Jing Huang

US Patent:

7133856, Nov 7, 2006

Filed:

May 19, 2003

Appl. No.:

10/441955

Inventors:

Jing Huang - Sunnyvale CA, US
Richard A. Olshen - Stanford CA, US

Assignee:

The Board of Trustees of the Leland Stanford Junior University - Palo Alto CA

International Classification:

G06E 1/00

US Classification:

706 21, 700104

Abstract:

The present invention provides a powerful and robust classification and prediction tool, methodology, and architecture for supervised learning, particularly applicable to complex datasets where multiple factors determine an outcome and yet many other factors are irrelevant to prediction. Among those features which are relevant to the outcome, they have complicated and influential interactions, though insignificant individual contributions. For example, polygenic diseases may be associated with genetic and environmental risk factors. This new approach allow us consider all risk factors simultaneously, including interactions and combined effects. Our approach has the strength of both binary classification trees and regression. A simple rooted binary tree model is created with each split defined by a linear combination of selected variables. The linear combination is achieved by regression with optimal scoring.

US Patent:

7424368, Sep 9, 2008

Filed:

Nov 12, 2003

Appl. No.:

10/712616

Inventors:

Jing Huang - Sunnyvale CA, US
Keith W Jones - Sunnyvale CA, US
Michael H. Shapero - Redwood City CA, US

Assignee:

Affymetix, Inc. - Santa Clara CA

International Classification:

G06F 19/00
G01N 33/48

US Classification:

702 19, 703 2, 435 6, 536 254, 211 4112

Abstract:

Methods of estimating genomic DNA copy number are disclosed. Amplified genomic DNA is hybridized to an array of allele specific SNP probes to generate a hybridization pattern. A value, S, is calculated for individual SNPs in the experimental sample, where S is the log of the arithmetic average of the intensities of the perfect match probes for the SNP. S is calculated for the SNP in reference samples that are matched to the experimental sample in genotype. The mean and standard deviation for the S values of the reference samples are calculated and a log intensity difference is calculated by subtracting the mean values for the reference and experimental samples. The copy number of the SNP region is estimated using the difference between the mean for the SNP in the reference samples and the S value for the SNP in the experimental sample in a log-log linear model.

US Patent:

7634363, Dec 15, 2009

Filed:

Dec 7, 2006

Appl. No.:

11/608233

Inventors:

Jing Huang - Sunnyvale CA, US
Keith W. Jones - Sunnyvale CA, US

Assignee:

Affymetrix, Inc. - Santa Clara CA

International Classification:

G06F 19/00
C12Q 1/68
G06F 15/00

US Classification:

702 20, 435 6, 700 1

Abstract:

Methods for genotyping polymorphisms using allele specific probes are disclosed. A training set is used to generate a model for each polymorphism to be interrogated. The training set is used to obtain an estimate of the asymmetry between an intensity measurement for a first allele and an intensity measurement for a second allele of the same polymorphism. The intensity measurement obtained for a test sample is adjusted using the estimate of asymmetry prior to using the intensity measurements to make a genotyping call. In preferred embodiments the adjustment is applied to polymorphisms that have a likelihood of being heterozygous that is above a specified threshold.

US Patent:

7822555, Oct 26, 2010

Filed:

Dec 5, 2005

Appl. No.:

11/295225

Inventors:

Jing Huang - Sunnyvale CA, US
Keith W. Jones - Sunnyvale CA, US
Michael H. Shapero - Redwood City CA, US

Assignee:

Affymetrix, Inc. - Santa Clara CA

International Classification:

G06F 7/00

US Classification:

702 19, 702 20, 703 11, 707102, 435 6, 536 245

Abstract:

Methods of identifying allele-specific changes in genomic DNA copy number are disclosed. Methods for identifying homozygous deletions and genetic amplifications are disclosed. An array of probes designed to detect presence or absence of a plurality of different sequences is also disclosed. The probes are designed to hybridize to sequences that are predicted to be present in a reduced complexity sample. The methods may be used to detect copy number changes in cancerous tissue compared to normal tissue. The methods may be used to diagnose cancer and other diseases associated with chromosomal anomalies.

US Patent:

7991564, Aug 2, 2011

Filed:

Dec 15, 2009

Appl. No.:

12/638939

Inventors:

Jing Huang - Sunnyvale CA, US
Keith W. Jones - Sunnyvale CA, US

Assignee:

Affymetrix, Inc. - Santa Clara CA

International Classification:

G06F 19/00
G06F 15/00
C12Q 1/68

US Classification:

702 20, 435 6, 700 1

Abstract:

Methods for genotyping polymorphisms using allele specific probes are disclosed. A training set is used to generate a model for each polymorphism to be interrogated. The training set is used to obtain an estimate of the asymmetry between an intensity measurement for a first allele and an intensity measurement for a second allele of the same polymorphism. The intensity measurement obtained for a test sample is adjusted using the estimate of asymmetry prior to using the intensity measurements to make a genotyping call. In preferred embodiments the adjustment is applied to polymorphisms that have a likelihood of being heterozygous that is above a specified threshold.

US Patent:

8190373, May 29, 2012

Filed:

Oct 12, 2010

Appl. No.:

12/902711

Inventors:

Jing Huang - Sunnyvale CA, US
Keith W. Jones - Sunnyvale CA, US
Michael H. Shapero - Redwood City CA, US

Assignee:

Affymetrix, Inc. - Santa Clara CA

International Classification:

G06F 7/00

US Classification:

702 19, 702 20, 703 11, 707700, 435 61

Abstract:

Methods of identifying allele-specific changes in genomic DNA copy number are disclosed. Methods for identifying homozygous deletions and genetic amplifications are disclosed. An array of probes designed to detect presence or absence of a plurality of different sequences is also disclosed. The probes are designed to hybridize to sequences that are predicted to be present in a reduced complexity sample. The methods may be used to detect copy number changes in cancerous tissue compared to normal tissue. The methods may be used to diagnose cancer and other diseases associated with chromosomal anomalies.

US Patent:

8498825, Jul 30, 2013

Filed:

Jun 23, 2011

Appl. No.:

13/167264

Inventors:

Jing Huang - Sunnyvale CA, US
Keith W. Jones - Sunnyvale CA, US

Assignee:

Affymetrix, Inc. - Santa Clara CA

International Classification:

G06F 19/00
C12Q 1/68

US Classification:

702 20, 435 611

Abstract:

Methods for genotyping polymorphisms using allele specific probes are disclosed. A training set is used to generate a model for each polymorphism to be interrogated. The training set is used to obtain an estimate of the asymmetry between an intensity measurement for a first allele and an intensity measurement for a second allele of the same polymorphism. The intensity measurement obtained for a test sample is adjusted using the estimate of asymmetry prior to using the intensity measurements to make a genotyping call. In preferred embodiments the adjustment is applied to polymorphisms that have a likelihood of being heterozygous that is above a specified threshold.

US Patent:

20050064476, Mar 24, 2005

Filed:

Aug 6, 2004

Appl. No.:

10/913928

Inventors:

Jing Huang - Sunnyvale CA, US
Michael Shapero - Redwood City CA, US
Keith Jones - Sunnyvale CA, US
Guoying Liu - San Ramon CA, US

Assignee:

Affymetrix, INC. - Santa Clara CA

International Classification:

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

US Classification:

435006000, 702020000

Abstract:

Methods of identifying changes in genomic DNA copy number are disclosed. Methods for identifying homozygous deletions and genetic amplifications are disclosed. An array of probes designed to detect presence or absence of a plurality of different sequences is also disclosed. The probes are designed to hybridize to sequences that are predicted to be present in a reduced complexity sample. The methods may be used to detect copy number changes in cancerous tissue compared to normal tissue. The methods may be used to diagnose cancer and other diseases associated with chromosomal anomalies.