Abstract: In certain aspects, the present invention provides methods for determining whether a Her-2 positive cancer is likely to respond to treatment with a Her2-acting agent and/or whether a patient with a Her-2 positive cancer is likely to have a slow disease progression. In other aspects, the present invention is drawn to methods for determining whether a subject with a Her-2 positive cancer is unlikely to respond to treatment with at least one chemotherapeutic agent in addition to a Her2-acting agent and/or whether a patient with a Her-2 positive cancer is likely to have a fast disease progression.

Abstract: The present invention provides an approach for developing an algorithm for determining the effectiveness of anti-viral drugs based on a comprehensive analysis of paired phenotypic and genotypic data guided by phenotypic clinical cut-offs. In one aspect, the algorithm allows one to provide a patient with effective treatment. It helps predict whether an infected individual will respond to treatment with an anti-viral compound, thereby allowing an effective treatment regimen to be designed without subjecting the patient to unnecessary side effects. Also, by avoiding the administration of ineffective drugs, considerable time and money is saved.

Abstract: This invention relates to methods for determining altered susceptibility of HIV-I viruses to protease inhibitors (PIs) based on the viral genotypes. The methods generally comprise detecting, in a gene encoding protease and/or gag of the HIV-I, the presence of mutations correlated with altered susceptibility to amprenavir and/or darunavir.

Abstract: The present invention provides methods and devices for predicting whether an HIV-I is likely to have a reduced susceptibility to an antiviral drug based on the HIV-I's genotype. In one aspect, the invention provides methods comprising determining whether a mutation or combination of mutations associated with altered susceptibility to protease inhibitors are present, as disclosed herein, thereby assessing the effectiveness of tipranavir therapy in the HIV-infected subject. Computer implemented methods comprising determining HIV-I's altered susceptibility are provided.

Abstract: In certain aspects, the present invention provides methods for determining whether a Her-2 positive cancer is likely to respond to treatment with a Her2-acting agent and/or whether a patient with a Her-2 positive cancer is likely to have a slow disease progression. In other aspects, the present invention is drawn to methods for determining whether a subject with a Her-2 positive cancer is unlikely to respond to treatment with at least one chemotherapeutic agent in addition to a Her2-acting agent and/or whether a patient with a Her-2 positive cancer is likely to have a fast disease progression.

Abstract: The present invention provides an approach for developing an algorithm for determining the effectiveness of anti-viral drugs based on a comprehensive analysis of paired phenotypic and genotypic data guided by phenotypic clinical cut-offs. In one aspect, the algorithm allows one to provide a patient with effective treatment. It helps predict whether an infected individual will respond to treatment with an anti-viral compound, thereby allowing an effective treatment regimen to be designed without subjecting the patient to unnecessary side effects. Also, by avoiding the administration of ineffective drugs, considerable time and money is saved.

Abstract: The present invention provides methods and devices for predicting whether an HIV-1 is resistant to an antiviral drug based on the HIV-1's genotype. In one aspect, the invention provides methods comprising determining whether a mutation or combination of mutations associated with NRTI resistance are present, as disclosed herein, thereby assessing the effectiveness of FTC therapy in the HIV-infected subject. Computer implemented methods comprising determining HIV-1 resistance are provided.

Abstract: The present invention provides an approach for developing an algorithm for determining the effectiveness of anti-viral drugs based on a comprehensive analysis of paired phenotypic and genotypic data guided by phenotypic clinical cut-offs. In one aspect, the algorithm allows one to provide a patient with effective treatment. It helps predict whether an infected individual will respond to treatment with an anti-viral compound, thereby allowing an effective treatment regimen to be designed without subjecting the patient to unnecessary side effects. Also, by avoiding the administration of ineffective drugs, considerable time and money is saved.

Abstract: This invention relates to methods for determining resistance or susceptibility of HIV-1 viruses to d4T based on the viral genotypes. The methods generally comprise detecting, in a gene encoding reverse transcriptase of the HIV-1, the presence of a mutation at codon 65 in combination with one or more mutations at certain other codons. Combinations of mutations associated with resistance and susceptibility to d4T are disclosed.

Abstract: The present invention provides methods and devices for predicting whether a HIV variant will be resistant to an antiviral drug based on the variant's genotype. In one aspect, methods are provided comprising determining whether a combination of protease inhibitor resistance mutations meet certain conditions, as disclosed herein, thereby assessing the effectiveness of ritonavir-boosted indinavir therapy in the HIV-infected subject. Computer implemented methods comprising determining HIV resistance are provided.

Abstract: This invention relates to methods for predicting replication capacity of a virus based on genotype and identifying targets for antiviral therapy by identifying mutations associated with altered replication capacity. The methods are useful, for example, for identifying previously unknown interactions among viral molecules or between viral molecules and host cell molecules that are essential to viral infection and/or replication. By identifying such interactions, novel targets for antiviral therapy can be identified. In another aspect, the invention provides a method for determining that an HIV has an altered replication capacity. In certain embodiments, the method comprises detecting a mutation in a codon of gag that is selected from the group consisting of 437, 439, 441, 442, 454, 478, 479, and 484.

Abstract: The present invention provides an approach for developing an algorithm for determining the effectiveness of anti-viral drugs based on a comprehensive analysis of paired phenotypic and genotypic data guided by phenotypic clinical cut-offs. In one aspect, the algorithm allows one to provide a patient with effective treatment. It helps predict whether an infected individual will respond to treatment with an anti-viral compound, thereby allowing an effective treatment regimen to be designed without subjecting the patient to unnecessary side effects. Also, by avoiding the administration of ineffective drugs, considerable time and money is saved.

Abstract: The present invention provides an approach for developing an algorithm for determining the effectiveness of anti-viral drugs based on a comprehensive analysis of paired phenotypic and genotypic data guided by phenotypic clinical cut-offs. In one aspect, the algorithm allows one to provide a patient with effective treatment. It helps predict whether an infected individual will respond to treatment with an anti-viral compound, thereby allowing an effective treatment regimen to be designed without subjecting the patient to unnecessary side effects. Also, by avoiding the administration of ineffective drugs, considerable time and money is saved.

Abstract: The present invention provides an approach for developing an algorithm for determining the effectiveness of anti-viral drugs based on a comprehensive analysis of paired phenotypic and genotypic data guided by phenotypic clinical cut-offs. In one aspect, the algorithm allows one to provide a patient with effective treatment. It helps predict whether an infected individual will respond to treatment with an anti-viral compound, thereby allowing an effective treatment regimen to be designed without subjecting the patient to unnecessary side effects. Also, by avoiding the administration of ineffective drugs, considerable time and money is saved.