Vivi Bich Truong

7504215, Mar 17, 2009

Nov 4, 2004

10/983046

Kyle B. Cole - Stanford CA, US
Vivi Truong - Mountain View CA, US
Glenn H. McGall - Palo Alto CA, US
Anthony D. Barone - San Jose CA, US

Affymetrix, Inc. - Santa Clara CA

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

435 6, 536 231, 536 243, 536 266, 435 911

In one aspect of the invention, a method is provided for end-labeling RNA (total RNA, mRNA, cRNA or fragmented RNA). In one aspect of the present invention, T4 RNA ligase is used to attach a 3′-labeled AMP or CMP donor to an RNA acceptor molecule. In another embodiment, a pyrophosphate molecule 3′-AppN-3′-linker-detectable moiety is used as donor molecule. In another aspect of the present invention, a method of detecting the presence of an RNA of interest in a sample is provided, the method having the following steps:.

7824863, Nov 2, 2010

Oct 22, 2008

12/256256

Kyle B. Cole - Stanford CA, US
Vivi Truong - Mountain View CA, US
Glenn H. McGall - Palo Alto CA, US
Anthony D. Barone - San Jose CA, US

Affymetrix, Inc. - Santa Clara CA

C12Q 1/68
C12P 19/34
C07H 15/00
C07H 21/00
C07H 19/04

435 6, 435 911, 435 912, 536 41, 536 2532, 536 266

In one aspect of the invention, a method is provided for end-labeling RNA (total RNA, mRNA, cRNA or fragmented RNA). In one aspect of the present invention, T4 RNA ligase is used to attach a 3′-labeled AMP or CMP donor to an RNA acceptor molecule. In another embodiment, a pyrophosphate molecule 3′-AppN-3′-linker-detectable moiety is used as donor molecule. In another aspect of the present invention, a method of detecting the presence of an RNA of interest in a sample is provided, the method having the following steps: providing the sample comprising RNA which may or may not have said RNA of interest; treating the sample with a fragmenting reagent to provide RNA fragments; removing phosphate groups from said fragments to provide fragments with free 3′ OH groups; ligating said fragment with a labeling reagent according to the instant invention; providing a nucleic acid array having probes directed to said RNA of interest; hybridizing the labeled nucleic acid fragments to said nucleic acid array; and determining the extent of hybridization to said probes to determine the presence of said RNA of interest.

20010051339, Dec 13, 2001

Mar 15, 2001

09/808352

Jonathan Oliner - Mountain View CA, US
Fred Christians - Los Altos CA, US
Vivi Truong - San Jose CA, US
Daniel Haber - Chestnut Hill MA, US
James Bean - Arlington MA, US
David Miklos - W. Roxbury MA, US
Denis Harkin - Knockhill Park, GB

C12Q001/68

435/006000

Analysis of the genes whose expression is affected by BRCA1 has identified a set of genes, each of which is up- or down-regulated by BRCA1. Each of these genes, alone or in groups, can be used to determine the mutational status of a BRCA1 gene, to determine whether a particular allelic variant affects BRCA1 function, to diagnose neoplasia, and to help identify candidate drugs which may be useful as anti-neoplastic agents.

20040086914, May 6, 2004

Jul 11, 2003

10/617992

Kyle Cole - Palo Alto CA, US
Vivi Truong - Mountain View CA, US
Glenn McGall - San Jose CA, US
Anthony Barone - San Jose CA, US

Affymetrix, INC. - Santa Clara CA

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

435/006000, 435/091200, 536/023100

In one aspect of the invention, a method is provided for end-labeling RNA (total RNA, mRNA, cRNA or fragmented RNA). In one embodiment, T4 RNA ligase is used to attach a 3′-biotinylated AMP or CMP donor to an RNA acceptor molecule. In another embodiment, a pyrophosphate molecule 3′-AppN-3′-linker-biotin is used as donor molecule. In another aspect of the invention, a method is provided for analyzing a nucleic acid population on a nucleic acid microarray comprising providing a nucleic acid population or converting the nucleic acid population into nucleic acid fragments; ligating the nucleic acid population or fragments to a labeled nucleic acid molecule to form labeled nucleic acid population or fragments using a ligase; hybridizing the labeled nucleic acid population or fragments to an array of nucleic acid probes, and determining hybridization signals of the probes as an indication of levels of the nucleic acids in the nucleic acid population.

20040234964, Nov 25, 2004

May 19, 2003

10/441864

Kyle Cole - Stanford CA, US
Vivi Truong - Mountain View CA, US
Glenn McGall - San Jose CA, US
Sumathi Venkatapathy - San Jose CA, US

Affymetrix, INC. - Santa Clara CA

C12Q001/68

435/006000, 525/054200

Methods are provided for reducing background signal associated with hybridization of nucleic acid arrays to nucleic acid samples, the method comprising hybridizing the array to the sample in the presence of a poly-anionic polymer (PAP). Background associated with hybridization of arrays to samples interferes with signal generated by specific binding to the probe array un-desirably lowers the signal to noise ratio (SNR) and generates an overall loss of sensitivity for nucleic acid arrays. Methods are also provided for hybridizing a nucleic acid sample to a nucleic acid array comprising incubating said sample with said array in the presence of a PAP. Hybridization buffers are also provided comprising a PAP.

20050069926, Mar 31, 2005

Aug 2, 2004

10/910158

Kyle Cole - Stanford CA, US
Vivi Truong - Mountain View CA, US

Affymetrix, INC. - Santa Clara CA

C12Q001/68
C12P019/34

435006000, 435091200

Methods are provided for enhancing generation of cDNA strands from mRNA. These methods are particularly useful for generating sufficient quantities of target for microarray hybridization.

20050136417, Jun 23, 2005

Mar 9, 2004

10/796323

Kyle Cole - Stanford CA, US
Vivi Truong - Mountain View CA, US
Glenn McGall - Palo Alto CA, US

Affymetrix, INC. - Santa Clara CA

C12Q001/68
C12P019/34

435006000, 435091200

Methods and kits for amplifying nucleic acids are provided. Double stranded cDNA with uridine residues incorporated into one strand is synthesized and the uridine containing strand is nicked at uridine residues. The DNA is extended from the nicks in the presence of dUTP using a strand displacing enzyme. Repeated cycles of nicking and extension result in amplification of the nucleic acid. Methods are also provided for analysis of the above sample by hybridization to an array, which may be specifically designed to interrogate the collection of target sequences for particular characteristics, such as, for example, the presence or absence of one or more polymorphisms or the presence or absence of a transcript.

62585363, Jul 10, 2001

Dec 1, 1998

9/203677

Jonathan Oliner - Mountain View CA
Fred Christians - Los Altos CA
Vivi Truong - San Jose CA
Daniel Haber - Chestnut Hill MA
James Bean - Arlington MA
David Miklos - W. Roxbury MA
Denis Paul Harkin - Belfast BT5 6HX, Northern Ireland, GB

C12Q 168
G01N 3353
C12P 2106
A61K 4900
C07H 2104

435 6

Analysis of the genes whose expression is affected by BRCA1 has identified a set of genes, each of which is up- or down-regulated by BRCA1. Each of these genes, alone or in groups, can be used to determine the mutational status of a BRCA1 gene, to determine whether a particular allelic variant affects BRCA1 function, to diagnose neoplasia, and to help identify candidate drugs which may be useful as anti-neoplastic agents.