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).
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Publication number: 20240229125Abstract: 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: ApplicationFiled: September 25, 2023Publication date: July 11, 2024Inventors: Xinghua Pan, Liyao Mai, Zhiwei Lian
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Publication number: 20240132949Abstract: 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: ApplicationFiled: September 24, 2023Publication date: April 25, 2024Inventors: Xinghua Pan, Liyao Mai, Zhiwei Lian
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Publication number: 20240043919Abstract: 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: ApplicationFiled: July 31, 2023Publication date: February 8, 2024Inventors: Xinghua Pan, Guanchuan Lin, Caiming Chen, Zhanying Dong
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Publication number: 20230104375Abstract: 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: ApplicationFiled: October 1, 2021Publication date: April 6, 2023Inventors: Xinghua PAN, Liyao MAI, Caiming CHEN, Yinbing QIU, Zhiwei LIAN
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Patent number: 10480021Abstract: 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: GrantFiled: June 23, 2015Date of Patent: November 19, 2019Assignee: YALE UNIVERSITYInventors: Xinghua Pan, Sherman M. Weissman
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Patent number: 10093970Abstract: 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: GrantFiled: March 14, 2014Date of Patent: October 9, 2018Assignees: New York University, Yale UniversityInventors: David Keefe, Sherman Weissman, Lin Liu, Fang Wang, Xinghua Pan
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Patent number: 10017761Abstract: 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: GrantFiled: December 23, 2013Date of Patent: July 10, 2018Assignee: Yale UniversityInventors: Sherman M. Weissman, Xinghua Pan
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Publication number: 20160032360Abstract: 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: ApplicationFiled: March 14, 2014Publication date: February 4, 2016Applicants: New york University, Yale UniversityInventors: David KEEFE, Sherman WEISSMAN, Lin LIU, Fang WANG, Xinghua PAN
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Publication number: 20150368694Abstract: 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: ApplicationFiled: June 23, 2015Publication date: December 24, 2015Inventors: Xinghua Pan, Sherman M. Weissman
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Publication number: 20140213485Abstract: 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: ApplicationFiled: December 23, 2013Publication date: July 31, 2014Applicant: YALE UNIVERSITYInventors: SHERMAN M. WEISSMAN, XINGHUA PAN
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Publication number: 20110318291Abstract: 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: ApplicationFiled: September 2, 2011Publication date: December 29, 2011Inventors: Frank P. Marchese, Xinghua Pan, Harold J. Mermelstein
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Patent number: 8067037Abstract: 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: GrantFiled: June 24, 2008Date of Patent: November 29, 2011Inventors: Frank P. Marchese, Xinghua Pan, Harold J. Mermelstein
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Publication number: 20090317493Abstract: 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: ApplicationFiled: June 24, 2008Publication date: December 24, 2009Inventors: Frank P. Marchese, Xinghua Pan, Harold J. Mermelstein
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Patent number: 6924104Abstract: 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: GrantFiled: October 29, 2001Date of Patent: August 2, 2005Assignee: Yale UniversityInventors: Sherman Weissman, Xinghua Pan
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Patent number: 6372434Abstract: 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: GrantFiled: May 1, 2000Date of Patent: April 16, 2002Assignee: Molecular Staging, Inc.Inventors: Sherman Weissman, Roger Lasken, Xinghua Pan
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Patent number: 6346399Abstract: 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: GrantFiled: May 1, 2000Date of Patent: February 12, 2002Assignees: Yale University, Molecular Staging, Inc.Inventors: Sherman Weissman, Roger Lasken, Xinghua Pan
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Patent number: 6287825Abstract: 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: GrantFiled: September 17, 1999Date of Patent: September 11, 2001Assignee: Molecular Staging Inc.Inventors: Sherman Weissman, Roger Lasken, Xinghua Pan