Patrick J Collins

US Patent:

6753145, Jun 22, 2004

Filed:

Jul 5, 2001

Appl. No.:

09/900084

Inventors:

Nelson R. Holcomb - San Jose CA
Patrick J. Collins - San Francisco CA
Karen W. Shannon - Los Gatos CA
Steven M. Lefkowitz - Millbrae CA

Assignee:

Agilent Technologies, Inc. - Palo Alto CA

International Classification:

C12Q 168

US Classification:

435 6, 4353201, 4352528, 435174, 435183, 382129, 382133, 382153, 382173, 382286, 382291, 702 19, 702 22, 935 10, 935 24, 935 72, 536 221

Abstract:

A buffer composition, method and kit for hybridizing microarrays of nucleic acids bound to an adsorbed polymer surface of a siliceous substrate provide an envelope of conditions to hybridize nucleic acid targets, while preserving theintactness of the adsorbed polymer surface of the array. The buffer composition comprises a non-chelating buffering agent, a pH within a range of pH 6. 4 and 7. 5, a monovalent cation having a monovalent cation concentration that ranges from about 0. 01 M to about 2. 0 M, and optionally relatively lower concentrations of a chelating agent and an ionic surfactant. The total cation concentration of the buffer composition ranges from about 0. 02 M to about 2. 0 M. The method comprises incubating the targets with the microarray in the buffer composition at a temperature between about 55Â C. and 70Â C.

US Patent:

7029854, Apr 18, 2006

Filed:

Nov 22, 2002

Appl. No.:

10/303151

Inventors:

Patrick J. Collins - Daly City CA, US
Keith C. Butler - Newark DE, US
Peter G. Webb - Menlo Park CA, US
Karen W. Shannon - Los Gatos CA, US
Sandra L. Tang - Saratoga CA, US

Assignee:

Agilent Technologies, Inc. - Palo Alto CA

International Classification:

C12Q 1/68

US Classification:

435 6, 435 911, 702 20, 536 243

Abstract:

Methods of identifying a sequence of a nucleic acid that is suitable for use as a surface immobilized probe for two or more mRNA transcripts encoded by the same gene are provided. In practicing the subject methods, a consensus region for the two or more transcripts is first identified, and this identified consensus region is then employed to identify the suitable nucleic acid sequence, e. g. , by using a probe design protocol. The subject invention also includes algorithms for performing the subject methods recorded on a computer readable medium, as well as computational analysis systems that include the same. Also provided are nucleic acid arrays produced with probes having sequences identified by the subject methods, as well as methods for using the same.

US Patent:

7302348, Nov 27, 2007

Filed:

Jun 2, 2004

Appl. No.:

10/859868

Inventors:

Jayati Ghosh - San Jose CA, US
Bill J. Peck - Mountain View CA, US
Eric M. Leproust - San Jose CA, US
Charles David Troup - Livermore CA, US
Glenda Choate Delenstarr - Redwood City CA, US
Patrick J. Collins - San Francisco CA, US
John F. Corson - Mountain View CA, US
Paul K. Wolber - Los Altos CA, US
Xiangyang Zhou - Mountain View CA, US

Assignee:

Agilent Technologies, Inc. - Santa Clara CA

International Classification:

G06F 19/00
G06F 15/00
G11C 17/00

US Classification:

702 19, 700 1, 365 94

Abstract:

A method and system for quantifying and correcting spatial-intensity trends for each channel of a microarray data set having one or more channels. The method and system of one embodiment of the present invention selects a set of features from each channel of the microarray data set. Based on the selected set of features, a surface is used to determine the intensities for all features in each channel of the microarray data set. Spatial-intensity trends within the microarray data set are quantified, based on the surface to the intensities for each channel of the microarray data set. After the surface has been determined, the spatial-intensity trend can be removed from the microarray data set.

US Patent:

20020192650, Dec 19, 2002

Filed:

May 30, 2001

Appl. No.:

09/870939

Inventors:

Douglas Amorese - Los Altos CA, US
Karen Shannon - Los Gatos CA, US
Patrick Collins - San Francisco CA, US
Paul Wolber - Los Altos CA, US

International Classification:

C12Q001/68
C12M001/34

US Classification:

435/006000, 435/287200

Abstract:

A polynucleotide array, and methods of making and using such arrays. The array may include a first set of multiple features each of which has first polynucleotide molecules of at least 400 nucleotides in length, and a second set of features each of which has second polynucleotide molecules of no more than 100 nucleotides in length. The second set of features can be used as control features, or to replace failed sequences in an enzymatic amplification to produce first polynucleotides, or to detect polymorphisms or splice variants which may not be detected by a particular first polynucleotide.

US Patent:

20040101846, May 27, 2004

Filed:

Nov 22, 2002

Appl. No.:

10/303160

Inventors:

Patrick Collins - Daly City CA, US
Anna Tsalenko - Chicago IL, US
Zohar Yakhini - Ramat Hasharon, IL
Peter Webb - Menlo Park CA, US
Karen Shannon - Los Gatos CA, US
Stephanie Fulmer-Smentek - Sunnyvale CA, US

International Classification:

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

US Classification:

435/006000, 702/020000

Abstract:

Methods of identifying a sequence of a probe, e.g., a biopolymeric probe, such as a nucleic acid, that is suitable for use as a surface immobilized probe for a target molecule of interest, e.g., a target nucleic acid, are provided. A feature of the subject methods is that a set of computationally determined initial candidate sequences are empirically evaluated to obtain functional data that is then employed to identify one or more clusters of candidate probe sequences from the initial set such that all candidate probe sequences within each identified cluster exhibitsubstantially the same performance under a plurality of different experiments, specifically a plurality of differential gene expression experiments. A candidate probe from the cluster that exhibits the best performance across the plurality of experimental sets is then selected as the optimum candidate probe, e.g., based on one or more performance metrics. The subject invention also includes algorithms for performing the subject methods recorded on a computer readable medium, as well as computational analysis systems that include the same. Also provided are nucleic acid arrays produced with probes having sequences identified by the subject methods, as well as methods for using the same.

US Patent:

20050136411, Jun 23, 2005

Filed:

Dec 22, 2003

Appl. No.:

10/744434

Inventors:

Patrick Collins - San Francisco CA, US
Khanh Nguyen - San Jose CA, US
Diane Ilsley - San Jose CA, US

International Classification:

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

US Classification:

435006000, 435091200, 702020000

Abstract:

Methods and compositions for linearly amplifying mRNA from small RNA samples to produce antisense RNA are provided In the subject methods, mRNA is converted to a transcription template product by using a promoter primer, where the resultant product at least includes a first strand cDNA template domain and a double-stranded RNA polymerase promoter. A feature of the subject methods is that the ratio of the promoter-primer to the input RNA is chosen to provide for a high yield of selective RNA product. Additional optional features include the use of a thermostabilizing agent, e.g., raffinose, trehalose, etc., in the reverse transcription step and/or the use of a polyalkylene oxide, e.g., a PEG, in the in vitro transcription step. Also provided are compositions and kits that find use in practicing the subject methods. The subject invention finds use a variety of different applications in which the preparation of linearly amplified amounts of cRNA is desired.

US Patent:

20050282174, Dec 22, 2005

Filed:

Jun 19, 2004

Appl. No.:

10/871303

Inventors:

Peter Webb - Menlo Park CA, US
Stephanie Fulmer-Smentek - Sunnyvale CA, US
Patrick Collins - San Francisco CA, US
Karen Shannon - Los Gatos CA, US
Jing Gao - Santa Clara CA, US

International Classification:

C12Q001/68

US Classification:

435006000

Abstract:

Methods and systems for identifying and selecting nucleic acid probes for detecting a target with a nucleic acid probe array or microarray, comprising selecting a plurality of candidate probes, forming a plurality of clusters from the plurality of candidate probes according to hybridization characteristics of the candidate probes, forming at least one SuperCluster from the clusters; and selecting at least one probe from each SuperCluster for the probe array.

US Patent:

20060040287, Feb 23, 2006

Filed:

May 26, 2005

Appl. No.:

11/139896

Inventors:

John Corson - Mountain View CA, US
Charles Troup - Livermore CA, US
Eric Leproust - San Jose CA, US
Glenda Delenstarr - Redwood City CA, US
Jayati Ghosh - Sunnyvale CA, US
Patrick Collins - San Francisco CA, US

International Classification:

C12Q 1/68
G06F 19/00

US Classification:

435006000, 702020000

Abstract:

A method and system for quantify random errors, sequence-dependent trends, and spatial-intensity trends in one or more channels of microarray data sets. The method and system of one embodiment of the present invention is directed to a method for quantifying random errors, sequence-dependent trends, and spatial-intensity trends present in microarray data sets. An additive error equation is employed to quantify background noise present in feature intensities due to random errors, sequence-dependent trends, and spatial-intensity trends.