Patents by Inventor Xinghua Pan

Xinghua Pan 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: 20240132949
    Abstract: Disclosed is a set of adhesive adapters containing sample barcodes for specifically tagging different samples. Further disclosed is a method for simultaneously detecting CpG methylation in a high number of samples, which is multi-sample reduced-representation bisulfite sequencing (msRRBS); and an alternative method thereof, which is multi-sample reduced-representation APOBEC sequencing (msRRAS). The adapters are used to specifically tag the plurality of samples, including all DNA fragments of the plurality of samples; then the plurality of samples are pooled to allow a single-tube reaction of the plurality of samples; and then the subsequent conversion, sequencing library construction and sequencing, distribution and decoding of readings of each sample, and downstream analysis are conducted. The library construction technology of the present application has advantages such as high efficiency, low cost, and stable and convenient operations.
    Type: Application
    Filed: September 24, 2023
    Publication date: April 25, 2024
    Inventors: Xinghua Pan, Liyao Mai, Zhiwei Lian
  • Publication number: 20240043919
    Abstract: A method for construction of a medium-throughput single-cell copy number sequencing (MT-scCNV-seq) library and sequencing includes: delivering single cells each to a tube, and independently lysing each cell; labeling each cell with a cell-specific barcode while tagmenting the gDNA with an innovative Tn5 transposome; pooling the reactions of a plurality of cells simultaneously treated above, and constructing a batch of sequencing libraries for the cells collectively in a single tube with primers containing a batch index. The specific tagmentation of the gDNA of a given cell by the Tn5 transposome enables early pooling of multiple cells in a single tube for collective library construction, without pre-whole-genome-amplification of each cell. The output library is compatible with a conventional NGS platform and program. Finally the sequencing data is disaggregated, and traced to each cell according to the barcode and index; the CNV profile for each cell of the panel is accurately identified.
    Type: Application
    Filed: July 31, 2023
    Publication date: February 8, 2024
    Inventors: Xinghua Pan, Guanchuan Lin, Caiming Chen, Zhanying Dong
  • Publication number: 20230104375
    Abstract: The invention discloses a primer set and a multiplexable library building scheme for constructing an RNA sequencing library with a related reagent kit and an application thereof. The invention also discloses a corresponding data analysis method and a related instrument. The primer set used for RNA sequencing library construction includes the reverse transcription primers containing poly-dT, the 2nd strand cDNA primers particularly contain a random or semi-random portion at their 3? end for universal initiation of the synthesis at multiple sites, or sequence capturing the 1st strand of a specific cDNA, as well as their corresponding PCR primer 1 and 2. By this method, the library construction process is simple and the operation is convenient; the time of building the database was significantly shortened; it can carry out a large number of samples in a single run; the analysis process is simpler; the cost of database building, sequencing and analysis is significantly reduced.
    Type: Application
    Filed: October 1, 2021
    Publication date: April 6, 2023
    Inventors: Xinghua PAN, Liyao MAI, Caiming CHEN, Yinbing QIU, Zhiwei LIAN
  • Patent number: 10480021
    Abstract: Methods of identifying DNase I Hyper-Resistant Sites (DHRS), or in board sense, highly compact chromatin and characterizing the DNA methylation status of DMRs such as CpG islands and CpG island shores are provided. The methods are particularly useful for analysis of genomic DNA from low quantities of cells, for example, less than 1,000 cells, less than 100 cells, less than 10 cells, or even one cell, and can be used to generate chromatin and methylation profiles. The downstream analyses include in parallel massive sequencing, microarray, PCR and Sanger sequencing, hybridization and other platforms. These methods can be used to generate chromatin and DNA methylation profiles in drug development, diagnostics, and therapeutic applications are also provided.
    Type: Grant
    Filed: June 23, 2015
    Date of Patent: November 19, 2019
    Assignee: YALE UNIVERSITY
    Inventors: Xinghua Pan, Sherman M. Weissman
  • Patent number: 10093970
    Abstract: The invention relates to a method for single cell analysis of relative telomere length using multiplex pre-PCR followed by a qPCR (SCT-pqPCR).
    Type: Grant
    Filed: March 14, 2014
    Date of Patent: October 9, 2018
    Assignees: New York University, Yale University
    Inventors: David Keefe, Sherman Weissman, Lin Liu, Fang Wang, Xinghua Pan
  • Patent number: 10017761
    Abstract: Methods for preparing cDNA libraries from single and low quantities of cells are disclosed. The methods are based on the principles of multi-strand displacement amplification or semi-random primed polymerase chain reaction. The methods typically include a step of reverse transcription and subsequent amplification of cDNA. The methods can be adapted for preparation of cDNA libraries that are representative of mRNA or whole RNA expressed by the cell or cells. The cDNA is suitable for sequencing or microarray analysis.
    Type: Grant
    Filed: December 23, 2013
    Date of Patent: July 10, 2018
    Assignee: Yale University
    Inventors: Sherman M. Weissman, Xinghua Pan
  • Publication number: 20160032360
    Abstract: The invention relates to a method for single cell analysis of relative telomere length using multiplex pre-PCR followed by a qPCR (SCT-pqPCR).
    Type: Application
    Filed: March 14, 2014
    Publication date: February 4, 2016
    Applicants: New york University, Yale University
    Inventors: David KEEFE, Sherman WEISSMAN, Lin LIU, Fang WANG, Xinghua PAN
  • Publication number: 20150368694
    Abstract: Methods of identifying DNase I Hyper-Resistant Sites (DHRS), or in board sense, highly compact chromatin and characterizing the DNA methylation status of DMRs such as CpG islands and CpG island shores are provided. The methods are particularly useful for analysis of genomic DNA from low quantities of cells, for example, less than 1,000 cells, less than 100 cells, less than 10 cells, or even one cell, and can be used to generate chromatin and methylation profiles. The downstream analyses include in parallel massive sequencing, microarray, PCR and Sanger sequencing, hybridization and other platforms. These methods can be used to generate chromatin and DNA methylation profiles in drug development, diagnostics, and therapeutic applications are also provided.
    Type: Application
    Filed: June 23, 2015
    Publication date: December 24, 2015
    Inventors: Xinghua Pan, Sherman M. Weissman
  • Publication number: 20140213485
    Abstract: Methods for preparing cDNA libraries from single and low quantities of cells are disclosed. The methods are based on the principles of multi-strand displacement amplification or semi-random primed polymerase chain reaction. The methods typically include a step of reverse transcription and subsequent amplification of cDNA. The methods can be adapted for preparation of cDNA libraries that are representative of mRNA or whole RNA expressed by the cell or cells. The cDNA is suitable for sequencing or microarray analysis.
    Type: Application
    Filed: December 23, 2013
    Publication date: July 31, 2014
    Applicant: YALE UNIVERSITY
    Inventors: SHERMAN M. WEISSMAN, XINGHUA PAN
  • Publication number: 20110318291
    Abstract: A topical drying composition is providing containing trehalose as the effective moisture (sweat) removing ingredient. The composition may be used in aqueous form or preferably as a cream and in addition to trehalose it contains several ingredients such as sorbitan monolaurate, polysorbitan, a moisturizer, a thickener, a softener, an antibacterial agent and a pH adjusting component to adjust the pH of the composition between about 5.5 to about 7.5. Sterilized water is used as the carrier for the composition. The topical composition can be applied to the area which is vulnerable to sweating after vigorous exercise in order to moisturize sweating on the skin.
    Type: Application
    Filed: September 2, 2011
    Publication date: December 29, 2011
    Inventors: Frank P. Marchese, Xinghua Pan, Harold J. Mermelstein
  • Patent number: 8067037
    Abstract: A topical drying composition is providing containing trehalose as the effective moisture (sweat) removing ingredient. The composition may be used in aqueous form or preferably as a cream and in addition to trehalose it contains several ingredients such as sorbitan monolaurate, polysorbitan, a moisturizer, a thickener, a softener, an antibacterial agent and a pH adjusting component to adjust the pH of the composition between about 5.5 to about 7.5. Sterilized water is used as the carrier for the composition. The topical composition can be applied to the area which is vulnerable to sweating after vigorous exercise in order to moisturize sweating on the skin.
    Type: Grant
    Filed: June 24, 2008
    Date of Patent: November 29, 2011
    Inventors: Frank P. Marchese, Xinghua Pan, Harold J. Mermelstein
  • Publication number: 20090317493
    Abstract: A topical drying composition is providing containing trehalose as the effective moisture (sweat) removing ingredient. The composition may be used in aqueous form or preferably as a cream and in addition to trehalose it contains several ingredients such as sorbitan monolaurate, polysorbitan, a moisturizer, a thickener, a softener, an antibacterial agent and a pH adjusting component to adjust the pH of the composition between about 5.5 to about 7.5. Sterilized water is used as the carrier for the composition. The topical composition can be applied to the area which is vulnerable to sweating after vigorous exercise in order to moisturize sweating on the skin.
    Type: Application
    Filed: June 24, 2008
    Publication date: December 24, 2009
    Inventors: Frank P. Marchese, Xinghua Pan, Harold J. Mermelstein
  • Patent number: 6924104
    Abstract: An improved method for screening genomic, cDNA, or any DNA fragments in general is described. Novel adapters are ligated to the ends of DNA fragments from two different individuals or two different pools of individuals. The DNA fragment-adapter complexes are mixed, denatured and reannealed to form homohybrid and heterohybrid DNA duplexes, which are separated based on characteristics of the adapters. Sequence differences between heterohybrids can be revealed as mismatched base pairs in the heterohybrid DNA duplex. Mismatch base pairs are discovered using genome mismatch scanning techniques that use thymine glycosylases and related enzymes that capture DNA containing mismatched base pairs. The perfectly base paired DNA or DNA containing mismatched base pairs can be further separated into homohybrids and heterohybrids using novel adapters that allow physical capture of either heterohybrid or homohybrid DNA.
    Type: Grant
    Filed: October 29, 2001
    Date of Patent: August 2, 2005
    Assignee: Yale University
    Inventors: Sherman Weissman, Xinghua Pan
  • Patent number: 6372434
    Abstract: Genomic or cDNA, or fragments and mixtures thereof, can be screened by generation of subsets and then subjecting the subsets to mismatch scanning procedures. Alternatively, DNA fragments can be generated by cutting with a restriction endonuclease that generates variable overhangs. For either of the above methods, Y-shaped adapters having a region of non-complementary single-stranded DNA at the end can be used. Heterohybrid DNA, containing one DNA strand derived from each of two different samples, or homohybrids, containing DNA strands from the same sample, can be selected. Adapters attached to the ends of the fragments are designed to allow the selective isolation of homohybrid or heterohybrid DNA.
    Type: Grant
    Filed: May 1, 2000
    Date of Patent: April 16, 2002
    Assignee: Molecular Staging, Inc.
    Inventors: Sherman Weissman, Roger Lasken, Xinghua Pan
  • Patent number: 6346399
    Abstract: Genomic or cDNA, or fragments and mixtures thereof, can be screened by generation of subsets and then subjecting the subsets to mismatch scanning procedures. Alternatively, DNA fragments can be generated by cutting with a restriction endonuclease that generates variable overhangs. For either of the above methods, Y-shaped adapters having a region of non-complementary single-stranded DNA at the end can be used. Heterohybrid DNA, containing one DNA strand derived from each of two different samples, or homohybrids, containing DNA strands from the same sample, can be selected. Adapters attached to the ends of the fragments are designed to allow the selective isolation of homohybrid or heterohybrid DNA.
    Type: Grant
    Filed: May 1, 2000
    Date of Patent: February 12, 2002
    Assignees: Yale University, Molecular Staging, Inc.
    Inventors: Sherman Weissman, Roger Lasken, Xinghua Pan
  • Patent number: 6287825
    Abstract: Genomic or cDNA, or fragments and mixtures thereof, can be screened by generation of subsets and then subjecting the subsets to mismatch scanning procedures. Alternatively, DNA fragments can be generated by cutting with a restriction endonuclease that generates variable overhangs. For either of the above methods, Y-shaped adapters having a region of non-complementary single-stranded DNA at the end can be used. Heterohybrid DNA, containing one DNA strand derived from each of two different samples, or homohybrids, containing DNA strands from the same sample, can be selected. Adapters attached to the ends of the fragments are designed to allow the selective isolation of homohybrid or heterohybrid DNA.
    Type: Grant
    Filed: September 17, 1999
    Date of Patent: September 11, 2001
    Assignee: Molecular Staging Inc.
    Inventors: Sherman Weissman, Roger Lasken, Xinghua Pan