Teresa A Webster

US Patent:

6699659, Mar 2, 2004

Filed:

Dec 21, 1998

Appl. No.:

09/217368

Inventors:

Teresa A. Webster - Loma Mar CA

Assignee:

Affymetrix, Inc. - Santa Clara CA

International Classification:

C12Q 168

US Classification:

435 6, 702 19, 702 20

Abstract:

Systems and methods for detecting monomer changes in a sample when an unknown quantity of expected monomers may also be present. Homogeneous and heterogeneous samples are exposed to polymer probes for hybridization. The hybridization affinities of the polymer probes to the samples are then compared to determine differences between the polymers in the samples. Accordingly, deletion, substitution and insertion mutations may be detected in a heterogeneous sample of nucleic acids.

US Patent:

6850846, Feb 1, 2005

Filed:

Jan 11, 2001

Appl. No.:

09/758872

Inventors:

Eugene Wang - Milpitas CA, US
Teresa Webster - Loma Mar CA, US

Assignee:

Affymetrix, Inc. - Santa Clara CA

International Classification:

G01N 3348

US Classification:

702 19, 702 20, 435 6

Abstract:

Methods, systems and computer software products are provided for determining genotype of a sample using a plurality of probes. In one preferred embodiment, a tentative genotype call is made based upon the relative allele signals. Pattern recognition is then used to validate the tentative call.

US Patent:

7031846, Apr 18, 2006

Filed:

Aug 15, 2002

Appl. No.:

10/219882

Inventors:

Shantanu Kaushikkar - San Jose CA, US
Teresa Webster - Loma Mar CA, US
Rui Mei - Santa Clara CA, US
Linda McAllister - San Francisco CA, US

Assignee:

Affymetrix, Inc. - Santa Clara CA

International Classification:

G01N 33/48
C12Q 1/68
G06F 7/00

US Classification:

702 19, 702 20, 707102, 435 6, 436501, 536 231

Abstract:

A computer program product, and related systems and methods, are described that processes emission intensity data corresponding to probes of a biological probe array. The computer program includes a genotype and statistical analysis manager that determines absolute or relative expression values based, at least in part, on a statistical measure of the emission intensity data and at least one user-selectable statistical parameter. The analysis manager may also determine genotype calls for one or more probes based, at least in part, on the emission intensity data, The analysis manager may further display the absolute or relative expression values based, at least in part, on at least one user-selectable display parameter and/or a measure of normalized change between genotype calls. The measure of normalized change may be based, at least in part, on a comparison of genotype calls and a reference value.

US Patent:

7280922, Oct 9, 2007

Filed:

Jul 14, 2005

Appl. No.:

11/181584

Inventors:

Rui Mei - Santa Clara CA, US
Teresa Webster - Loma Mar CA, US

Assignee:

Affymetrix, Inc. - Santa Clara CA

International Classification:

G06F 17/00
C12Q 1/68

US Classification:

702 20, 435 6, 702 19

Abstract:

Methods, systems and computer software products are provided for determining genotype of a sample using a plurality of probes. In one preferred embodiment, a tentative genotype call is made based upon the relative allele signals. Pattern recognition is then used to validate the tentative call.

US Patent:

7881875, Feb 1, 2011

Filed:

Jul 13, 2006

Appl. No.:

11/457452

Inventors:

Teresa A. Webster - Santa Clara CA, US
Hajime Matsuzaki - Palo Alto CA, US
Xiaojun Di - Cupertino CA, US
Earl A. Hubbell - Palo Alto CA, US
Rui Mei - Santa Clara CA, US
Simon Cawley - Oakland CA, US
Gregory Marcus - San Carlos CA, US
Keith W. Jones - Sunnyvale CA, US

Assignee:

Affymetrix, Inc. - Santa Clara CA

International Classification:

G06F 7/00

US Classification:

702 19, 702 20, 703 11, 703 13, 435 6, 536 245

Abstract:

The invention relates to the selection of a collection of relevant single nucleotide polymorphisms across a genome to design a nucleic acid probe array. As such, the invention relates to diverse fields impacted by the nature of genetics, including biology, medicine, and medical diagnostics.

US Patent:

7991560, Aug 2, 2011

Filed:

Feb 10, 2006

Appl. No.:

11/352008

Inventors:

Shantanu V. Kaushikkar - San Jose CA, US
Teresa Webster - Loma Mar CA, US
Rui Mei - Santa Clara CA, US
Linda McAllister - San Francisco CA, US

Assignee:

Affymetrix, Inc. - Santa Clara CA

International Classification:

G06F 7/00

US Classification:

702 19, 702 20, 703 11, 707700, 435 6, 536 245

Abstract:

A computer program product, and related systems and methods, are described that processes emission intensity data corresponding to probes of a biological probe array. The computer program includes a genotype and statistical analysis manager that determines absolute or relative expression values based, at least in part, on a statistical measure of the emission intensity data and at least one user-selectable statistical parameter. The analysis manager may also determine genotype calls for one or more probes based, at least in part, on the emission intensity data. The analysis manager may further display the absolute or relative expression values based, at least in part, on at least one user-selectable display parameter and/or a measure of normalized change between genotype calls. The measure of normalized change may be based, at least in part, on a comparison of genotype calls and a reference value.

US Patent:

8467974, Jun 18, 2013

Filed:

Jun 15, 2011

Appl. No.:

13/161150

Inventors:

Shantanu V. Kaushikkar - San Jose CA, US
Teresa A. Webster - Santa Clara CA, US
Rui Mei - Santa Clara CA, US
Linda McAllister - San Francisco CA, US

Assignee:

Affymetrix, Inc. - Santa Clara CA

International Classification:

G06F 7/00

US Classification:

702 19, 702 20, 703 11, 707700, 436501

Abstract:

A computer program product, and related systems and methods, are described that processes emission intensity data corresponding to probes of a biological probe array. The computer program includes a genotype and statistical analysis manager that determines absolute or relative expression values based, at least in part, on a statistical measure of the emission intensity data and at least one user-selectable statistical parameter. The analysis manager may also determine genotype calls for one or more probes based, at least in part, on the emission intensity data. The analysis manager may further display the absolute or relative expression values based, at least in part, on at least one user-selectable display parameter and/or a measure of normalized change between genotype calls. The measure of normalized change may be based, at least in part, on a comparison of genotype calls and a reference value.

US Patent:

7361468, Apr 22, 2008

Filed:

Jul 5, 2005

Appl. No.:

11/175859

Inventors:

Guoying Liu - Emeryville CA, US
Simon Cawley - Oakland CA, US
Hajime Matsuzaki - Palo Alto CA, US
Earl A. Hubbell - Palo Alto CA, US
Geoffrey Yang - San Jose CA, US
Teresa A. Webster - Santa Clara CA, US
Rui Mei - Santa Clara CA, US
Xiaojun Di - Cupertino CA, US
Richard Chiles - Castro Valley CA, US

Assignee:

Affymetrix, Inc. - Santa Clara CA

International Classification:

C12Q 1/68
C07H 21/04
C12M 3/00
C12M 1/34

US Classification:

435 6, 4352872, 435 911, 536 231, 536 243

Abstract:

Methods, kits and arrays of nucleic acid probes for genotyping large numbers of human SNPs in parallel are provided. A set of more than 100,000 human SNPs, known to be biallelic in at least two populations is provided. Allele specific perfect match probes and genotyping probe sets are provided for each allele of each biallelic SNP in a set of human SNPs that is useful for genetic analysis within and across populations. Probe sets that include perfect match and mismatch probes are provided. The probe sets are suitable for inclusion in an array. The invention provides the SNP and surrounding sequence and provides the sequences in such a way as to make them available for a variety of analyses including genotyping. As such, the invention relates to diverse fields impacted by the nature of genetics, including biology, medicine, and medical diagnostics.