Colombe E Chappey

US Patent:

7553618, Jun 30, 2009

Filed:

Jul 1, 2003

Appl. No.:

10/612600

Inventors:

Neil T. Parkin - Belmont CA, US
Ellen Paxinos - San Jose CA, US
Colombe Chappey - San Francisco CA, US
Mary T. Wrin - Fremont CA, US
Andrea Gamarnik - Chandler AZ, US
Christos J. Petropoulos - Half Moon Bay CA, US

Assignee:

Monogram Biosciences, Inc. - South San Francisco CA

International Classification:

C12Q 1/70
A61K 39/21

US Classification:

435 5, 4242081

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.

US Patent:

7993824, Aug 9, 2011

Filed:

Jul 1, 2003

Appl. No.:

10/612603

Inventors:

Colombe Chappey - San Francisco CA, US
Christos J. Petropoulos - Half Moon Bay CA, US
Neil T. Parkin - Belmont CA, US

Assignee:

Monogram Biosciences, Inc. - South San Francisco CA

International Classification:

C12Q 1/70
C12Q 1/68
G01N 33/00

US Classification:

435 5, 435 6, 436 89

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.

US Patent:

20040224307, Nov 11, 2004

Filed:

Feb 13, 2003

Appl. No.:

10/367223

Inventors:

Neil Parkin - Belmont CA, US
Colombe Chappey - San Francisco CA, US
Christos Petropoulos - South San Francisco CA, US

International Classification:

C12Q001/70
C12Q001/68

US Classification:

435/005000, 435/006000

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.

US Patent:

20050214749, Sep 29, 2005

Filed:

Feb 4, 2005

Appl. No.:

11/051812

Inventors:

Colombe Chappey - San Francisco CA, US
Christos Petropoulos - Half Moon Bay CA, US
Neil Parkin - Belmont CA, US

International Classification:

C12Q001/70
C12Q001/68

US Classification:

435005000, 435006000

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.

US Patent:

20050214750, Sep 29, 2005

Filed:

Feb 4, 2005

Appl. No.:

11/052741

Inventors:

Neil Parkin - Belmont CA, US
Colombe Chappey - San Francisco CA, US
Michael Bates - San Carlos CA, US

International Classification:

C12Q001/70
C12Q001/68
G06F019/00
G01N033/48
G01N033/50

US Classification:

435005000, 435006000, 702019000

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. In certain embodiments, the mutation is selected from the group consisting of I437L, P439S, E454V, P478L, and I479K In certain embodiments, the mutation is in a codon of gag that is selected from the group consisting of 418, 456, 456, 453, 418, 483, 481, 465, 429, 484, 481, 483, 484, 465, 454, 442, 479, 418, 479, and 486.

US Patent:

20060094020, May 4, 2006

Filed:

Oct 29, 2004

Appl. No.:

10/976721

Inventors:

Neil Parkin - Belmont CA, US
Colombe Chappey - San Francisco CA, US

International Classification:

C12Q 1/70
C12Q 1/68

US Classification:

435006000, 435005000

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.

US Patent:

20080293038, Nov 27, 2008

Filed:

May 25, 2006

Appl. No.:

11/915307

Inventors:

Neil T. Parkin - Belmont CA, US
Colombe Chappey - San Francisco CA, US
Jeannette Whitcomb - San Mateo CA, US

International Classification:

C12Q 1/70

US Classification:

435 5

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.

US Patent:

20090191559, Jul 30, 2009

Filed:

Dec 19, 2008

Appl. No.:

12/340436

Inventors:

Weidong Huang - Pleasanton CA, US
Jeff Sperinde - El Granada CA, US
Michael Bates - San Carlos CA, US
Colombe Chappey - San Francisco CA, US

Assignee:

MONOGRAM BIOSCIENCES, INC. - South San Francisco CA

International Classification:

C12Q 1/68
C12Q 1/02
G01N 33/574

US Classification:

435 6, 435 29, 435 723

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.