Patents by Inventor Yunqing Ma
Yunqing Ma 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).
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Publication number: 20120172246Abstract: Methods of detecting various types of nucleic acids, including methods of detecting two or more nucleic acids in multiplex branched-chain DNA assays, are provided. Detection assays may be conducted at least in vitro, in cellulo, and in situ. Nucleic acids which are optionally captured on a solid support are detected, for example, through cooperative hybridization events that result in specific association of a label probe system with the nucleic acids. Various label probe system embodiments are provided. Compositions, kits, and systems related to the methods are also described.Type: ApplicationFiled: January 3, 2012Publication date: July 5, 2012Applicant: AFFYMETRIX, INC.Inventors: Quan N. Nguyen, Robert J. Lipshutz, Gary K. McMaster, Yunqing Ma, Yen-Chieh Wu, Audrey Lin, Chunfai Lai, Cung-Tuong Nguyen
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Publication number: 20120052498Abstract: Methods of detecting various types of nucleic acids, including methods of detecting two or more nucleic acids in multiplex branched-chain DNA assays, are provided. Detection assays may be conducted at least in vitro, in cellulo, and in situ. Nucleic acids which are optionally captured on a solid support are detected, for example, through cooperative hybridization events that result in specific association of a label probe system with the nucleic acids. Various label probe system embodiments are provided. Compositions, kits, and systems related to the methods are also described.Type: ApplicationFiled: July 1, 2011Publication date: March 1, 2012Applicant: Affymetrix, INC.Inventors: Quan N. Nguyen, Gary K. McMaster, Yunqing Ma, Yen-Chieh Wu, Audrey Lin, Chunfai Lai, Cung-Tuong Nguyen
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Publication number: 20120003648Abstract: Disclosed are methods, compositions and kits for amplifying signals for detecting the presence, quantity and/or sequence of nucleic acids and proteins, as well as methods, compositions and kits for increasing the number of such targets simultaneously detectable in a sample. Detection may be, for instance, in vivo, in cellulo or in situ. Amplification of signal is achieved by way of hybridization of nucleic acid label probe systems and structures. Increase in target multiplex capacity is achieved by way of varying the type of labels utilized in the nucleic acid label probe system.Type: ApplicationFiled: July 1, 2011Publication date: January 5, 2012Applicant: Affymetrix, INC.Inventors: Yunqing Ma, Gary K. McMaster, Aiguo Zhang, Quan N. Nguyen
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Publication number: 20120004132Abstract: Methods of detecting various types of nucleic acids, including methods of detecting two or more nucleic acids in multiplex branched-chain DNA assays, are provided. Detection assays may be conducted at least in vitro, in cellulo, and in situ. Nucleic acids which are optionally captured on a solid support are detected, for example, through cooperative hybridization events that result in specific association of a label probe system with the nucleic acids. Various label probe system embodiments are provided. Embodiments are directed to concurrent detection of one or more nucleic acids and one or more proteins. Embodiments also are directed to determining the methylation state of a target sequence. Other embodiments are directed to detection of one or more proteins using DNA barcodes. Compositions, kits, and systems related to the methods are also described.Type: ApplicationFiled: July 5, 2011Publication date: January 5, 2012Applicant: Affymetrix, INC.Inventors: Aiguo Zhang, Yunqing Ma, Quan N. Nguyen, Franklin R. Witney, Gary K. McMaster, Glenn H. McGall
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Publication number: 20110256536Abstract: This invention provides methods, compositions and systems to detect a nucleic acid of interest in a two-stage amplification. The two-stage amplification begins with a first non-enzymatic accumulation of an amplification oligomer that is the target substrate for a second nucleic acid amplification or assay. Two or more amplification oligomers can be used to allow multiplexed amplifications of two or more nucleic acids of interest with deconvolution based on unique detection signals or unique signal locations.Type: ApplicationFiled: April 21, 2011Publication date: October 20, 2011Applicant: Panomics, Inc.Inventors: Gary McMaster, Yunqing Ma
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Publication number: 20110237449Abstract: Methods of capturing two or more nucleic acids simultaneously from a single sample are provided. Different nucleic acids are captured through cooperative hybridization events on a substrate, or different subsets of particles, or at different selected positions on a spatially addressable solid support. Methods described include enrichment and purification of nucleic acids prior to downstream steps including sequencing of target nucleic acids. Compositions, kits, and systems related to the methods are also described.Type: ApplicationFiled: January 7, 2011Publication date: September 29, 2011Applicant: AFFYMETRIX, INC.Inventors: Gary K. McMaster, Quan N. Nguyen, Franklin R. Witney, Yunqing Ma
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Publication number: 20110223606Abstract: This invention provides methods of quantitating nucleic acids from problematic samples, such as aged samples, formalin fixed samples, paraffin embedded samples, samples with aneuploid cells, and cells with fragmented nucleic acids. Methods include techniques to efficiently solubilize the nucleic acids under non-denaturing conditions from preserved clinical samples without resort to organic extractions, to normalize cell counts regardless of aneuploidy, to access the fragmentation state of the nucleic acids, and to provide standard curves for degraded nucleic acid samples.Type: ApplicationFiled: May 17, 2011Publication date: September 15, 2011Applicant: Panomics, Inc.Inventors: Gary McMaster, Joan Davies, Yunqing Ma, Yuling Luo
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Publication number: 20110195864Abstract: Methods of detecting copy number of a repeated sequence element, including methods of determining telomere length, are provided. The methods can be multiplexed for detection of repeated sequence element copy number on two or more nucleic acid targets simultaneously. Compositions, kits, and systems related to the methods are also described.Type: ApplicationFiled: April 8, 2011Publication date: August 11, 2011Applicant: Affymetrix, Inc.Inventor: Yunqing Ma
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Publication number: 20110171644Abstract: Methods of capturing two or more nucleic acids simultaneously from a single sample are provided. Different nucleic acids are captured through cooperative hybridization events on different subsets of particles or at different selected positions on a spatially addressable solid support. Methods of capturing one or more long nucleic acids and methods of capturing one or more nucleic acid for sequencing are also provided. Compositions, kits, and systems related to the methods are also described.Type: ApplicationFiled: December 23, 2010Publication date: July 14, 2011Applicant: Affymetrix, Inc.Inventors: Yuling Luo, Yunqing Ma, Gary McMaster, Quan Ngoc Nguyen, Frank Witney, Wen Yang
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Patent number: 7968327Abstract: This invention provides methods of quantitating nucleic acids from problematic samples, such as aged samples, formalin fixed samples, paraffin embedded samples, samples with aneuploid cells, and cells with fragmented nucleic acids. Methods include techniques to efficiently solublize the nucleic acids under non-denaturing conditions from preserved clinical samples without resort to organic extractions, to normalize cell counts regardless of aneuploidy, to access the fragmentation state of the nucleic acids, and to provide standard curves for degraded nucleic acid samples.Type: GrantFiled: August 14, 2007Date of Patent: June 28, 2011Inventors: Gary McMaster, Joan Davies, Yunqing Ma, Yuling Luo
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Patent number: 7951539Abstract: This invention provides methods, compositions and systems to detect a nucleic acid of interest in a two-stage amplification. The two-stage amplification begins with a first non-enzymatic accumulation of an amplification oligomer that is the target substrate for a second nucleic acid amplification or assay. Two or more amplification oligomers can be used to allow multiplexed amplifications of two or more nucleic acids of interest with deconvolution based on unique detection signals or unique signal locations.Type: GrantFiled: October 7, 2009Date of Patent: May 31, 2011Assignee: Panomics, Inc.Inventors: Gary McMaster, Yunqing Ma
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Publication number: 20110059866Abstract: Methods of detecting nucleic acids, including methods of detecting two or more nucleic acids in multiplex branched-chain DNA assays, are provided. Nucleic acids captured on a solid support are detected, for example, through cooperative hybridization events that result in specific association of a label with the nucleic acids. Compositions, kits, and systems related to the methods are also described.Type: ApplicationFiled: February 26, 2010Publication date: March 10, 2011Applicant: Advanced Cell Diagnostics, Inc.Inventors: Yuling Luo, Yunqing Ma, Cung-Tuong Nguyen
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Publication number: 20110059442Abstract: Methods of detecting nucleic acids, including methods of detecting two or more nucleic acids in multiplex branched-chain DNA assays, are provided. Nucleic acids captured on a solid support are detected, for example, through cooperative hybridization events that result in specific association of a label with the nucleic acids. Compositions, kits, and systems related to the methods are also described.Type: ApplicationFiled: February 26, 2010Publication date: March 10, 2011Applicant: Advanced Cell Diagnostics, Inc.Inventors: Yuling Luo, Yunqing Ma, Cung-Tuong Nguyen
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Patent number: 7709198Abstract: Methods of detecting nucleic acids, including methods of detecting two or more nucleic acids in multiplex branched-chain DNA assays, are provided. Nucleic acids captured on a solid support are detected, for example, through cooperative hybridization events that result in specific association of a label with the nucleic acids. Compositions, kits, and systems related to the methods are also described.Type: GrantFiled: June 19, 2006Date of Patent: May 4, 2010Assignee: Advanced Cell Diagnostics, Inc.Inventors: Yuling Luo, Yunqing Ma, Cung-Tuong Nguyen
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Publication number: 20100099175Abstract: This invention provides methods, compositions and systems to detect a nucleic acid of interest in a two-stage amplification. The two-stage amplification begins with a first non-enzymatic accumulation of an amplification oligomer that is the target substrate for a second nucleic acid amplification or assay. Two or more amplification oligomers can be used to allow multiplexed amplifications of two or more nucleic acids of interest with deconvolution based on unique detection signals or unique signal locations.Type: ApplicationFiled: October 7, 2009Publication date: April 22, 2010Inventors: Gary McMaster, Yunqing Ma
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Publication number: 20090298709Abstract: Methods of detecting copy number of a repeated sequence element, including methods of determining telomere length, are provided. The methods can be multiplexed for detection of repeated sequence element copy number on two or more nucleic acid targets simultaneously. Compositions, kits, and systems related to the methods are also described.Type: ApplicationFiled: May 21, 2009Publication date: December 3, 2009Applicant: Affymetrix, Inc.Inventor: Yunqing Ma
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Patent number: 7615351Abstract: This invention provides methods, compositions and systems to detect a nucleic acid of interest in a two-stage amplification. The two-stage amplification begins with a first non-enzymatic accumulation of an amplification oligomer that is the target substrate for a second nucleic acid amplification or assay. Two or more amplification oligomers can be used to allow multiplexed amplifications of two or more nucleic acids of interest with deconvolution based on unique detection signals or unique signal locations.Type: GrantFiled: November 6, 2007Date of Patent: November 10, 2009Assignee: Panomics, Inc.Inventors: Gary McMaster, Yunqing Ma
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Publication number: 20080176242Abstract: This invention provides methods, compositions and systems to detect a nucleic acid of interest in a two-stage amplification. The two-stage amplification begins with a first non-enzymatic accumulation of an amplification oligomer that is the target substrate for a second nucleic acid amplification or assay. Two or more amplification oligomers can be used to allow multiplexed amplifications of two or more nucleic acids of interest with deconvolution based on unique detection signals or unique signal locations.Type: ApplicationFiled: November 6, 2007Publication date: July 24, 2008Applicant: Panomics, Inc.Inventors: Gary McMaster, Yunqing Ma
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Publication number: 20080050746Abstract: This invention provides methods of quantitating nucleic acids from problematic samples, such as aged samples, formalin fixed samples, paraffin embedded samples, samples with aneuploid cells, and cells with fragmented nucleic acids. Methods include techniques to efficiently solublize the nucleic acids under non-denaturing conditions from preserved clinical samples without resort to organic extractions, to normalize cell counts regardless of aneuploidy, to access the fragmentation state of the nucleic acids, and to provide standard curves for degraded nucleic acid samples.Type: ApplicationFiled: August 14, 2007Publication date: February 28, 2008Applicant: Panomics, Inc.Inventors: Gary McMaster, Joan Davies, Yunqing Ma, Yuling Luo
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Publication number: 20070042392Abstract: The present invention provides novel nucleic acids, novel polypeptide sequences encoded by these nucleic acids and uses thereof.Type: ApplicationFiled: August 31, 2005Publication date: February 22, 2007Applicant: NUVELO, Inc.Inventors: Y. Tang, Chenghua Liu, Vinod Asundi, Rui-hong Chen, Yunqing Ma, Feiyan Ren, Jian-Rui Wang, Thomas Wehrman, Chongjun Xu, Aidong Xue, Yonghong Yang, Jie Zhang, Qing Zhao, Ping Zhou, Radoje Drmanac, Yi-Cheng Cao, Dunrui Wang, Zhi Wang, Ryle Goodrich