information available at the time of publication.