Daniel J Shoemaker

US Patent:

6962821, Nov 8, 2005

Filed:

Dec 5, 2002

Appl. No.:

10/309814

Inventors:

John Lewis Danssaert - San Diego CA, US
Robert James Shopes - San Diego CA, US
Daniel Davis Shoemaker - Stanford CA, US

Assignee:

Stratagene California - La Jolla CA

International Classification:

G01N033/566
C12Q001/00
C12M001/34

US Classification:

436501, 435 4, 4352884, 422 63, 422 67, 422 99

Abstract:

A method in which a temperature gradient is generated across a “gradient” block, and an apparatus comprising a block across which a temperature gradient can be generated. By setting up such a gradient, multiple reaction mixtures held in wells on the gradient block can be simultaneously run at temperatures which differ only slightly, thereby permitting an optimum temperature for the reaction to be quickly identified. In a preferred embodiment the gradient block is integrated into a thermal cycler used for nucleic acid amplification reactions.

US Patent:

7432084, Oct 7, 2008

Filed:

Jul 17, 2002

Appl. No.:

10/485008

Inventors:

Daniel D. Shoemaker - San Diego CA, US
Christopher D. Armour - Kirkland WA, US
Philip W. Garrett-Engele - Seattle WA, US

Assignee:

Rosetta Inpharmatics LLC - Seattle WA

International Classification:

C12P 19/34

US Classification:

435 913, 435 9121

Abstract:

In one aspect the present invention provides methods of synthesizing a preparation of nucleic acid molecules, the methods comprising the steps of: (a) utilizing an RNA template to enzymatically synthesize a first DNA molecule that is complementary to at least 50 contiguous bases of the RNA template; (b) utilizing the first DNA molecule as a template to enzymatically synthesize a second DNA molecule, thereby forming a double-stranded DNA molecule wherein the first DNA molecule is hybridized to the second DNA molecule; (c) utilizing the first or second DNA molecule of the double-stranded DNA molecule as a template to enzymatically synthesize a first RNA molecule that is complementary to either the first DNA molecule or to the second DNA molecule; and (d) utilizing the first RNA molecule as a template to enzymatically synthesize a third DNA molecule that is complementary to the first RNA molecule. In another aspect, the present invention provides processed DNA samples prepared by a method of the invention for synthesizing a preparation of nucleic acid molecules. In another aspect, the present invention provides methods for hybridizing a processed DNA sample to a population of immobilized nucleic acid molecules.

US Patent:

7501254, Mar 10, 2009

Filed:

Jul 19, 2007

Appl. No.:

11/879966

Inventors:

Daniel D. Shoemaker - San Diego CA, US

Assignee:

GHC Technologies, Inc. - La Jolla CA

International Classification:

C12Q 1/68
C12P 19/34

US Classification:

435 6, 435 911, 435 912

Abstract:

Methods for amplification and capture of nucleic acid sequences include annealing a forward primer to a DNA or RNA template in a first reaction vessel including fewer than four different dNTPs; forming an extended primer that terminates when an omitted dNTP is required for further extension; releasing the extended primer; exponentially amplifying the extended primer in a second reaction vessel that includes a reverse primer, four different dNTPs and a capture probe that includes n oligonucleotides having fewer than n locking nucleic acids; and concurrently capturing one of the extended primers with the capture probe while amplifying the extended primer. The steps of annealing, extending and releasing can occur at a first reaction temperature that is substantially isothermal and in the absence of a helicase. The steps of exponentially amplifying and capturing can occur at a second reaction temperature that is substantially isothermal.

US Patent:

7794985, Sep 14, 2010

Filed:

Mar 27, 2008

Appl. No.:

12/079851

Inventors:

Daniel D. Shoemaker - San Diego CA, US

Assignee:

GHC Technologies, Inc. - La Jolla CA

International Classification:

C12Q 1/68
C12P 19/34

US Classification:

435 912, 435 6, 435 911

Abstract:

A method for detecting the presence of a nucleic acid template () in a sample includes the steps of combining the sample in a reaction vessel with a first primer (F) and a second primer (R) having a first section (), a second section () and a spacer (). The method also includes one or more of the steps of extending the first section () with additional nucleotides, binding the first primer (F) to the extended first section, extending the first primer (F) with additional nucleotides and terminating extension of the first primer (F) with the spacer (). The first section () includes a plurality of nucleotides that bind with a portion of the nucleic acid template (). The second section () is spaced-apart from the first section () and includes a plurality of nucleotides that do not bind with the nucleic acid template (). The spacer () couples the first section () to the second section (). The invention is also directed toward the second primer (R).

US Patent:

7930406, Apr 19, 2011

Filed:

Oct 31, 2007

Appl. No.:

11/981425

Inventors:

Daniel D. Shoemaker - San Diego CA, US
Lee Thomas O'Donnell - Tarzana CA, US
James P. Broder - San Diego CA, US
Scott D. Shoemaker - San Diego CA, US

Assignee:

BOSS Logic, LLC - San Diego CA

International Classification:

G06F 17/30

US Classification:

709227, 709228, 709229

Abstract:

A system for transmission of mode of access information between a first device operated by a first user and a second device operated by a second user includes a database that is in network communication with the first device and the second device. The database stores a plurality of different modes of access for contacting the first user that are devoid of alpha-numeric identifiers specific to the first user. The database allows the first user to select one of the modes of access as a current mode of access of the first user. The current mode of access of the first user can be communicated to the second device once the second device queries the database. The current mode of access of the first user can be selected from the group consisting of mobile phone, text message and electronic mail. The current mode of access of the first user can change automatically over time according to a schedule input into the database by the first user. In some embodiments, at least one of the first device and the second device is a web-based mobile phone.

US Patent:

7958144, Jun 7, 2011

Filed:

Aug 29, 2003

Appl. No.:

10/651733

Inventors:

Daniel D. Shoemaker - San Diego CA, US
Lee Thomas O'Donnell - Tarzana CA, US
James P. Broder - San Diego CA, US
Scott D. Shoemaker - San Diego CA, US

Assignee:

Boss Logic, LLC - San Diego CA

International Classification:

G06F 17/30

US Classification:

707781, 707785, 709223, 709225, 709227, 709229

Abstract:

A system for transmission of data between a first device operated by a first user and a second device includes a database that receives a first set of data input by the first user and a second set of data input by the second user. In one embodiment, the first set of data includes an immediate mode of access and/or one or more future modes of access of the first user which correlate to one or more specific time periods during which the future mode of access will become the immediate mode of access. Additionally, the first set of data can include a time-dependent schedule of the future mode of access of the first user.

US Patent:

8137912, Mar 20, 2012

Filed:

Jun 14, 2007

Appl. No.:

11/763245

Inventors:

Ravi Kapur - Sharon MA, US
Mehmet Toner - Wellesley MA, US
Roland Stoughton - The Sea Ranch CA, US
Daniel Shoemaker - San Diego CA, US
Ronald W. Davis - Palo Alto CA, US

Assignee:

The General Hospital Corporation - Boston MA
GPB Scientific, LLC - Richmond VA
Verinata Health, Inc. - Redwood City CA

International Classification:

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

US Classification:

435 61, 435 912, 536 231, 536 243

Abstract:

The present invention relates to methods for detecting, enriching, and analyzing rare cells that are present in the blood, e. g. fetal cells. The invention further features methods of analyzing rare cell(s) to determine the presence of an abnormality, disease or condition in a subject, e. g. a fetus by analyzing a cellular sample from the subject.

US Patent:

8168389, May 1, 2012

Filed:

Sep 2, 2008

Appl. No.:

12/230628

Inventors:

Daniel Shoemaker - San Diego CA, US
Ravi Kapur - Sharon MA, US
Mehmet Toner - Wellesley MA, US
Roland Stoughton - The Sea Ranch CA, US
Ronald W. Davis - Palo Alto CA, US

Assignee:

The General Hospital Corporation - Boston MA
GPB Scientific, LLC - Richmond VA
Verinata Health, Inc. - Redwood City CA

International Classification:

C12Q 1/68

US Classification:

435 612

Abstract:

The present invention provides systems, apparatuses, and methods to detect the presence of fetal cells when mixed with a population of maternal cells in a sample and to test fetal abnormalities, e. g. aneuploidy. The present invention involves labeling regions of genomic DNA in each cell in said mixed sample with different labels wherein each label is specific to each cell and quantifying the labeled regions of genomic DNA from each cell in the mixed sample. More particularly the invention involves quantifying labeled DNA polymorphisms from each cell in the mixed sample.