Abstract: The present invention concerns a method for predicting quantitative phenotype, e.g. gag-phenotype, integrase phenotype or tropism in a patient infected by Human Immunodeficiency Virus (HIV).

Abstract: The present invention concerns the determination of weighted phenotypic sensitivity score (wPSS) for a combination therapy as being the combination of information about the inherent anti-viral potency of each drug, as determined through statistical analysis of response to anti-retroviral therapy combination regimens, with resistance information on the individual patient's virus to each anti-retroviral drug as well as the use of this wPSS for predicting the efficacy of a patient's therapy or for evaluating or optimizing a therapy.

Abstract: The instant disclosure describes a novel genotype and phenotype assay to elucidate and/or evaluate new potential HIV integrase inhibitors, but also currently approved and experimental compounds that target protease, reverse transcriptase, and RNaseH. This assay allows studying linked mutations and mutational patterns that occur under HAART and experimental therapies.

Abstract: The instant disclosure describes a novel genotype and phenotype assay to elucidate and/or evaluate new potential HIV integrase inhibitors, but also currently approved and experimental compounds that target protease, reverse transcriptase, and RNaseH. This assay allows studying linked mutations and mutational patterns that occur under HAART and experimental therapies.

Abstract: The present invention relates to methods for the evaluation of HIV-1 Subtype C (HIV-1-C) treatment. The methods are based on evaluating molecular events at the HIV-1-C gag-protease-reverse transcriptase (GPRT) resulting in altered therapeutic efficacy of investigated anti-retroviral compounds. The methods rely on providing HIV-1-C GPRT RNA and evaluating a treatment either through genotyping or phenotyping methods. Said methods may find a use in the field of diagnostics, drug screening, pharmacogenetics and drug development.

Abstract: Methods and systems for improving the accuracy of predicting resistance of a disease to a drug are described. More specifically, methods for assessing the impact of pre-existing variations in drug susceptibility, whether naturally occurring or selected by previous drug exposure, on treatment response in order to establish clinically relevant cut-off values for phenotypic or genotypic resistance tests are described.

Abstract: The present invention provides methods and kits for the rapid exponential amplification of nucleic acid molecules using a padlock probe. The present invention improves upon the existing methods for amplifying padlock probes by eliminating or delaying the appearance of artifact products that cause false positive results, and also increase the sensitivity and speed of the assay. Further provided are nucleic acid amplification primers containing non-informative base analogs.

Abstract: The invention relates to a method for obtaining clonal HIV-1 sequence information from a clinical isolate derived from an HIV-1 infected individual to guide highly active anti-retroviral therapy (HAART) comprising the following steps; a) extracting cell-associated viral nucleic acid b) amplifying said nucleic acid c) obtaining clonal sequence information d) interpreting the clonal sequence information and determining the ratio of the minority viral species by bio-informatics means whereby the ratio obtained is used to guide HAART.

Abstract: The present invention concerns methods and systems for improving the accuracy of predicting resistance of a disease to a therapy. In one embodiment of the invention, mean and standard deviation (SD) values of fold change in normalized sensitivity, relative to a laboratory wild type standard pathogen or malignant cell are calculated to demonstrate that the patient samples display inherently different degrees of variation in susceptibility to each therapy. In another embodiment, the 2×SD value for each therapy is used as the cut-off between sensitive (within normal susceptible range) and resistant (above normal susceptible range).

Abstract: The present invention relates to a method for mutation analysis of the HIV pol gene of HIV virions comprising amplifying virion RNA or DNA via nested PCR using outer primers as represented in SEQ ID No. 1 and 2, amplifying said PCR product via nested PCR using a 5? and 3? primer chosen from the inner primers SEQ ID No. 3, 4, 5, and 6, and sequencing this secondary obtained PCR product using at least one sequencing primer chosen from any of SEQ ID No. 7 to 12 or variants thereof. In the alternative, at least one secondary sequencing primer may be used chosen from any of SEQ ID No. 13 to 24. The benefit of the sequences present in the invention resides in the fact that, with the aid of the oligonucleotides, the sequences of all presently known HIV subtypes and all mutations of the pol gene presently known to yield resistance towards antiretroviral therapy can be determined. The present invention also relates to kits for performing such a method as well as primers for performing the same.

Abstract: A method and system for predicting the resistance of a disease to a therapeutic agent is provided. Further provided is a method and system for designing a therapeutic treatment agent for a patient afflicted with a disease. Specifically, the methods use a trained neural network to interpret genotypic information obtained from the disease. The trained neural network is trained using a database of known or determined genotypic mutations that are correlated with phenotypic therapeutic agent resistance. The present invention also provides methods and systems for predicting the probability of a patient developing a genetic disease. A trained neural network for making such predictions is also provided.

Abstract: The present invention relates to a method of for mutation analysis of the HIV pol gene of HIV-1 virions comprising amplifying viral RNA or DNA via nested PCR using outer primers as represented in SEQ ID No: 1 and 2, amplifying said PCR product via nested PCR using a 5′ and 3′ primer chosen from the inner primers SEQ ID No: 3, 4, 5, and 6, and sequencing this secondary obtained PCR product using at least one sequencing primer chosen from any of SEQ ID No: 7 to 12 or variants thereof. In the alternative, at least one secondary sequencing primer may be used chosen from any of SEQ ID No: 13 to 24. The present invention also relates to kits for performing such a method as well as primers for performing the same.