Andrew George Sparks

US Patent:

7897344, Mar 1, 2011

Filed:

Nov 6, 2008

Appl. No.:

12/266385

Inventors:

Fredrik Dahl - Menlo Park CA, US
Radoje Drmanac - Los Altos Hills CA, US
Andrew Sparks - Los Gatos CA, US

Assignee:

Complete Genomics, Inc. - Mountain View CA

International Classification:

C12Q 1/68
C12P 19/34

US Classification:

435 6, 435 912, 435 914

Abstract:

Aspects described and claimed herein provide methods to insert multiple DNA adaptors into a population of circular target DNAs at defined positions and orientations with respect to one another. The resulting multi-adaptor constructs are then used in massively-parallel nucleic acid sequencing techniques.

US Patent:

7901890, Mar 8, 2011

Filed:

Nov 5, 2008

Appl. No.:

12/265593

Inventors:

Fredrik Dahl - Menlo Park CA, US
Radoje Drmanac - Los Altos Hills CA, US
Andrew Sparks - Los Gatos CA, US

Assignee:

Complete Genomics, Inc. - Mountain View CA

International Classification:

C12Q 1/68
C12P 19/34

US Classification:

435 6, 435 912, 435 914

Abstract:

Aspects described and claimed herein provide methods to insert multiple DNA adaptors into a population of circular target DNAs at defined positions and orientations with respect to one another. The resulting multi-adaptor constructs are then used in massively-parallel nucleic acid sequencing techniques.

US Patent:

20050100911, May 12, 2005

Filed:

Aug 6, 2003

Appl. No.:

10/635175

Inventors:

Nila Patil - Woodside CA, US
David Cox - Belmont CA, US
Charit Pethiyagoda - Sunnyvale CA, US
Andrew Sparks - Saratoga CA, US
Huang-Tsu Chen - Cupertino CA, US

Assignee:

Perlegen Sciences, Inc. - Mountain View CA

International Classification:

C12Q001/68
C12P019/34

US Classification:

435006000, 435091200

Abstract:

The invention provides several methods for reducing the complexity of a population of nucleic acids prior to performing an analysis of the nucleic acids on a nucleic acid probe array. The methods result in a subset of the initial population enriched for a desired property, or lacking nucleic acids having an undesired properly. The resulting nucleic acids in the subset are then applied to the array for various types of analysis. The methods are particularly useful for analyzing populations having a high decree of complexity, for example, chromosomal-derived DNA, or whole genomic DNA, or mRNA population. In addition, such methods allow for analysis of pooled samples.

US Patent:

20060183132, Aug 17, 2006

Filed:

Feb 14, 2005

Appl. No.:

11/058432

Inventors:

Glenn Fu - Dublin CA, US
Laura Stuve - San Jose CA, US
John Sheehan - Mountain View CA, US
Amy Ollmann - Redwood City CA, US
Naiping Shen - Saratoga CA, US
Andrew Sparks - Saratoga CA, US
Dennis Ballinger - Menlo Park CA, US

Assignee:

Perlegen Sciences, Inc. - Mountain View CA

International Classification:

C12Q 1/68
C12P 19/34

US Classification:

435006000, 435091200

Abstract:

Multiple unique selection probes are provided in a single medium. Each selection probe has a sequence that is complementary to a unique target sequence that may be present in a sample under consideration. For example, each selection probe may be complementary to a sequence that includes one of the SNPs used to genotype an organism. Single-stranded selection probes anneal or hybridize with sample sequences having the unique target sequences specified by the selection probe sequences. Sequences from the sample that do not anneal or hybridize with the selection probes are separated from the bound sequences by an appropriate technique. The bound sequences can then be freed to provide a mixture of isolated target sequences, which can be used as needed for the application at hand.

US Patent:

20090075343, Mar 19, 2009

Filed:

Nov 2, 2007

Appl. No.:

11/934695

Inventors:

Andrew Sparks - Los Gatos CA, US
Steven Huang - San Jose CA, US
Radoje Drmanac - Los Altos Hills CA, US
Arnold Oliphant - Sunnyvale CA, US

Assignee:

COMPLETE GENOMICS, INC. - Mountain View CA

International Classification:

C12P 19/34

US Classification:

435 912

Abstract:

Aspects described and claimed herein provide methods to insert multiple DNA adaptors into a population of circular target DNAs at defined positions and orientations with respect to one another using nicking reactions. The resulting multi-adaptor constructs are then used in massively-parallel nucleic acid sequencing techniques.

US Patent:

20090111705, Apr 30, 2009

Filed:

Nov 2, 2007

Appl. No.:

11/934697

Inventors:

Andrew Sparks - Los Gatos CA, US
Arnold Oliphant - Sunnyvale CA, US
George Yeung - Mountain View CA, US

Assignee:

Complete Genomics, Inc. - Mountain View CA

International Classification:

C40B 30/04
C12N 15/00
C40B 40/08
C12N 9/00

US Classification:

506 9, 4353201, 506 17, 435183

Abstract:

Aspects described and claimed herein provide methods to insert multiple DNA adaptors into a population of circular target DNAs at defined positions and orientations with respect to one another by employing selective capture of defined molecules. The resulting multi-adaptor constructs are then used in massively-parallel nucleic acid sequencing techniques.

US Patent:

20090111706, Apr 30, 2009

Filed:

Nov 2, 2007

Appl. No.:

11/934703

Inventors:

Andrew Sparks - Los Gatos CA, US
Arnold Oliphant - Sunnyvale CA, US
Radoje Drmanac - Los Altos Hills CA, US

Assignee:

Complete Genomics, Inc. - Mountain View CA

International Classification:

C40B 30/04
C12N 15/11
C40B 40/08

US Classification:

506 9, 536 231, 506 17

Abstract:

Aspects described and claimed herein provide methods to insert multiple DNA adaptors into a population of circular target DNAs at defined positions and orientations with respect to one another by employing amplification procedures. The resulting multi-adaptor constructs are then used in massively-parallel nucleic acid sequencing techniques.

US Patent:

20090124514, May 14, 2009

Filed:

Oct 24, 2008

Appl. No.:

12/258244

Inventors:

Glenn Fu - Dublin CA, US
Laura Stuve - San Jose CA, US
Julie Montgomery - Santa Cruz CA, US
John Sheehan - Mountain View CA, US
Charit Pethiyagoda - Santa Clara CA, US
Amy Ollmann - San Carlos CA, US
Naiping Shen - Saratoga CA, US
Michael Kennemer - Los Gatos CA, US
Andrew B. Sparks - Los Gatos CA, US
Dennis Ballinger - Menlo Park CA, US

Assignee:

PERLEGEN SCIENCES, INC. - Mountain View CA

International Classification:

C40B 30/04

US Classification:

506 9

Abstract:

Multiple unique selection probes are provided in a single medium. Each selection probe has a sequence that is complementary to a unique target sequence that may be present in a sample under consideration. For example, each selection probe may be complementary to a sequence that includes one of the SNPs used to genotype an organism. Single-stranded selection probes anneal or hybridize with sample sequences having the unique target sequences specified by the selection probe sequences. Sequences from the sample that do not anneal or hybridize with the selection probes are separated from the bound sequences by an appropriate technique. The bound sequences can then be freed to provide a mixture of isolated target sequences, which can be used as needed for the application at hand.