Christopher J Becker

US Patent:

6468748, Oct 22, 2002

Filed:

Feb 29, 2000

Appl. No.:

09/515277

Inventors:

Joseph A. Monforte - Berkeley CA
Thomas A. Shaler - Fremont CA
Yuping Tan - Fremont CA
Christopher H. Becker - Palo Alto CA

Assignee:

Sequenom, Inc. - San Diego CA

International Classification:

C12Q 168

US Classification:

435 6, 435 911, 435 912, 536 221, 536 231, 536 2433, 250281, 250282, 250283, 250280, 250287, 210635, 210656

Abstract:

This invention relates to methods for screening nucleic acids for mutations by analyzing nonrandomly fragmented nucleic acids using mass spectrometric techniques and to procedures for improving mass resolution and mass accuracy of these methods of detecting mutations.

US Patent:

6635452, Oct 21, 2003

Filed:

Dec 10, 1997

Appl. No.:

08/988024

Inventors:

Joseph A. Monforte - Berkeley CA
Christopher H. Becker - Palo Alto CA
Daniel J. Pollart - Menlo Park CA
Thomas A. Shaler - Menlo Park CA

Assignee:

Sequenom Inc. - San Diego CA

International Classification:

C12Q 168

US Classification:

435 911, 435 912, 435 6, 536 221, 536 231, 536 243, 536 2431, 536 2433, 536 253, 536 2532, 436172

Abstract:

Using nonvolatile, releasable, mass-labels, the present invention provides for the synthesis and use of mass-labeled compounds to specifically interact with biomolecular targets. Following binding of the mass-labeled compounds to the target molecule, the unique mass-label can be analyzed using mass spectrometry to identify and characterize the target molecule. In one embodiment of the invention, a mass-labeled oligonucleotide probe is used to identify a specific gene sequence. A myriad of mass-labeled compounds may be produced for use in a wide variety of interactions such as oligonucleotide-oligonucleotide hybridization, polynucleotide-polynucleotide interactions, enzyme-substrate or substrate analog/intermediate interactions, polypeptide-nucleic acid interactions, protein-ligand interactions, receptor-ligand interactions, polypeptide-metal interactions, nucleic acid-metal interactions or antigen-antibody interactions. Also contemplated are combinatorial processes for creating large libraries of compounds permitting rapid screening for a wide variety of targets.

US Patent:

6764822, Jul 20, 2004

Filed:

Apr 3, 2000

Appl. No.:

09/541210

Inventors:

John M. Butler - Menlo Park CA
Jia Li - Union City CA
Joseph A. Monforte - Berkeley CA
Christopher H. Becker - Palo Alto CA

Assignee:

Sequenom, Inc. - San Diego CA

International Classification:

C12Q 168

US Classification:

435 6, 435 912, 436 94, 436173, 536 253, 536 254

Abstract:

The present invention is related to the fields of genetic mapping and genetic identity detection, including forensic identification and paternity testing. This invention is more specifically directed to the use of mass spectrometry to detect length variation in DNA nucleotide sequence repeats (including variants of common alleles), such as microsatellites and short tandem repeats, and to DNA sequences provided as primers for the analysis of DNA tandem nucleotide repeat polymorphisms at specific loci on specific chromosomes.

US Patent:

6835927, Dec 28, 2004

Filed:

Oct 15, 2002

Appl. No.:

10/272425

Inventors:

Christopher H. Becker - Palo Alto CA
Curtis A. Hastings - Arlington VA
Scott M. Norton - Sunnyvale CA

Assignee:

Surromed, Inc. - Menlo Park CA

International Classification:

B01D 5944

US Classification:

250282, 250281, 250288

Abstract:

Relative quantitative information about components of chemical or biological samples can be obtained from mass spectra by normalizing the spectra to yield peak intensity values that accurately reflect concentrations of the responsible species. A normalization factor is computed from peak intensities of those inherent components whose concentration remains constant across a series of samples. Relative concentrations of a component occurring in different samples can be estimated from the normalized peak intensities. Unlike conventional methods, internal standards or additional reagents are not required. The methods are particularly useful for differential phenotyping in proteomics and metabolomics research, in which molecules varying in concentration across samples are identified. These identified species may serve as biological markers for disease or response to therapy.

US Patent:

6949633, Sep 27, 2005

Filed:

Aug 25, 1998

Appl. No.:

09/139386

Inventors:

Joseph Albert Monforte - Berkeley CA, US
Christopher Hank Becker - Palo Alto CA, US
Thomas Andrew Shaler - Menlo Park CA, US
Daniel Joseph Pollart - Alameda CA, US

Assignee:

Sequenom, Inc. - San Diego CA

International Classification:

C07H019/00
C07H021/00
C07H021/04

US Classification:

536 221, 536 231, 536 2433, 536 2532

Abstract:

The present invention provides modified oligonucleotide primers designed to incorporate a cleavable moiety so that a 3′ portion of the primer (linked to an extension product) can be released from an upstream 5′ portion of the primer. Upon selective cleavage of the cleavable site, primer extension products that contain about five or fewer base pairs of the primer sequence are released, to provide more useful sizing and sequence information per fragment than extension products containing the entire primer.

US Patent:

7087896, Aug 8, 2006

Filed:

Dec 27, 2004

Appl. No.:

11/023234

Inventors:

Christopher H. Becker - Palo Alto CA, US
Curtis A. Hastings - Bethesda MD, US
Scott M. Norton - Durham NC, US
Sushmita Mimi Roy - Santa Clara CA, US
Weixun Wang - Mountain View CA, US
Haihong Zhou - Mountain View CA, US
Thomas Andrew Shaler - Fremont CA, US
Praveen Kumar - Santa Clara CA, US
Markus Anderle - Campbell CA, US
Hua Lin - Sunnyvale CA, US

Assignee:

PPD Biomarker Discovery Sciences, LLC - Wilmington NC

International Classification:

B01D 59/44
H01J 49/00

US Classification:

250282, 250281

Abstract:

Relative quantitative information about components of chemical or biological samples can be obtained from mass spectra by normalizing the spectra to yield peak intensity values that accurately reflect concentrations of the responsible species. A normalization factor is computed from peak intensities of those inherent components whose concentration remains constant across a series of samples. Relative concentrations of a component occurring in different samples can be estimated from the normalized peak intensities. Unlike conventional methods, internal standards or additional reagents are not required. The methods are particularly useful for differential phenotyping in proteomics and metabolomics research, in which molecules varying in concentration across samples are identified. These identified species may serve as biological markers for disease or response to therapy.

US Patent:

7108985, Sep 19, 2006

Filed:

Apr 3, 2002

Appl. No.:

10/115301

Inventors:

Christopher Becker - Palo Alto CA, US
James R. LaDine - Whitinsville MA, US
Thomas A. Shaler - Fremont CA, US
Chia-Hui Paul Shieh - Fremont CA, US

Assignee:

Thermo Finnigan, LLC - San Jose CA

International Classification:

G01N 33/53
G01N 24/00
G01N 33/532
G01N 33/534
C12Q 1/37
C07K 1/10
C07K 1/14

US Classification:

435 71, 435 75, 435 23, 436173, 436544, 436545, 436824, 530402, 530409, 530412

Abstract:

Methods and reagents for obtaining simplified mixtures of peptides from a sample containing a number of peptides are disclosed. The simplified sample can be easier to analyze than the original peptide sample yet it is representative of all or nearly all of the proteins present in the mixed protein sample from which the original and more complex peptide sample was derived. The methods entail the use of tagging moieties that include an amino-acid-specific reactive group (R). The tagging moieties “tag” peptides or proteins at specific amino acids (e. g. , by reacting with an amino acid to form a covalent bond), ultimately allowing the isolation of peptides that contain those specific amino acids. Other methods entail the used of a reactive moiety (R) that comprises a reagent that selectively interacts with selected proteins, either covalently or noncovalently. For example, Rcan be a natural ligand for a receptor that is to be tagged or a protein that interacts with a second protein that is to be tagged.

US Patent:

7132519, Nov 7, 2006

Filed:

Jul 22, 2002

Appl. No.:

10/202189

Inventors:

Joseph A. Monforte - Berkeley CA, US
Christopher H. Becker - Palo Alto CA, US
Daniel J. Pollart - Menlo Park CA, US
Thomas A. Shaler - Menlo Park CA, US

Assignee:

Sequenom, Inc. - San Diego CA

International Classification:

C07H 21/00
C07H 21/02
A61K 38/00
C07K 1/00
C12Q 1/68

US Classification:

536 221, 536 231, 536 253, 536 266, 435 6, 530300, 530350

Abstract:

Releasable tag reagents for use in the detection and analysis of target molecules, particular in mass spectrometric analyses are provided. Also provided are methods of detection that employ releasable tag reagents.