Patents by Inventor Shivani Nautiyal
Shivani Nautiyal has filed for patents to protect the following inventions. This listing includes patent applications that are pending as well as patents that have already been granted by the United States Patent and Trademark Office (USPTO).
-
Publication number: 20210147903Abstract: Methods for determining the methylation status of a plurality of cytosines are disclosed. In some aspects genomic DNA target sequences containing CpGs are targeted for analysis by multiplex amplification using target specific probes that can be specifically degraded prior to amplification. The targets may be modified with bisulfite prior to amplification. In another aspect targets are cut with methylation sensitive or insensitive restriction enzymes and marked with a tag using the target specific probes. The presence or absence of methylation may be determined using methylation sensitive restriction enzyme or bisulfite treatment. Detection in many embodiments employs hybridization to tag arrays, genotyping arrays or resequencing arrays.Type: ApplicationFiled: October 26, 2020Publication date: May 20, 2021Inventors: Shivani Nautiyal, Malek Faham
-
Patent number: 10822659Abstract: Arrays for genome-wide analysis of methylation are disclosed. In a preferred aspect arrays comprising a plurality of probes complementary to a plurality of identified CpG islands in the human, mouse and rat genome are disclosed. The arrays may be used to detect methylation within CpG islands in samples from human, mouse and rat genomes.Type: GrantFiled: October 24, 2017Date of Patent: November 3, 2020Assignee: AFFYMETRIX, INC.Inventors: Yanxiang Cao, Shivani Nautiyal, Charles G. Miyada, Christopher Davies, Gangwu Mei, Alan J. Williams, Eric B. Schell, John E. Blume
-
Patent number: 10822642Abstract: Methods for determining the methylation status of a plurality of cytosines are disclosed. In some aspects genomic DNA target sequences containing CpGs are targeted for analysis by multiplex amplification using target specific probes that can be specifically degraded prior to amplification. The targets may be modified with bisulfite prior to amplification. In another aspect targets are cut with methylation sensitive or insensitive restriction enzymes and marked with a tag using the target specific probes. The presence or absence of methylation may be determined using methylation sensitive restriction enzyme or bisulfite treatment. Detection in many embodiments employs hybridization to tag arrays, genotyping arrays or resequencing arrays.Type: GrantFiled: July 31, 2019Date of Patent: November 3, 2020Assignee: Affymetrix, Inc.Inventors: Shivani Nautiyal, Malek Faham
-
Publication number: 20200024640Abstract: Methods for determining the methylation status of a plurality of cytosines are disclosed. In some aspects genomic DNA target sequences containing CpGs are targeted for analysis by multiplex amplification using target specific probes that can be specifically degraded prior to amplification. The targets may be modified with bisulfite prior to amplification. In another aspect targets are cut with methylation sensitive or insensitive restriction enzymes and marked with a tag using the target specific probes. The presence or absence of methylation may be determined using methylation sensitive restriction enzyme or bisulfite treatment. Detection in many embodiments employs hybridization to tag arrays, genotyping arrays or resequencing arrays.Type: ApplicationFiled: July 31, 2019Publication date: January 23, 2020Inventors: Shivani Nautiyal, Malek Faham
-
Patent number: 10407717Abstract: Methods for determining the methylation status of a plurality of cytosines are disclosed. In some aspects genomic DNA target sequences containing CpGs are targeted for analysis by multiplex amplification using target specific probes that can be specifically degraded prior to amplification. The targets may be modified with bisulfite prior to amplification. In another aspect targets are cut with methylation sensitive or insensitive restriction enzymes and marked with a tag using the target specific probes. The presence or absence of methylation may be determined using methylation sensitive restriction enzyme or bisulfite treatment. Detection in many embodiments employs hybridization to tag arrays, genotyping arrays or resequencing arrays.Type: GrantFiled: September 30, 2016Date of Patent: September 10, 2019Assignee: Affymetrix, Inc.Inventors: Shivani Nautiyal, Malek Faham
-
Publication number: 20180251841Abstract: Arrays for genome-wide analysis of methylation are disclosed. In a preferred aspect arrays comprising a plurality of probes complementary to a plurality of identified CpG islands in the human, mouse and rat genome are disclosed. The arrays may be used to detect methylation within CpG islands in samples from human, mouse and rat genomes.Type: ApplicationFiled: October 24, 2017Publication date: September 6, 2018Inventors: Yanxiang Cao, Shivani Nautiyal, Charles G. Miyada, Christopher Davies, Gangwu Mei, Alan J. Williams, Eric B. Schell, John E. Blume
-
Patent number: 9828640Abstract: Arrays for genome-wide analysis of methylation are disclosed. In a preferred aspect arrays comprising a plurality of probes complementary to a plurality of identified CpG islands in the human, mouse and rat genome are disclosed. The arrays may be used to detect methylation within CpG islands in samples from human, mouse and rat genomes.Type: GrantFiled: October 2, 2013Date of Patent: November 28, 2017Assignee: Affymetrix, Inc.Inventors: Yanxiang Cao, Shivani Nautiyal, Charles G. Miyada, Christopher Davies, Gangwu Mei, Alan J. Williams, Eric B. Schell, John E. Blume
-
Publication number: 20170081703Abstract: Methods for determining the methylation status of a plurality of cytosines are disclosed. In some aspects genomic DNA target sequences containing CpGs are targeted for analysis by multiplex amplification using target specific probes that can be specifically degraded prior to amplification. The targets may be modified with bisulfite prior to amplification. In another aspect targets are cut with methylation sensitive or insensitive restriction enzymes and marked with a tag using the target specific probes. The presence or absence of methylation may be determined using methylation sensitive restriction enzyme or bisulfite treatment. Detection in many embodiments employs hybridization to tag arrays, genotyping arrays or resequencing arrays.Type: ApplicationFiled: September 30, 2016Publication date: March 23, 2017Inventors: Shivani Nautiyal, Malek Faham
-
Publication number: 20150038352Abstract: Arrays for genome-wide analysis of methylation are disclosed. In a preferred aspect arrays comprising a plurality of probes complementary to a plurality of identified CpG islands in the human, mouse and rat genome are disclosed. The arrays may be used to detect methylation within CpG islands in samples from human, mouse and rat genomes.Type: ApplicationFiled: October 2, 2013Publication date: February 5, 2015Applicant: AFFYMETRIX, INC.Inventors: Yanxiang Cao, Shivani Nautiyal, Charles G. Miyada, Christopher Davies, Gangwu Mei, Alan J. Williams, Eric B. Schell, Jonh E. Blume
-
Patent number: 8709716Abstract: Arrays for genome-wide analysis of methylation are disclosed. IN a preferred aspect arrays comprising a plurality of probes complementary to a plurality of identified CpG islands in the human, mouse and rat genome are disclosed. The arrays may be used to detect methylation within cpG islands in samples from human, mouse and rat genomes.Type: GrantFiled: January 27, 2011Date of Patent: April 29, 2014Assignee: Affymetrix, Inc.Inventors: Yanxiang Cao, Shivani Nautiyal, Charles G. Miyada, Christopher Davies, Gangwu Mei, Alan J Williams, Eric B. Schell, John E. Blume
-
Publication number: 20110166037Abstract: Arrays for genome-wide analysis of methylation are disclosed. IN a preferred aspect arrays comprising a plurality of probes complementary to a plurality of identified CpG islands in the human, mouse and rat genome are disclosed. The arrays may be used to detect methylation within cpG islands in samples from human, mouse and rat genomes.Type: ApplicationFiled: January 27, 2011Publication date: July 7, 2011Applicant: AFFYMETRIX, INC.Inventors: Yanxiang Cao, Shivani Nautiyal, Charles G. Miyada, Christopher Davies, Gangwu Mei, Alan J Williams, Eric B. Schell, John E. Blume
-
Publication number: 20110151438Abstract: Methods for determining the methylation status of a plurality of cytosines are disclosed. In some aspects genomic DNA target sequences containing CpGs are targeted for analysis by multiplex amplification using target specific probes that can be specifically degraded prior to amplification. The targets may be modified with bisulfite prior to amplification. In another aspect targets are cut with methylation sensitive or insensitive restriction enzymes and marked with a tag using the target specific probes. The presence or absence of methylation may be determined using methylation sensitive restriction enzyme or bisulfite treatment. Detection in many embodiments employs hybridization to tag arrays, genotyping arrays or resequencing arrays.Type: ApplicationFiled: October 24, 2007Publication date: June 23, 2011Applicant: AFFYMETRIX, INC.Inventors: Shivani Nautiyal, Malek Faham
-
Patent number: 7901882Abstract: Arrays for genome-wide analysis of methylation are disclosed. In a preferred aspect arrays comprising a plurality of probes complementary to a plurality of identified CpG islands in the human, mouse and rat genome are disclosed. The arrays may be used to detect methylation within CpG islands in samples from human, mouse and rat genomes.Type: GrantFiled: April 2, 2007Date of Patent: March 8, 2011Assignee: Affymetrix, Inc.Inventors: Yanxiang Cao, Shivani Nautiyal, Charles G. Miyada, Christopher Davies, Gangwu Mei, Alan J. Williams, Eric B. Schell, John E. Blume
-
Publication number: 20080254453Abstract: Methods of analyzing DNA to identify regions of the genome that are methylated in a genomic sample are disclosed. In one aspect genomic DNA is fragmented using a restriction enzyme with a degenerate recognition site, methylated restriction fragments are separated from unmethylated fragments by affinity purification. The complexity of the methylated fragments is reduced by amplification of a subset of the fragments using adaptors that ligate to a subset of the fragments. The amplified product is fragmented, labeled and hybridized to an array of probes. The hybridization pattern is analyzed to determine methylation status of cytosines.Type: ApplicationFiled: April 12, 2007Publication date: October 16, 2008Applicant: AFFYMETRIX, INCInventors: Michael H. Shapero, Shivani Nautiyal
-
Publication number: 20080108073Abstract: Methods for determining the methylation status of a plurality of cytosines are disclosed. In some aspects genomic DNA target sequences containing CpGs are targeted for analysis by multiplex amplification using target specific probes that can be specifically degraded prior to amplification. The targets may be modified with bisulfite prior to amplification. In another aspect targets are cut with methylation sensitive or insensitive restriction enzymes and marked with a tag using the target specific probes. The presence or absence of methylation may be determined using methylation sensitive restriction enzyme or bisulfite treatment. Detection in many embodiments employs hybridization to tag arrays, genotyping arrays or resequencing arrays.Type: ApplicationFiled: October 24, 2007Publication date: May 8, 2008Applicant: AFFYMETRIX, INC.Inventors: Shivani Nautiyal, Malek Faham
-
Publication number: 20070243546Abstract: Arrays for genome-wide analysis of methylation are disclosed. In a preferred aspect arrays comprising a plurality of probes complementary to a plurality of identified CpG islands in the human, mouse and rat genome are disclosed. The arrays may be used to detect methylation within CpG islands in samples from human, mouse and rat genomes.Type: ApplicationFiled: April 2, 2007Publication date: October 18, 2007Applicant: AFFYMETRIX, INCInventors: Yanxiang Cao, Shivani Nautiyal, Charles Miyada, Christopher Davies, Gangwu Mei, Alan Williams, Eric Schell, John Blume
-
Publication number: 20060292585Abstract: Methods of analyzing DNA to determine the methylation status of a plurality of cytosines are disclosed. In one aspect genomic DNA is fragmented, fragments are circularized, the circles are treated with a methylation sensitive enzyme to enrich for circles with methylated sites or with a methylation dependent enzyme to enrich for circles with unmethylated sites, and the circles are amplified. The amplified product is fragmented, labeled and hybridized to an array of probes. The array of probes may be a tiling array or an array of junction probes. The hybridization pattern is analyzed to determine methylation status of cytosines.Type: ApplicationFiled: August 26, 2005Publication date: December 28, 2006Applicant: Affymetrix, INC.Inventors: Shivani Nautiyal, John Blume
-
Publication number: 20050196792Abstract: Methods for amplifying a nucleic acid sample while preserving the methylation status of cytosines are disclosed. In some aspects the amplified methylated sample is modified by methylation sensitive modification and analyzed by hybridization to an array to identify cytosines that were methylated in the starting material and cytosines that were not methylated in the starting material. Methods for detecting methylation status are also disclosed. In one embodiment a DNA methyltransferase activity is included in the amplification reaction and this activity methylates the newly synthesized DNA using the methylated genomic template strand as a guide.Type: ApplicationFiled: February 14, 2005Publication date: September 8, 2005Applicant: Affymetrix, INC.Inventors: Stephen Fodor, Robert Lipshutz, Shivani Nautiyal
-
Patent number: 6303317Abstract: Methods for creating and using polypeptide probes with high affinity for any desirable coiled coil region are described, as well as heterospecific polypeptide probes directed to the coiled coil region of a target polypeptide. Core residue packing rules are provided for selective amino acid pairing and packing in the hydrophobic core of the interhelical interface.Type: GrantFiled: January 28, 1998Date of Patent: October 16, 2001Assignee: The Regents of the University of CaliforniaInventors: Thomas C. Alber, Victoria Allen, Shivani Nautiyal