Patents by Inventor Zihua Wang
Zihua Wang 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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Patent number: 10041119Abstract: 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.Type: GrantFiled: May 6, 2015Date of Patent: August 7, 2018Assignees: Verinata Health, Inc., GPB Scientific, LLC, The General Hospital CorporationInventors: Ravi Kapur, Mehmet Toner, Zihua Wang, Martin Fuchs
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Patent number: 9956562Abstract: The invention features devices and methods for the deterministic separation of particles. Exemplary methods include the enrichment of a sample in a desired particle or the alteration of a desired particle in the device. The devices and methods are advantageously employed to enrich for rare cells, e.g., fetal cells, present in a sample, e.g., maternal blood and rare cell components, e.g., fetal cell nuclei. The invention further provides a method for preferentially lysing cells of interest in a sample, e.g., to extract clinical information from a cellular component, e.g., a nucleus, of the cells of interest. In general, the method employs differential lysis between the cells of interest and other cells (e.g., other nucleated cells) in the sample.Type: GrantFiled: November 2, 2015Date of Patent: May 1, 2018Assignees: The General Hospital Corporation, GPB Scientific, LLCInventors: Lotien Richard Huang, Thomas A. Barber, Bruce L. Carvalho, Ravi Kapur, Paul Vernucci, Mehmet Toner, Zihua Wang
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Publication number: 20170152548Abstract: The present invention, SMASH (Short Multiply Aggregated Sequence Homologies), is a technique designed to pack multiple independent mappings into every read. Specifically, the invention relates to a composition comprising a first mixture of different chimeric genomic nucleic acid fragments, wherein each different fragment in the mixture comprises randomly ligated DNA segments, wherein each DNA segment in the fragment is a nucleic acid molecule at least 27 base pairs in length resulting from random fragmentation of a single genome. The invention also relates to methods for generating said composition and use of said composition to obtain genomic information, for example, copy number variation.Type: ApplicationFiled: January 30, 2017Publication date: June 1, 2017Applicant: Cold Spring Harbor LaboratoryInventors: Michael H. Wigler, Dan Levy, Zihua Wang
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Publication number: 20170140096Abstract: A method for determining the presence of a biological entity. The method may include entering into a digital computer, at least a plurality of first input values associated with a first genetic element, a plurality of second input values associated with a second genetic element, and a plurality of third input values associated with a third genetic element associated with a plurality of samples. The method also includes determining a threshold value associated with the third genetic element, separating the samples using the threshold value into a first set of samples and a second set of samples, clustering the first set of samples in a feature space defined by the first genetic element and the second genetic element, defining a first boundary space using the first set of samples, and defining a second boundary space using the second set of samples.Type: ApplicationFiled: November 11, 2016Publication date: May 18, 2017Inventors: Jiuliu Lu, Zihua Wang, Antonio Arevalo Reyes, Erik Alan Gustafson, John Steven Riley
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Patent number: 9519751Abstract: A method for determining the presence of a biological entity. The method may include entering into a digital computer, at least a plurality of first input values associated with a first genetic element, a plurality of second input values associated with a second genetic element, and a plurality of third input values associated with a third genetic element associated with a plurality of samples. The method also includes determining a threshold value associated with the third genetic element, separating the samples using the threshold value into a first set of samples and a second set of samples, clustering the first set of samples in a feature space defined by the first genetic element and the second genetic element, defining a first boundary space using the first set of samples, and defining a second boundary space using the second set of samples.Type: GrantFiled: March 29, 2013Date of Patent: December 13, 2016Assignee: Beckman Coulter, Inc.Inventors: Jiuliu Lu, Zihua Wang, Antonio Arevalo Reyes, Erik Alan Gustafson, John Steven Riley
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Publication number: 20160251715Abstract: A method for obtaining from genomic material genomic copy number information unaffected by amplification distortion, comprising obtaining segments of the genomic material, tagging the segments with substantially unique tags to generate tagged nucleic acid molecules, such that each tagged nucleic acid molecule comprises one segment of the genomic material and a tag, subjecting the tagged nucleic acid molecules to amplification by polymerase chain reaction (PCR), generating tag associated sequence reads by sequencing the product of the PCR reaction, assigning each tagged nucleic acid molecule to a location on a genome associated with the genomic material by mapping the subsequence of each tag associated sequence read corresponding to a segment of the genomic material to a location on the genome, and counting the number of tagged nucleic acid molecules having a different tag that have been assigned to the same location on the genome, thereby obtaining genomic copy number information unaffected by amplification dType: ApplicationFiled: March 7, 2016Publication date: September 1, 2016Applicant: Cold Spring Harbor LaboratoryInventors: James Hicks, Nicholas Navin, Jennifer Troge, Zihua Wang, Michael Wigler
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Patent number: 9404156Abstract: A method for obtaining from genomic material genomic copy number information unaffected by amplification distortion, comprising obtaining segments of the genomic material, tagging the segments with substantially unique tags to generate tagged nucleic acid molecules, such that each tagged nucleic acid molecule comprises one segment of the genomic material and a tag, subjecting the tagged nucleic acid molecules to polymerase chain reaction (PCR) amplification, generating tag associated sequence reads by sequencing the product of the PCR reaction, assigning each tagged nucleic acid molecule to a location on a genome associated with the genomic material by mapping the subsequence of each tag associated sequence read corresponding to a segment of the genomic material to a location on the genome, and counting the number of tagged nucleic acid molecules assigned to the same location on the genome having a different tag, thereby obtaining genomic copy number information unaffected by amplification distortion.Type: GrantFiled: October 21, 2011Date of Patent: August 2, 2016Assignee: Cold Spring Harbor LaboratoryInventors: James Hicks, Nicholas Navin, Jennifer Troge, Zihua Wang, Michael Wigler
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Publication number: 20160144378Abstract: The invention features devices and methods for the deterministic separation of particles. Exemplary methods include the enrichment of a sample in a desired particle or the alteration of a desired particle in the device. The devices and methods are advantageously employed to enrich for rare cells, e.g., fetal cells, present in a sample, e.g., maternal blood and rare cell components, e.g., fetal cell nuclei. The invention further provides a method for preferentially lysing cells of interest in a sample, e.g., to extract clinical information from a cellular component, e.g., a nucleus, of the cells of interest. In general, the method employs differential lysis between the cells of interest and other cells (e.g., other nucleated cells) in the sample.Type: ApplicationFiled: November 2, 2015Publication date: May 26, 2016Inventors: Lotien Richard Huang, Thomas A. Barber, Bruce L. Carvalho, Ravi Kapur, Paul Vernucci, Mehmet Toner, Zihua Wang
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Patent number: 9317655Abstract: Systems and methods for identifying Methicillin resistant strains of Staphylococcus aureus (MRSA) in a sample are used that are based on the fact that an MRSA positive sample should have roughly the same copy numbers of mecA, SCCmec, and a Staphylococcus aureus-specific target gene sequence. The systems and methods may further present the three assays simultaneously on a 2-D plot with each axis of the plot 120 degrees apart. According to one embodiment, a Y plot is used for the 2-D display. If a given sample has similar readings of mecA, SCCmec, and a Staphylococcus aureus-specific target gene sequence, the sample's measured copy numbers of mecA, SCCmec, and the Staphylococcus aureus-specific target gene sequence can plot close to the origin regardless of the sample's absolute assay readings. With the help of this transformation, a boundary function can be defined that can be used to distinguish MRSA-positive samples from MRSA-negative samples.Type: GrantFiled: November 11, 2010Date of Patent: April 19, 2016Assignee: Beckman Coulter, Inc.Inventors: Jiuliu Lu, Zihua Wang, Antonio Arevalo Reyes, Erik Alan Gustafson, John Steven Riley
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Publication number: 20160002737Abstract: The present invention relates to methods for detecting, enriching, and analyzing rare cells that are present in the blood, e.g., epithelial cells. The invention further features methods of analyzing rare cell(s) to determine the presence of an abnormality, disease or condition in a subject by analyzing a cellular sample from the subject.Type: ApplicationFiled: July 8, 2015Publication date: January 7, 2016Inventors: Martin Fuchs, Ravi Kapur, Mehmet Toner, Zihua Wang
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Publication number: 20150344956Abstract: 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.Type: ApplicationFiled: May 6, 2015Publication date: December 3, 2015Inventors: Ravi Kapur, Mehmet Toner, Zihua Wang, Martin Fuchs
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Patent number: 9174222Abstract: The invention features devices and methods for the deterministic separation of particles. Exemplary methods include the enrichment of a sample in a desired particle or the alteration of a desired particle in the device. The devices and methods are advantageously employed to enrich for rare cells, e.g., fetal cells, present in a sample, e.g., maternal blood and rare cell components, e.g., fetal cell nuclei. The invention further provides a method for preferentially lysing cells of interest in a sample, e.g., to extract clinical information from a cellular component, e.g., a nucleus, of the cells of interest. In general, the method employs differential lysis between the cells of interest and other cells (e.g., other nucleated cells) in the sample.Type: GrantFiled: September 14, 2011Date of Patent: November 3, 2015Assignees: The General Hospital Corporation, GPB Scientific, LLCInventors: Lotien Richard Huang, Thomas Barber, Bruce L. Carvalho, Ravi Kapur, Paul Vernucci, Mehmet Toner, Zihua Wang
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Publication number: 20140065609Abstract: A method for obtaining from genomic material genomic copy number information unaffected by amplification distortion, comprising obtaining segments of the genomic material, tagging the segments with substantially unique tags to generate tagged nucleic acid molecules, such that each tagged nucleic acid molecule comprises one segment of the genomic material and a tag, subjecting the tagged nucleic acid molecules to polymerase chain reaction (PCR) amplification, generating tag associated sequence reads by sequencing the product of the PCR reaction, assigning each tagged nucleic acid molecule to a location on a genome associated with the genomic material by mapping the subsequence of each tag associated sequence read corresponding to a segment of the genomic material to a location on the genome, and counting the number of tagged nucleic acid molecules assigned to the same location on the genome having a different tag, thereby obtaining genomic copy number information unaffected by amplification distortion.Type: ApplicationFiled: October 21, 2011Publication date: March 6, 2014Inventors: James Hicks, Nicholas Navin, Jennifer Troge, Zihua Wang, Michael Wigler
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Publication number: 20130324418Abstract: The present invention relates to methods for detecting, enriching, and analyzing rare cells that are present in the blood, e.g., epithelial cells. The invention further features methods of analyzing rare cell(s) to determine the presence of an abnormality, disease or condition in a subject by analyzing a cellular sample from the subject.Type: ApplicationFiled: January 9, 2013Publication date: December 5, 2013Inventors: Martin Fuchs, Ravi Kapur, Mehmet Toner, Zihua Wang
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Patent number: 8585971Abstract: The invention features devices and methods for the deterministic separation of particles. Exemplary methods include the enrichment of a sample in a desired particle or the alteration of a desired particle in the device. The devices and methods are advantageously employed to enrich for rare cells, e.g., fetal cells, present in a sample, e.g., maternal blood and rare cell components, e.g., fetal cell nuclei. The invention further provides a method for preferentially lysing cells of interest in a sample, e.g., to extract clinical information from a cellular component, e.g., a nucleus, of the cells of interest. In general, the method employs differential lysis between the cells of interest and other cells (e.g., other nucleated cells) in the sample.Type: GrantFiled: April 20, 2012Date of Patent: November 19, 2013Assignees: The General Hospital Corporation, GPB Scientific, LLCInventors: Lotien Richard Huang, Thomas A. Barber, Bruce L. Carvalho, Ravi Kapur, Paul Vernucci, Mehmet Toner, Zihua Wang
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Publication number: 20130288903Abstract: 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.Type: ApplicationFiled: March 14, 2013Publication date: October 31, 2013Inventors: Ravi Kapur, Mehmet Toner, Zihua Wang, Martin Fuchs
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Patent number: 8442924Abstract: A method for determining the presence of a biological entity. The method may include entering into a digital computer, at least a plurality of first input values associated with a first genetic element (e.g., mecA), a plurality of second input values associated with a second genetic element (femA), and a plurality of third input values associated with a third genetic element (e.g., orfX) associated with a plurality of samples. Each sample includes a first input value in the plurality of first input values, a second input value in the plurality of second input values, and a third input value in the plurality of third input values.Type: GrantFiled: November 12, 2010Date of Patent: May 14, 2013Assignee: Beckman Coulter, Inc.Inventors: Jiuliu Lu, Zihua Wang, Antonio Arevalo Reyes, Erik Alan Gustafson, John Steven Riley
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Publication number: 20120283957Abstract: Systems and methods for identifying Methicillin resistant strains of Staphylococcus aureus (MRSA) in a sample are used that are based on the fact that an MRSA positive sample should have roughly the same copy numbers of mecA, SCCmec, and a Staphylococcus aureus-specific target gene sequence. The systems and methods may further present the three assays simultaneously on a 2-D plot with each axis of the plot 120 degrees apart. According to one embodiment, a Y plot is used for the 2-D display. If a given sample has similar readings of mecA, SCCmec, and a Staphylococcus aureus-specific target gene sequence, the sample's measured copy numbers of mecA, SCCmec, and the Staphylococcus aureus-specific target gene sequence can plot close to the origin regardless of the sample's absolute assay readings. With the help of this transformation, a boundary function can be defined that can be used to distinguish MRSA-positive samples from MRSA-negative samples.Type: ApplicationFiled: November 11, 2010Publication date: November 8, 2012Applicant: Beckman Coulter, Inc.Inventors: Jiuliu Lu, Zihua Wang, Antonio Arevalo Reyes, Erik Alan Gustafson, John Steven Riley
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Publication number: 20120225473Abstract: The invention features devices and methods for the deterministic separation of particles. Exemplary methods include the enrichment of a sample in a desired particle or the alteration of a desired particle in the device. The devices and methods are advantageously employed to enrich for rare cells, e.g., fetal cells, present in a sample, e.g., maternal blood and rare cell components, e.g., fetal cell nuclei. The invention further provides a method for preferentially lysing cells of interest in a sample, e.g., to extract clinical information from a cellular component, e.g., a nucleus, of the cells of interest. In general, the method employs differential lysis between the cells of interest and other cells (e.g., other nucleated cells) in the sample.Type: ApplicationFiled: April 20, 2012Publication date: September 6, 2012Inventors: Lotien Richard Huang, Thomas A. Barber, Bruce L. Carvalho, Ravi Kapur, Paul Vernucci, Mehmet Toner, Zihua Wang
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Publication number: 20120208186Abstract: 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.Type: ApplicationFiled: November 29, 2011Publication date: August 16, 2012Inventors: Ravi Kapur, Mehmet Toner, Zihua Wang, Martin Fuchs