Jeffrey Stephen Sampson

US Patent:

7291471, Nov 6, 2007

Filed:

Nov 21, 2005

Appl. No.:

11/284495

Inventors:

Jeffrey R. Sampson - San Francisco CA, US
Joel Myerson - Berkeley CA, US

Assignee:

Agilent Technologies, Inc. - Santa Clara CA

International Classification:

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

US Classification:

435 6, 4352872, 536 253

Abstract:

Oligonucleotide arrays having features that include cleavable oligonucleotides are disclosed, as well as methods of making such arrays. Methods of synthesizing an oligonucleotide on a surface of a substrate are described.

US Patent:

7371580, May 13, 2008

Filed:

Aug 24, 2001

Appl. No.:

09/938937

Inventors:

Zohar H. Yakhini - Ya′acov, IL
Jeffrey R Sampson - Burlingame CA, US
Joel Myerson - Berkeley CA, US

Assignee:

Agilent Technologies, Inc. - Santa Clara CA

International Classification:

G01N 33/00
C12Q 1/68
C12M 1/36

US Classification:

436 94, 435 6, 4352872, 536 231, 536 243, 436800

Abstract:

The present invention provides a system and methods for assaying nucleic acid molecules with reduced levels of background signal and enhanced specificity and sensitivity. In particular, the present invention provides a system and methods for detecting, sorting, tracking and characterizing nucleic acid molecules using hybridization assays with reduced levels of undesirable cross hybridization and reduced levels of intramolecular secondary structure.

US Patent:

7399844, Jul 15, 2008

Filed:

Apr 17, 2001

Appl. No.:

09/836012

Inventors:

Jeffrey R. Sampson - Burlingame CA, US
Joel Myerson - Berkeley CA, US
Anna M. Tsalenko - Chicago IL, US
Nicholas M. Sampas - San Jose CA, US
Peter G. Webb - Menlo Park CA, US
Zohar H. Yakhini - Ya'Acov, IL

Assignee:

Agilent Technologies, Inc. - Santa Clara CA

International Classification:

C07H 19/00
C12Q 1/68

US Classification:

536 221, 435 6

Abstract:

Methods and reagents are disclosed which provide for more sensitive, more accurate and higher through-put analyses of target nucleic acid sequences. The methods and reagents of the present invention may be generically applied to generally any target nucleic acid sequence and do not require a priori information about the presence, location or identity of mutations in the target nucleic acid sequence. The reagents of the invention are mixtures of oligonucleotide precursors having a high level of coverage and mass number complexity, and also having tags analyzable by mass spectrometry which are covalently linked to the precursors through cleavable bonds. A method is also disclosed for analyzing a target nucleic acid sequence employing the mixtures of oligonucleotide precursors having tags analyzable by mass spectrometry covalently linked to the oligonucleotide precursors through cleavable bonds, and chemical or enzymatic assays to alter the mass of the oligonucleotide precursors prior to mass spectral analysis. The enzymatic assay may be a polymerase extension assay or a ligation-based assay. The kits for carrying out the methods of the invention are also disclosed.

US Patent:

7544471, Jun 9, 2009

Filed:

Jul 30, 2005

Appl. No.:

11/193271

Inventors:

Hui Wang - Palo Alto CA, US
Jeffrey R. Sampson - San Francisco CA, US

Assignee:

Agilent Technologies, Inc. - Santa Clara CA

International Classification:

C12Q 1/68

US Classification:

435 6

Abstract:

In particular embodiments in accordance with the present invention, a wax-embedded tissue specimen is digested and the resulting digested tissue specimen is purified to provide a purified RNA fraction. The purified RNA fraction is treated with one or more enzymes to provide a sample containing dephosphorylated RNA; the sample is contacted with an enzyme having an RNA ligation activity in the presence of a labeled substrate to provide labeled RNA. Kits for performing the described methods are described. Methods of performing an array analysis of a labeled RNA sample are also described.

US Patent:

7682809, Mar 23, 2010

Filed:

Jan 11, 2008

Appl. No.:

12/013377

Inventors:

Jeffrey R. Sampson - San Francisco CA, US

Assignee:

Agilent Technologies, Inc. - Santa Clara CA

International Classification:

C12P 19/34
C12Q 1/68
G01N 15/06
C07H 21/04

US Classification:

435 911, 435 6, 536 231, 536 243, 422 681

Abstract:

A method for sequencing a nucleic acid is provided. In certain embodiments, the method includes contacting a nucleic acid duplex comprising a nucleic acid template and a primer annealed to the template with a reagent mix under primer extension conditions to produce an extended primer and ATP. The reagent mix may contain an adenosine-2′-deoxynucleoside tetraphosphate moiety and a polymerase. The method further includes detecting the produced ATP. Also provided are adenosine-2′-deoxynucleoside tetraphosphate moieties that find use in the subject methods. Also provided are kits containing the adenosine-2′-deoxynucleoside tetraphosphate moieties for use in the subject methods.

US Patent:

7807356, Oct 5, 2010

Filed:

Mar 9, 2006

Appl. No.:

11/372971

Inventors:

Jeffrey R. Sampson - San Francisco CA, US
Hui Wang - Palo Alto CA, US

Assignee:

Agilent Technologies, Inc. - Santa Clara CA

International Classification:

C12Q 1/68

US Classification:

435 6

Abstract:

Embodiments of labeled nucleotide compositions are described. Methods are described in which a sample containing RNA is contacted with an enzyme having an RNA ligation activity in the presence of a labeled nucleotide composition to provide labeled RNA. Methods of performing an array analysis of a labeled RNA sample are also described.

US Patent:

7867703, Jan 11, 2011

Filed:

Aug 26, 2004

Appl. No.:

10/927809

Inventors:

Jeffrey R. Sampson - San Francisco CA, US
Barney E. Saunders - Cupertino CA, US

Assignee:

Agilent Technologies, Inc. - Santa Clara CA

International Classification:

C12Q 1/68
C12P 19/34
C12M 1/34
C07H 21/02
C07H 21/04

US Classification:

435 6, 435 912, 4352872, 536 231, 536 243, 536 2433

Abstract:

A method for providing defined mixtures of nucleic acids is described. In certain embodiments, the method uses oligonucleotide probes attached to a solid support as a sequence-specific affinity agent to isolate and facilitate the amplification of defined nucleic acid fragment mixtures.

US Patent:

20020197618, Dec 26, 2002

Filed:

Jan 16, 2002

Appl. No.:

10/052926

Inventors:

Jeffrey Sampson - Burlingame CA, US

International Classification:

C12Q001/68
C12M001/34

US Classification:

435/006000, 435/287200

Abstract:

The present invention provides an improved method of nanopore sequencing by generating a nucleic acid molecule to be sequenced having tandem repeats of a sequence, and also having modified nucleotides which reduce the levels of secondary structure. The presence of tandemly repeated sequence and the absence of secondary structure increases the rate of sequencing and accuracy of sequences generated by nanopore sequencing.