Mark Steven Andersen

US Patent:

7364855, Apr 29, 2008

Filed:

May 2, 2005

Appl. No.:

11/119985

Inventors:

Mark R. Andersen - Carlsbad CA, US
Michael W. Hunkapiller - San Carlos CA, US
Steven M. Menchen - Fremont CA, US

Assignee:

Applera Corporation - Foster City CA

International Classification:

C12Q 1/68
C07H 21/02
C07H 21/04

US Classification:

435 6, 536 231, 536 243

Abstract:

Ligation-based methods and kits are disclosed for determining the degree of methylation of one or more target nucleotides. In certain embodiments, the methylation status of one or more target nucleotides is determined by generating misligation products. In certain embodiments, at least one target nucleotide is amplified prior to the ligation reaction. In certain embodiments, at least one ligation product, at least one ligation product surrogate, at least one misligation product, at least one misligation product surrogate, or combinations thereof are amplified. In certain embodiments, one or more ligation probes comprise at least one nucleotide analog, at least one Modification, at least one mismatched nucleotide, or combinations thereof.

US Patent:

7601821, Oct 13, 2009

Filed:

Mar 24, 2005

Appl. No.:

11/090830

Inventors:

Mark R. Andersen - Carlsbad CA, US
Kenneth J. Livak - San Jose CA, US
Adam Broomer - Foster City CA, US
Caifu Chen - Palo Alto CA, US

Assignee:

Applied Biosystems, LLC - Carlsbad CA

International Classification:

C07H 21/04
C12Q 1/68

US Classification:

536 221, 435 6

Abstract:

The present invention is directed to methods, reagents, and kits for detecting the presence or absence of (or quantifying) target polynucleotide sequences and proteins in at least one sample using encoding and decoding reactions. When a particular target polynucleotide is present in a sample for example, a reaction product is formed in the encoding reaction that includes addressable primer portions. At least one labeling probe and at least one address primer can be employed in the decoding amplification reaction thereby providing a detectable signal value depending upon whether a sequence is present or absent. In some embodiments, the encoding comprises a ligation reaction with linker probes, and single nucleotide polymorphisms (SNPs) are analyzed.

US Patent:

20060234252, Oct 19, 2006

Filed:

Jul 1, 2005

Appl. No.:

11/173569

Inventors:

Mark Andersen - Carlsbad CA, US

Assignee:

Applera Corporation - Foster City CA

International Classification:

C12Q 1/68

US Classification:

435006000

Abstract:

Methods for determining the methylation state of at least one target nucleotide that employ a reaction catalyzed by a structure-specific nuclease, typically coupled with a ligation reaction are disclosed. By detecting the cleaved flap, a ligation product, a ligation product surrogate, a hybridization complex, or combinations thereof, one can infer the degree to which the corresponding target nucleotide is methylated. Certain of the disclosed methods are particularly useful for evaluating bisulfite-treated target sequences and determining the degree of target nucleotide methylation. The disclosed methods are well suited for rapidly analyzing a large number of target sequences, typically in one or more multiplex reactions. Kits for performing coupled nuclease and ligase methylation detection assays are also disclosed.

US Patent:

20070026430, Feb 1, 2007

Filed:

Jun 30, 2006

Appl. No.:

11/428191

Inventors:

Mark Andersen - Carlsbad CA, US
Benjamin Schroeder - San Mateo CA, US
Kai Lao - Pleasanton CA, US

Assignee:

APPLERA CORPORATION - Foster City CA

International Classification:

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

US Classification:

435006000, 435091200, 536024300

Abstract:

The present teachings provide methods, compositions, and kits for detecting target analytes, including proteins. In some embodiments, cleavage reactions are performed in the context of proximity probe reactions that query target proteins, wherein the presence and/or quantity of cleavage products is indicative of the presence and/or quantity of a target protein. In some embodiments, the cleavage fragments are quantitated using a real time PCR assay comprising a stem-loop primer, wherein the stem-loop primer comprises a self-complementary hairpin structure and a free 3′ end end complementary to the cleavage product. In some embodiments, polymerase extension approaches are employed in the context of proximity probe reactions.

US Patent:

20070219364, Sep 20, 2007

Filed:

Dec 22, 2006

Appl. No.:

11/615626

Inventors:

Mark Andersen - Carlsbad CA, US
Michael Hunkapiller - San Carlos CA, US
Kenneth Livak - San Jose CA, US
Eugene Spier - Palo Alto CA, US
H. Wenz - Redwood City CA, US

Assignee:

APPLERA CORPORATION - Foster City CA

International Classification:

C07H 21/00

US Classification:

536024300

Abstract:

The present invention relates to methods and kits for detecting the presence or absence of (or quantitating) target nucleic acid sequences using ligation and amplification. The invention also relates to methods, reagents, and kits that employ addressable portions and labeled probes.

US Patent:

20090142761, Jun 4, 2009

Filed:

Apr 28, 2008

Appl. No.:

12/111008

Inventors:

Mark R. Andersen - Carlsbad CA, US
Michael W. Hunkapiller - San Carlos CA, US
Steven M. Menchen - Fremont CA, US

Assignee:

Applera Corporation - Foster City CA

International Classification:

C12Q 1/68

US Classification:

435 6

Abstract:

Ligation-based methods and kits are disclosed for determining the degree of methylation of one or more target nucleotides. In certain embodiments, the methylation status of one or more target nucleotides is determined by generating misligation products. In certain embodiments, at least one target nucleotide is amplified prior to the ligation reaction. In certain embodiments, at least one ligation product, at least one ligation product surrogate, at least one misligation product, at least one misligation product surrogate, or combinations thereof are amplified. In certain embodiments, one or more ligation probes comprise at least one nucleotide analog, at least one Modification, at least one mismatched nucleotide, or combinations thereof.

US Patent:

20090247425, Oct 1, 2009

Filed:

Mar 28, 2008

Appl. No.:

12/058531

Inventors:

Hua Zhang - Carlsbad CA, US
Mark Andersen - Carlsbad CA, US

Assignee:

INVITROGEN CORPORATION - Carlsbad CA

International Classification:

C40B 40/06
C40B 50/00
C12N 9/24
C12N 9/12
C12N 9/16
C40B 50/14

US Classification:

506 16, 506 23, 506 30, 435200, 435196, 435194

Abstract:

The present disclosure relates generally to compositions and methods for the reuse of arrays, including microarrays. Specifically, the present disclosure discloses polynucleotide targets comprising nucleotide analogs that are not present within the probe polynucleotides immobilized on the array. The nucleotide-analog containing targets can be chemically modified to reduce their thermal stability and thus easier to remove from the array. In preferred embodiments, the disclosure relates to DNA probes hybridized to single-stranded deoxyribouridine-containing targets, the targets subsequently being chemically modified using a uracil DNA glycosylase and/or nuclease. Accordingly, the disclosure allows for the glycosylase treated, deoxyuridine-containing targets to be removed from the array by exposure to less stringent denaturing conditions than otherwise would have been required. Using less stringent denaturing conditions permits reuse of the array by reducing damage to the probe polynucleotides immobilized on the array during target removal.

US Patent:

20110143343, Jun 16, 2011

Filed:

Jul 26, 2010

Appl. No.:

12/843877

Inventors:

MARK R. ANDERSEN - CARLSBAD CA, US
MICHAEL W. HUNKAPILLER - SAN CARLOS CA, US
STEVEN M. MENCHEN - FREMONT CA, US

Assignee:

Applied Biosystems, LLC - Carlsbad CA

International Classification:

C12Q 1/68

US Classification:

435 611

Abstract:

Ligation-based methods and kits are disclosed for determining the degree of methylation of one or more target nucleotides. In certain embodiments, the methylation status of one or more target nucleotides is determined by generating misligation products. In certain embodiments, at least one target nucleotide is amplified prior to the ligation reaction. In certain embodiments, at least one ligation product, at least one ligation product surrogate, at least one misligation product, at least one misligation product surrogate, or combinations thereof are amplified. In certain embodiments, one or more ligation probes comprise at least one nucleotide analog, at least one Modification, at least one mismatched nucleotide, or combinations thereof.