Mostafa Ronaghi

US Patent:

6828100, Dec 7, 2004

Filed:

Dec 4, 2001

Appl. No.:

09/889812

Inventors:

Mostafa Ronaghi - Palo Alto CA

Assignee:

Biotage AB - Uppsala

International Classification:

C12Q 168

US Classification:

435 6, 435 911, 435 912

Abstract:

The present invention relates to a method of identifying a base at a target position in a sample nucleic acid sequence wherein a primer, which hybridizes to the sample nucleic acid immediately adjacent to the target position, is provided and the sample nucleic acid and primer are subjected to a polymerase reaction in the presence of a nucleotide whereby the nucleotide will only become incorporated if it is complementary to the base in the target position, and said incorporation is detected, characterized in that, a single-stranded nucleic acid binding protein is included in the polymerase reaction step.

US Patent:

6858412, Feb 22, 2005

Filed:

Oct 24, 2001

Appl. No.:

09/999362

Inventors:

Thomas D. Willis - San Francisco CA, US
Paul Hardenbol - Los Altos CA, US
Maneesh Jain - Menlo Park CA, US
Viktor Stolc - Cupertino CA, US
Mostafa Ronaghi - Palo Alto CA, US
Ronald W. Davis - Palo Alto CA, US

Assignee:

The Board of Trustees of the Leland Stanford Junior University - Palo Alto CA

International Classification:

C12P019/34
C12Q001/68
C07H021/02
C07H021/04

US Classification:

435 911, 435 6, 435 912, 536 243, 536 231

Abstract:

The invention is directed to novel methods of multiplexing nucleic acid reactions, including amplification, detection and genotyping. The invention relies on the use of precircle probes that are circularized in the presence of the corresponding target nucleic acids, cleaved, and then amplified.

US Patent:

7459311, Dec 2, 2008

Filed:

Sep 7, 2001

Appl. No.:

10/363231

Inventors:

Pål Nyren - Stockholm, SE
Mostafa Ronaghi - Palo Alto CA, US
Annika Tallsjö - Uppsala, SE

Assignee:

Biotage AB - Uppsala

International Classification:

C12Q 1/68

US Classification:

436 6, 536 221

Abstract:

The present invention provides a method of identifying a base at a target position in a sample nucleic acid sequence, said method comprising: subjecting a primer hybridised to said sample nucleic acid immediately adjacent to the target position, to a polymerase primer extension reaction in the presence of a nucleotide, whereby the nucleotide will only become incorporated if it is complementary to the base in the target position, and determining whether or not said nucleotide is incorporated by detecting whether Ppi is released, the identity of the target base being determined from the identity of any nucleotide incorporated, wherein, where said nucleotide comprises an adenine base, an α-thio triphosphate analogue of said nucleotide is used, and the Rp isomer of said analogue and/or the degradation products of said analogue are eliminated from the polymerase reaction step.

US Patent:

7622281, Nov 24, 2009

Filed:

May 19, 2005

Appl. No.:

11/134683

Inventors:

Mostafa Ronaghi - Palo Alto CA, US
Foad Mashayekhi - San Francisco CA, US

Assignee:

The Board of Trustees of the Leland Stanford Junior University - Palo Alto CA

International Classification:

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

US Classification:

435 912, 435 6, 536 231, 536 243

Abstract:

Described herein are methods and compositions relating to amplifying nucleic acid. In certain embodiments, the invention provides methods for labeling and amplifying a nucleic acid molecule.

US Patent:

7648824, Jan 19, 2010

Filed:

Nov 26, 2008

Appl. No.:

12/323706

Inventors:

Pal Nyren - Stockholm, SE
Mostafa Ronaghi - Palo Alto CA, US
Annika Tallsjo - Uppsala, SE

Assignee:

Qiagen GmbH - Hilden

International Classification:

C12Q 1/68

US Classification:

435 6, 435 911, 536 221, 536 2433

Abstract:

The present invention provides a method of identifying a base at a target position in a sample nucleic acid sequence, said method comprising: subjecting a primer hybridised to said sample nucleic acid immediately adjacent to the target position, to a polymerase primer extension reaction in the presence of a nucleotide, whereby the nucleotide will only become incorporated if it is complementary to the base in the target position, and determining whether or not said nucleotide is incorporated by detecting whether PPi is released, the identity of the target base being determined from the identity of any nucleotide incorporated, wherein, where said nucleotide comprises an adenine base, an α-thio triphosphate analogue of said nucleotide is used, ant the Rp isomer of said analogue and/or the degradation products of said analogue are eliminated from the polymerase reaction step.

US Patent:

7700323, Apr 20, 2010

Filed:

Apr 15, 2004

Appl. No.:

10/826633

Inventors:

Thomas D Willis - San Francisco CA, US
Paul Hardenbol - Los Altos CA, US
Maneesh Jain - Menlo Park CA, US
Viktor Stolc - Cupertino CA, US
Mostafa Ronaghi - Palo Alto CA, US
Ronald W Davis - Palo Alto CA, US

Assignee:

The Board of Trustees of the Leland Stanford Junior University - Stanford CA

International Classification:

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

US Classification:

435 911, 435 6, 435 912, 536 243, 536 231

Abstract:

The invention is directed to novel methods of multiplexing nucleic acid reactions, including amplification, detection and genotyping. The invention relies on the use of precircle probes that are circularized in the presence of the corresponding target nucleic acids, cleaved, and then amplified.

US Patent:

7782237, Aug 24, 2010

Filed:

Jun 13, 2008

Appl. No.:

12/139299

Inventors:

Mostafa Ronaghi - Los Altos Hills CA, US
Ali Agah - Campbell CA, US

Assignee:

The Board of Trustees of the Leland Stanford Junior University - Palo Alto CA

International Classification:

H03M 1/66

US Classification:

341143, 341118, 341155, 341120

Abstract:

An error-corrected representation of an input signal, such as a bioluminescence signal, is generated. An analog representation of the input signal is oversampled and quantized to provide a first-stage digital output and a residual error. The residual error is provided as a second-stage digital output using successive approximation. The first-stage and second-stage digital outputs are used to generate an error-corrected representation of the bioluminescence signal.

US Patent:

7932034, Apr 26, 2011

Filed:

Dec 18, 2007

Appl. No.:

11/959317

Inventors:

Mostafa Ronaghi - Los Altos Hills CA, US

Assignee:

The Board of Trustees of the Leland Stanford Junior University - Palo Alto CA

International Classification:

C12Q 1/68
C12P 19/34

US Classification:

435 6, 435 912

Abstract:

The present method involves sequencing by synthesis in which a template strand having an attached primer is immobilized in a small volume reaction mixture. In one embodiment, the reaction mixture is in contact with a sensitive heat sensor, which detects the heat of reaction from incorporation of a complementary base (dNTP) in the presence of appropriate reagents (DNA polymerase, and polymerase reaction buffer). Alternatively, or in addition, a change in pH resulting from the incorporation of nucleotides in the DNA polymerase reaction is measured. A device is provided having delivery channels for appropriate reagents, including dNTPs, which may be delivered sequentially or in a mixture. Preferably, the dNTPs are added in a predetermined sequence, and the dNTP is incorporated or not depending on the template sequence.