James A Hicks

US Patent:

20070207481, Sep 6, 2007

Filed:

Dec 14, 2006

Appl. No.:

11/639674

Inventors:

Michael Wigler - Cold Spring Harbor NY, US
James Hicks - Cold Spring Harbor NY, US
Larry Norton - New York NY, US
Anders Zettenberg - Djursholm, SE

International Classification:

C12Q 1/68
G06F 19/00
C07H 21/04

US Classification:

435006000, 702020000, 536024300

Abstract:

The present invention relates to methods and compositions for detecting genomic rearrangements (e.g., amplification) at one or more genetic loci and various applications of such methods and compositions. Examples of genetic loci include HER2, TOP2A and other loci on the human chromosome 17.

US Patent:

20100227768, Sep 9, 2010

Filed:

Dec 14, 2006

Appl. No.:

11/639712

Inventors:

Michael H. Wigler - Cold Spring Harbor NY, US
James B. Hicks - Cold Spring Harbor NY, US
Alexander Krasnitz - Cold Spring Harbor NY, US
Anders P. Zettenberg - Stockholm, SE

International Classification:

C40B 30/02

US Classification:

506 8

Abstract:

The present invention provides methods and compositions related to genomic profiling, and in particular, to assigning probabilistic measure of clinical outcome for a patient having a disease or a tumor using segmented genomic profiles such as those produced by representational oligonucleotide microarray analysis (ROMA).

US Patent:

20100273674, Oct 28, 2010

Filed:

Sep 16, 2008

Appl. No.:

12/678423

Inventors:

Sitharthan Kamalakaran - Pelham NY, US
Robert Lucito - East Meadow NY, US
James Bruce Hicks - Lattingtown NY, US

International Classification:

C40B 30/04
C12Q 1/68
C40B 40/06

US Classification:

506 9, 435 6, 506 16

Abstract:

The invention relates to a method for the analysis of ovarian cancer disorders, comprising determining the genomic methylation status of one or more CpG dinucleotides in a sequence selected from the group of sequences according to SEQ ID NO. 1 to 10 and/or SEQ ID NO. 50 to SEQ ID NO. 60. Optionally, additionally following steps are performed, the one or more results from the methylation status test is input into a classifier that is obtained from a Diagnostic Multi Variate Model, calculating a likelihood as to whether the sample is from a normal tissue or an ovarian cancer tissue and/or, calculating an associated p-value for the confidence in the prediction.

US Patent:

20100279879, Nov 4, 2010

Filed:

Sep 16, 2008

Appl. No.:

12/678628

Inventors:

Sitharthan Kamalakaran - Pelham NY, US
Robert Lucito - East Meadow NY, US
James Bruce Hicks - Lattingtown NY, US
Xiaoyue Zhao - Fremont CA, US
Jude Kendall - Bronx NY, US

Assignee:

KONINKLIJKE PHILIPS ELECTRONICS N.V. - EINDHOVEN
COLD SPRING HARBOR LABORATORIES - COLD SPRING HARBOR NY

International Classification:

C12Q 1/68
C40B 30/00
C40B 40/06
C07H 21/04

US Classification:

506 7, 435 6, 506 16, 536 231

Abstract:

Method for the analysis of breast cancer disorders, comprising determining the genomic methylation status of one or more CpG dinucleotides in a sequence selected from the group of sequences according to SEQ ID NO. 1 to 10 and/or SEQ ID NO. 50 to SEQ ID NO. 60. Optionally, additionally following steps are performed, the one or more results from the methylation status test is input into a classifier that is obtained from a Diagnostic Multi Variate Model, calculating a likelihood as to whether the sample is from a normal tissue or an breast cancer tissue and/or, calculating an associated p-value for the confidence in the prediction.

US Patent:

20120004118, Jan 5, 2012

Filed:

Jan 25, 2010

Appl. No.:

13/147105

Inventors:

Sitharthan Kamalakaran - Pelham NY, US
Angel Janevski - New York NY, US
James Bruce Hicks - Cold Spring Harbor NY, US

Assignee:

COLD SPRING HARBOR LABORATORIES - COLD SPRING HARBOR NY
KONINKLIJKE PHILIPS ELECTRONICS N.V. - EINDHOVEN

International Classification:

C40B 30/00
C12Q 1/68
B01J 19/00
C40B 60/12
C12M 1/34
G01N 33/50
H01J 49/26

US Classification:

506 7, 436 94, 435 612, 250282, 506 39, 4352872, 422 681

Abstract:

Provided is a method for the analysis of breast cancer disorders, comprising determining the genomic methylation status of one or more CpG dinucleotides. Furthermore, a computer program product stored on a computer-readable medium comprising software code adapted to perform the steps of the method when executed on a data-processing apparatus is provided. A device comprising means for supporting a clinician is also provided.

US Patent:

20120004855, Jan 5, 2012

Filed:

Dec 22, 2009

Appl. No.:

13/141343

Inventors:

Sitharthan Kamalakaran - Pelham NY, US
Vinay Varadan - New York NY, US
James B. Hicks - Lattingtown NY, US

Assignee:

KONINKLIJKE PHILIPS ELECTRONICS N.V. - EINDHOVEN

International Classification:

G06F 19/00
C40B 40/06

US Classification:

702 19, 506 16

Abstract:

A methylation classification list comprising loci DNA, for which loci the methylation status of the DNA is indicative of likelihood of recurrence of cancer, is provided. Furthermore, a method, apparatus and use for predicting probability of relapse free survival of a subject diagnosed with cancer, are provided.

US Patent:

20120149593, Jun 14, 2012

Filed:

Jan 22, 2010

Appl. No.:

13/145829

Inventors:

James B. Hicks - Cold Spring Harbor NY, US
Gregory J. Hannon - Huntington NY, US
Emily Hodges - Huntington NY, US
Jude Kendall - Bronx NY, US
Andrew D. Smith - Santa Monica CA, US

International Classification:

C40B 30/04
G06F 19/20
C40B 40/06

US Classification:

506 9, 506 16, 702 20

Abstract:

This invention provides methods and arrays for determination of the methylation patterns at single-nucleotide resolution by array-based hybrid selection and next-generation sequencing of bisulfite-treated DNA.

US Patent:

20120172238, Jul 5, 2012

Filed:

Sep 15, 2010

Appl. No.:

13/497062

Inventors:

Vinay Varadan - New York NY, US
Sitharthan Kamalakaran - Pelham NY, US
James Bruce Hicks - Lattingtown NY, US

Assignee:

COLD SPRING HARBOR LABORATORIES - COLD SPRING HARBOR NY
KONINKLIJKE PHILIPS ELECTRONICS N.V. - EINDHOVEN

International Classification:

C40B 20/00
C40B 40/06

US Classification:

506 2, 506 16

Abstract:

The present invention relates to a method for assisting in diagnosing breast cancer and/or monitoring breast cancer progression in a given sample based on the analysis of differential DNA methylation patterns. More particularly, the method is directed to the identification of one or more epigenetic markers that derive from the application of a variety of statistical methods in order to point out the prognostic significance of the difference in methylation states at one or more genomic loci and predict whether the sample analyzed has a good or bad prognosis following treatment.