Brendan J Tarrier

8071312, Dec 6, 2011

Sep 28, 2010

12/892359

Vladimir L. Makarov - Ann Arbor MI, US
Emmanuel Kamberov - Ann Arbor MI, US
Brendan J. Tarrier - Belleville MI, US

Rubicon Genomics, Inc. - Ann Arbor MI

C12Q 1/68
C12P 19/34

435 612, 435 911, 435 912

The present invention concerns preparation of DNA molecules, such as a library, using a stem-loop oligonucleotide. In particular embodiments, the invention employs a single reaction mixture and conditions. In particular, at least part of the inverted palindrome is removed during the preparation of the molecules to facilitate amplification of the molecules. Thus, in specific embodiments, the DNA molecules are suitable for amplification and are not hindered by the presence of the palindrome.

8399199, Mar 19, 2013

Nov 1, 2011

13/286937

Vladimir L. Makarov - Ann Arbor MI, US
Emmanuel Kamberov - Ann Arbor MI, US
Brendan J. Tarrier - Belleville MI, US

Rubicon Genomics - Ann Arbor MI

C12Q 1/68
C12P 19/34

435 612, 435 911, 435 912

The present invention concerns preparation of DNA molecules, such as a library, using a stem-loop oligonucleotide. In particular embodiments, the invention employs a single reaction mixture and conditions. In particular, at least part of the inverted palindrome is removed during the preparation of the molecules to facilitate amplification of the molecules. Thus, in specific embodiments, the DNA molecules are suitable for amplification and are not hindered by the presence of the palindrome.

8409804, Apr 2, 2013

Mar 2, 2006

11/367046

Vladimir L. Makarov - Ann Arbor MI, US
Emmanuel Kamberov - Ann Arbor MI, US
Brendan J. Tarrier - Whitmore Lake MI, US

Rubicon Genomics, Inc. - Ann Arbor MI

C12Q 1/68
C12P 19/34

435 612, 435 912

The present invention concerns isolation, library preparation and selective amplification from a compositionally heterogeneous pool of DNA fragments of a fraction of molecules, such as those originating from promoter CpG islands and characterized by a high GC content. In particular, the process utilizes a heat-induced segregation of DNA molecules into GC-poor, single-stranded molecule fractions and GC-rich, double-stranded molecule fractions, with subsequent enzymatic conversion of the GC-rich, double-stranded DNA molecules into a library, and, optionally, amplification. In specific embodiments, the isolation process is used to generate promoter-enriched genomic and methylome libraries for research and diagnostic applications, for example.

8440404, May 14, 2013

Mar 3, 2005

11/071864

Vladimir L. Makarov - Ann Arbor MI, US
Emmanuel Kamberov - Ann Arbor MI, US
Tong Sun - Novi MI, US
Jonathon H. Pinter - Ypsilanti MI, US
Brendan J. Tarrier - Whitmore Lake MI, US
Eric E. Bruening - Chelsea MI, US
Takao Kurihara - Ann Arbor MI, US
Tim Tesmer - Whittaker MI, US
Joseph M'Mwirichia - Ypsilanti MI, US

Rubicon Genomics - Ann Arbor MI

C12Q 1/68
C12P 19/34

435 611, 435 61, 435 612, 435 911, 435 912

The present invention regards a variety of methods and compositions for obtaining epigenetic information, such as DNA methylation patterns, through the preparation, amplification and analysis of Methylome libraries. In particular, the method employs preparation of a DNA molecule by digesting the DNA molecule with at least one methylation-sensitive restriction enzyme; incorporating a nucleic acid molecule into at least some of the digested DNA molecules by either (1) incorporating at least one primer from a plurality of primers that have a 5′ constant sequence and a 3′ variable sequence, wherein the primers are substantially non-self-complementary and substantially non-complementary to other primers in the plurality; or (2) incorporating an oligonucleotide having an inverted repeat and a loop under conditions wherein the oligonucleotide becomes blunt-end ligated to one strand of the digested DNA molecule, followed by polymerization from a 3′ hydroxyl group present in a nick in the oligonucleotide-linked molecule; and amplifying one or more of the DNA molecules.

20070031857, Feb 8, 2007

Mar 2, 2006

11/366222

Vladimir Makarov - Ann Arbor MI, US
Emmanuel Kamberov - Ann Arbor MI, US
Brendan Tarrier - Whitmore Lake MI, US

Rubicon Genomics, Inc. - Ann Arbor MI

C12Q 1/68
C12P 19/34

435006000, 435091200

The present invention concerns preparation of DNA molecules, such as a library, using a stem-loop oligonucleotide. In particular embodiments, the invention employs a single reaction mixture and conditions. In particular, at least part of the inverted palindrome is removed during the preparation of the molecules to facilitate amplification of the molecules. Thus, in specific embodiments, the DNA molecules are suitable for amplification and are not hindered by the presence of the palindrome.

20100021973, Jan 28, 2010

Nov 13, 2008

12/270850

Vladimir L. Makarov - Ann Arbor MI, US
Emmanuel Kamberov - Ann Arbor MI, US
Brendan J. Tarrier - Belleville MI, US

C12P 19/34
C07H 21/04

435 9121, 536 231, 435 911

The present invention concerns preparation of DNA molecules, such as a library, using a stem-loop oligonucleotide. In particular embodiments, the invention employs a single reaction mixture and conditions. In particular, at least part of the inverted palindrome is removed during the preparation of the molecules to facilitate amplification of the molecules. Thus, in specific embodiments, the DNA molecules are suitable for amplification and are not hindered by the presence of the palindrome.

20130303407, Nov 14, 2013

Feb 13, 2013

13/766607

Emmanuel KAMBEROV - Ann Arbor MI, US
Brendan J. TARRIER - Belleville MI, US

C12N 15/10
C12P 19/34

506 26, 435 9152, 435 912, 435 9121, 435 913, 435 9141

The present invention concerns preparation of DNA molecules, such as a library, using a stem-loop oligonucleotide. In particular embodiments, the invention employs a single reaction mixture and conditions. In particular, at least part of the inverted palindrome is removed during the preparation of the molecules to facilitate amplification of the molecules. Thus, in specific embodiments, the DNA molecules are suitable for amplification and are not hindered by the presence of the palindrome.

20130309668, Nov 21, 2013

Apr 9, 2013

13/859034

Rubicon Genomics, Inc. - , US
Emmanuel KAMBEROV - Ann Arbor MI, US
Tong SUN - Novi MI, US
Jonathan H. PINTER - Ypsilanti MI, US
Brendan J. TARRIER - Whitmore Lake MI, US
Eric E. BRUENING - Chelsea MI, US
Takao KURIHARA - Ann Arbor MI, US
Tim TESMER - Whittaker MI, US
Joseph M'Mwirichia - Ypsilanti MI, US

Rubicon Genomics, Inc. - Ann Arbor MI

C12Q 1/68

435 611

The present invention regards a variety of methods and compositions for obtaining epigenetic information, such as DNA methylation patterns, through the preparation, amplification and analysis of Methylome libraries. In particular, the method employs preparation of a DNA molecule by digesting the DNA molecule with at least one methylation-sensitive restriction enzyme; incorporating a nucleic acid molecule into at least some of the digested DNA molecules by either (1) incorporating at least one primer from a plurality of primers that have a 5′ constant sequence and a 3′ variable sequence, wherein the primers are substantially non-self-complementary and substantially non-complementary to other primers in the plurality; or (2) incorporating an oligonucleotide having an inverted repeat and a loop under conditions wherein the oligonucleotide becomes blunt-end ligated to one strand of the digested DNA molecule, followed by polymerization from a 3′ hydroxyl group present in a nick in the oligonucleotide-linked molecule; and amplifying one or more of the DNA molecules