Rui En Mei

US Patent:

6988040, Jan 17, 2006

Filed:

Aug 15, 2002

Appl. No.:

10/219503

Inventors:

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

Assignee:

Affymetrix, Inc. - Santa Clara CA

International Classification:

G06F 17/00

US Classification:

702 20, 702 19, 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:

7297778, Nov 20, 2007

Filed:

Oct 4, 2002

Appl. No.:

10/264945

Inventors:

Hajime Matsuzaki - Palo Alto CA, US
Xing Su - Cupertino CA, US
Sean Walsh - Danville CA, US
Giulia Kennedy - San Francisco CA, US
Rui Mei - Santa Clara CA, US

Assignee:

Affymetrix, Inc. - Santa Clara CA

International Classification:

C07H 21/00
C12Q 1/68

US Classification:

536 221, 536 2432, 435 6

Abstract:

The presently claimed invention provides for novel methods and kits for analyzing a collection of target sequences in a nucleic acid sample. A sample is amplified under conditions that enrich for a subset of fragments that includes a collection of target sequences. The invention further provides for analysis of the above sample by hybridization to an array, which may be specifically designed to interrogate the collection of target sequences for particular characteristics, such as, for example, the presence or absence of one or more polymorphisms.

US Patent:

7300788, Nov 27, 2007

Filed:

Oct 7, 2003

Appl. No.:

10/681773

Inventors:

Hajime Matsuzaki - Palo Alto CA, US
Rui Mei - Santa Clara CA, US
Mei-Mei Shen - Cupertino CA, US
Giulia C. Kennedy - San Francisco CA, US

Assignee:

Affymetrix, Inc. - Santa Clara CA

International Classification:

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

US Classification:

4352872, 536 231, 536 243, 435 911

Abstract:

The invention provides nucleic acid sequences that are complementary, in one embodiment, to a wide variety of human polymorphisms. The invention provides the sequences in such a way as to make them available for a variety of analyses including genotyping a large number of SNPs in parallel. The invention also provides a collection of human SNPs that is useful for genetic analysis within and across populations. As such, the invention relatesd to diverse fields impacted by the nature of genetics, including biology, medicine, and medical diagnostics.

US Patent:

7629164, Dec 8, 2009

Filed:

Jul 13, 2004

Appl. No.:

10/891260

Inventors:

Hajime Matsuzaki - Palo Alto CA, US
Rui Mei - Santa Clara CA, US

Assignee:

Affymetrix, Inc. - Santa Clara CA

International Classification:

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

US Classification:

4352872, 536 231, 536 243, 435 911

Abstract:

The invention provides nucleic acid sequences that are complementary, in one embodiment, to a collection of human single nucleotide polymorphisms. The invention provides the sequences in such a way as to make them available for a variety of analyses including genotyping a large number of SNPs in parallel by, for example, allele specific hybridization. The invention also provides a collection of human SNPs that is useful for genetic analysis within and across populations. As such, the invention relates to diverse fields impacted by the nature of genetics, including biology, medicine, and medical diagnostics.

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.