Elaine M Weidenhammer

US Patent:

6492122, Dec 10, 2002

Filed:

Oct 10, 2001

Appl. No.:

09/975408

Inventors:

Elaine M. Weidenhammer - San Diego CA
Ling Wang - San Diego CA
Xiao Xu - San Diego CA
Michael J. Heller - Encinitas CA
Brenda F. Kahl - San Diego CA

Assignee:

Nanogen, Inc. - San Diego CA

International Classification:

C12Q 168

US Classification:

435 6, 435 71, 435 911, 435 912, 4352872, 536 221, 536 231, 536 243, 536 2431, 536 2432, 536 2433

Abstract:

The present invention presents techniques useful in methods for gene expression monitoring, and other nucleic acid hybridization assays, that utilize microelectronic arrays to drive the transport and hybridization of nucleic acids. Particularly, methods for normalizing the signals of individual microlocations by the use of an internal control sequence probe are provided. These methods are particularly useful for hybridization assays in which a quantitative comparison of the hybridization of several different sequences at a plurality of microlocations is desired, such as in gene expression analyses.

US Patent:

20020119484, Aug 29, 2002

Filed:

Feb 12, 2002

Appl. No.:

10/075579

Inventors:

Elaine Weidenhammer - San Diego CA, US
Xiao Xu - San Diego CA, US
Michael Heller - Encinitas CA, US
Brenda Kahl - San Diego CA, US

Assignee:

Nanogen, Inc. - San Diego CA

International Classification:

C12Q001/68
G06F019/00
C12P019/34
G01N033/48
G01N033/50

US Classification:

435/006000, 702/020000, 435/091200

Abstract:

The present invention presents methods for gene expression monitoring that utilize microelectronic arrays to drive the transport and hybridization of nucleic acids. Procedures are described for generating mRNA expression samples for use in these methods from populations of cells, tissues, or other biological source materials, that may differ in their physiological and/or pathological state. Provided in the invention are methods for generating a reusable nucleic acid transcript library from mRNA in a sample of biological material. In order to improve gene expression monitoring on the microelectronic arrays, the transcripts are amplified to produce sample nucleic acid amplicons of a defined length. Because multiple sample amplicons may be selectively hybridized to controlled sites in the electronic array, the gene expression profiles of the polynucleotide populations from different sources can be directly compared in an array format using electronic hybridization methodologies. Also provided in the invention are methods for detecting the level of sample amplicons using electronically assisted primer extension detection, and utilizing individual test site hybridization controls. The hybridization data collected utilizing the improved methods of the present invention will allow the correlation of changes in mRNA level with the corresponding expression of the encoded protein in the biological source material, and thus aid in studying the role of gene expression in disease.

US Patent:

6379897, Apr 30, 2002

Filed:

Nov 9, 2000

Appl. No.:

09/710200

Inventors:

Elaine M. Weidenhammer - San diego CA
Ling Wang - San diego CA
Xiao Xu - San diego CA
Michael J. Heller - Encinitas CA
Brenda F. Kahl - San Diego CA

Assignee:

Nanogen, Inc. - San Diego CA

International Classification:

C12Q 168

US Classification:

435 6, 435 71, 435 911, 435 912, 4352852, 4352872, 536 221, 536 231, 536 243, 536 2431, 536 2432, 536 2433

Abstract:

The present invention presents methods for gene expression monitoring that utilize microelectronic arrays to drive the transport and hybridization of nucleic acids. Procedures are described for generating mRNA expression samples for use in these methods from populations of cells, tissues, or other biological source materials, that may differ in their physiological and/or pathological state. Provided in the invention are methods for generating a reusable nucleic acid transcript library from mRNA in a sample of biological material. In order to improve gene expression monitoring on the microelectronic arrays, the transcripts are amplified to produce sample nucleic acid amplicons of a defined length. Because multiple sample amplicons may be selectively hybridized to controlled sites in the electronic array, the gene expression profiles of the polynucleotide populations from different sources can be directly compared in an array format using electronic hybridization methodologies. Also provided in the invention are methods for detecting the level of sample amplicons using electronically assisted primer extension detection, and utilizing individual test site hybridization controls.