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.
Encoding And Decoding Reactions For Determining Target Molecules
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.
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.
Proximity Probing Of Target Proteins Comprising Restriction And/Or Extension
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.
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.
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.
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.
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.
Dr. Andersen graduated from the University of South Dakota Sanford School of Medicine in 1989. He works in Omaha, NE and specializes in Family Medicine. Dr. Andersen is affiliated with CHI Health Lakeside Hospital.
Dr. Andersen graduated from the University of Arkansas College of Medicine at Little Rock in 1990. He works in Little Rock, AR and specializes in Psychiatry. Dr. Andersen is affiliated with Arkansas Childrens Hospital and University Arkansas Of Medical Sciences.
Apr 2012 to 2000 Consultant under contractCTI Foods Wilder, ID Jun 2010 to Mar 2012 Director of Technical ServicesJohn Soules Foods Tyler, TX Jan 2007 to Jun 2010 Director of Quality AssuranceBox, Inc San Diego, CA Mar 1995 to Dec 2006 Senior Product Manager, Quality Assurance, JackMedical Biology Institute La Jolla, CA Jan 1993 to Jan 1995 Post-doctorial FellowAndersen's Red Mountain Durocs Valley Center, CA 1980 to 1994 Owner OperatorUniversity of Wyoming
1990 to 1992 Graduate Teaching and Research AssistantUniversity of Georgia
1987 to 1989 Graduate Teaching and Research AssistantCalifornia State Polytechnic University Pomona, CA 1987 to 1987California State Polytechnic University
1982 to 1987 Student Employee
Education:
University of Wyoming Laramie, WY 1992 Ph.D. in Animal Science/Food ScienceUniversity of Georgia Athens, GA 1989 MS in Animal Science/Meats and Muscle BiologyCalifornia State Polytechnic University Pomona, CA 1987 BS in Animal Science/Animal Production
Mar 2011 to 2000 Return to Vendor ClerkAndersen General Contracting
Dec 1977 to 2000Woodbridge Middle School Woodbridge, VA Jan 1979 to Jun 2009 A technology education instructor and managerWoodbridge Middle School
2001 to 2004
Education:
Northern Virginia Community College Jan 2002 to Jan 2008 Computer TechnologyVirigina Tech Falls Church, VA Jan 1988 to Jan 1993 MS in Curriculum and InstructionState University of New York at Oswego Oswego, NY Dec 1977 B.S. in Teacher Education
Apr 2012 to 2000 Consultant under contractCTI Foods Wilder, ID Jun 2010 to Mar 2012 Director of Technical ServicesJohn Soules Foods Tyler, TX Jan 2007 to Jun 2010 Director of Quality AssuranceBox, Inc San Diego, CA Mar 1995 to Dec 2006 Senior Product Manager, Quality Assurance, JackMedical Biology Institute La Jolla, CA Jan 1993 to Jan 1995 Post-doctorial Fellow
Education:
University of Wyoming Laramie, WY 1992 Ph.D. in Animal Science/Food ScienceUniversity of Georgia Athens, GA 1989 MS in Animal Science/Meats and Muscle BiologyCalifornia State Polytechnic University Pomona, CA 1987 BS in Animal Science/Animal Production
The Meridian Group, Inc. Andersen Roofing Contractor (OLD). Meridian Group. Mark Andersen Construction. Mark Anderson. Mark Andersen. Anderson & Associates. The Project Planning Center. Themco. Thrempco Construction & Remodeling Services. Interior Finishing. Contractor - Remodel & Repair
Indeed, policy watchers were scratching their heads over the series of conflicting announcements. The PBoC is scrambling to ensure stability in China's notoriously volatile share market, said Mark Andersen, global co-head of Asset Allocation at UBS CIO Wealth Management.
Date: Apr 20, 2015
Category: Business
Source: Google
Asian Stocks Follow US Equities Higher as Yen Holds Decline
As valuations get stretched we have to dampenexpectations a little bit, Mark Andersen, co-head of globalasset allocation at UBS Group AGs wealth management unit, saidin a Bloomberg TV interview in Hong Kong. We see a very, verydivergent world. Central banks are going to have to err on theca
Date: Dec 03, 2014
Category: Business
Source: Google
European Stocks Decline as Violence in Iraq Escalates
The developments in Iraq will continue to be oninvestors radars as a spike in oil prices always holds thepotential to spook market participants, said Mark Andersen,co-head of global asset allocation at UBS AGs wealth-managementunit in Hong Kong.
With lower inflation and some soft housing data there is no rush to do any strong tapering. The Fed doesnt want to make a policy mistake by tapering too aggressively, said Mark Andersen, head of asset allocation at UBS.
Date: Sep 18, 2013
Category: Business
Source: Google
European Stocks Are Little Changed as Danone Rallies
European equity markets are still holding up well on theback of last weeks PMI numbers, which hints that growth inEurope will advance in the coming quarters, said Mark Andersen, who helps oversee $1.7 trillion as head of assetallocation at UBS AG in Zurich. Earnings still need to come instro
Date: Jul 29, 2013
Category: Business
Source: Google
European Stocks Retreat the Most in Two Weeks After Fed Minutes
The FOMC minutes may have started an adjustment process for the markets, with a bit of realism setting in with investors, Mark Andersen, who helps oversee $1.7 trillion as co-head of asset allocation at UBS AG in Zurich, said in a telephone interview. You cant have both stronger growth and ever
Mark Andersen, Bay County supervisor, said he had at least eight suspicious forms from Strategic Allied Consulting and was still looking. He said the forms were easy to spot because they had all been filled out by one person and then signed by others.
Date: Sep 28, 2012
Category: U.S.
Source: Google
Raul Rallies Phils | Philadelphia Inquirer | 2011-08-01
around Philadelphia, and bought him coffee. ("This is a great team," Pence said.) He originally packed for a 10-game road trip with Houston, and those clothes are all he has. His black cleats were spray-painted red by assistant athletic trainer Mark Andersen. That'll have to do until later this week.
University of Wisconsin-Stevens Point - Psychology
Mark Andersen
Relationship:
Single
About:
Born and Bred in Western Australia currently living in the burbs of Perth. Not much of a sport fanatic mostly in to motorsport Moto GP V8 Tourers, for the most part a bike guy. All in all laid back an...
Bragging Rights:
Father of 3 children that just light up my day.Own a ducati 900ss that I'm trying to get back on the road not soon enough hanging out to get back on 2 wheels..