Patents by Inventor Sudhir Sinha

Sudhir Sinha 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: 20230054587
    Abstract: A retrotransposable element-based multiplexed quantitative polymerase chain reaction (qPCR) assay system to quantitate and distinguish cell free DNA integrity and concentration in blood, plasma, and serum as a measure of minimum residual disease, therapeutic effectiveness, neoadjuvant effectiveness in a patient having stage I, stage II, stage III, or stage IV cancer, and disease progression, thereby improving patient outcomes.
    Type: Application
    Filed: December 18, 2020
    Publication date: February 23, 2023
    Inventors: Sudhir SINHA, Gary SPITZER, Hiromi BROWN, Patrick HALL
  • Patent number: 11345953
    Abstract: A process of quantifying the extent of degradation present in a human DNA sample is described. The process makes use of a real time PCR system to separately quantitate within a sample a first retrotransposon interspersed element and a relatively longer second retrotransposon interspersed element, where the longer element is expected to be disrupted at a faster pace than is the shorter element as the sample degrades. In one embodiment, the process makes use of the appearance of the relatively young (on an evolutionary scale) Alu Yb-lineage subfamily sequences appearing in every human genome and their virtual absence in non-human samples. In a preferred embodiment, the process quantifies longer 290 bp sequences of “SVA” elements and shorter 80 bp sequences of Alu Yb8-lineage. Newly designed primers and TaqMan probes that are useful in the process are presented. A related process additionally quantifies male specific human DNA.
    Type: Grant
    Filed: March 13, 2018
    Date of Patent: May 31, 2022
    Inventor: Sudhir Sinha
  • Publication number: 20210292811
    Abstract: A retrotransposable element based multiplexed qPCR assay to robustly quantitate and distinguish cell free DNA integrity and concentration in blood plasma and serum is described. The multiplexed system for characterizing cancer in humans includes a sample of serum, plasma, urine, or other biological fluid, the sample comprising cell free DNA, the cell free DNA comprising long and short retrotransposable element targets and an added internal positive control, the long and short targets being independent of each other, a distinctly labeled TaqMan probe corresponding to each target, a forward primer and a reverse primer corresponding to each target, a DNA standard for generating standard curves, a qPCR system for amplifying the targets and a qPCR data analysis system.
    Type: Application
    Filed: March 12, 2021
    Publication date: September 23, 2021
    Inventor: Sudhir SINHA
  • Patent number: 10993418
    Abstract: Kits and methods providing measurement of tumor burden in a patient derived xenograft (PDX) mouse are described. Exemplary embodiments contemplate taking a sample, typically a blood sample, from a PDX mouse and using a real-time polymerase chain reaction (PCR) system to quantitate both human patient circulating tumor DNA (ctDNA) and mouse DNA. In preferred embodiments, both PCR amplifications are done simultaneously in a multiplex, and a highly polymorphic human DNA target sequence is amplified for high sensitivity, allowing for small volume samples, typically 50-100 ?L, of mouse blood. Serial evaluations are possible because the mouse can survive withdrawal of these small volumes of blood. A related method allows for quantitation of ctDNA in the presence of human immune cells added to a “humanized” mouse. These relatively quick and easy methods of determining tumor burden in PDX mice can have predictive value for the efficacy of cancer treatments in human patients.
    Type: Grant
    Filed: April 30, 2018
    Date of Patent: May 4, 2021
    Inventor: Sudhir Sinha
  • Patent number: 10988803
    Abstract: A retrotransposable element based multiplexed qPCR assay to robustly quantitate and distinguish cell free DNA integrity and concentration in blood plasma and serum is described. The multiplexed system for characterizing cancer in humans includes a sample of serum, plasma, urine, or other biological fluid, the sample comprising cell free DNA, the cell free DNA comprising long and short retrotransposable element targets and an added internal positive control, the long and short targets being independent of each other, a distinctly labeled TaqMan probe corresponding to each target, a forward primer and a reverse primer corresponding to each target, a DNA standard for generating standard curves, a qPCR system for amplifying the targets and a qPCR data analysis system.
    Type: Grant
    Filed: December 29, 2015
    Date of Patent: April 27, 2021
    Assignee: Life Genetics Lab, LLC
    Inventor: Sudhir Sinha
  • Patent number: 10968477
    Abstract: By utilizing a Mini-Primer strategy targeting the target site duplication (TSD) sequence of retrotransposons, insertion and null allele (INNUL) markers, which include short interspersed nuclear elements (SINEs), long interspersed nuclear elements (LINEs), and composite SVA retrotransposons (SINE/VNTR/Alu, where VNTR represents “variable number of tandem repeats” and Alu represents a type of primate specific SINE that has reached a copy number in excess of one million in the human genome), can be effectively used as markers for human identification and bio-ancestry studies regardless of the size of the inserted element. The size of the amplicons for INNULs and the difference between allelic states can be reduced substantially such that these markers have utility for analyzing high and low quality human DNA samples. Multiplexes including either 15 or 20 retrotransposable element (RE) markers plus Amelogenin for single tube amplification of DNA in four color detection were successfully designed.
    Type: Grant
    Filed: October 26, 2015
    Date of Patent: April 6, 2021
    Inventor: Sudhir Sinha
  • Patent number: 10415031
    Abstract: A method for processing forensic samples that include sperm cells from a perpetrator of sexual assault and epithelial cells that are primarily contributed by the victim is provided. The method includes providing a nanofiber filter that is formed of intermingled nanofibers having diameters of about 700 nm or less, selectively digesting the epithelial cells of a forensic sample and separating the sperm cells of the sample from the digested epithelial cells by filtration of the digest mixture through the nanofiber filter, the sperm cells becoming entrapped in the nanofiber filter. The captured sperm cells may then be digested to form a second digest mixture including digested sperm cell DNA. Using the first digest mixture filtrate and the second digest mixture, respectively, DNA samples may be isolated and DNA profiles may be obtained, the DNA profiles being useful for human identification. An apparatus and a kit for processing forensic samples obtained in sexual assault cases are also provided.
    Type: Grant
    Filed: February 4, 2016
    Date of Patent: September 17, 2019
    Assignee: InnoGenomics Technologies, LLC
    Inventor: Sudhir Sinha
  • Publication number: 20180288982
    Abstract: Kits and methods providing measurement of tumor burden in a patient derived xenograft (PDX) mouse are described. Exemplary embodiments contemplate taking a sample, typically a blood sample, from a PDX mouse and using a real-time polymerase chain reaction (PCR) system to quantitate both human patient circulating tumor DNA (ctDNA) and mouse DNA. In preferred embodiments, both PCR amplifications are done simultaneously in a multiplex, and a highly polymorphic human DNA target sequence is amplified for high sensitivity, allowing for small volume samples, typically 50-100 ?L, of mouse blood. Serial evaluations are possible because the mouse can survive withdrawal of these small volumes of blood. A related method allows for quantitation of ctDNA in the presence of human immune cells added to a “humanized” mouse. These relatively quick and easy methods of determining tumor burden in PDX mice can have predictive value for the efficacy of cancer treatments in human patients.
    Type: Application
    Filed: April 30, 2018
    Publication date: October 11, 2018
    Inventor: Sudhir Sinha
  • Publication number: 20180230525
    Abstract: A process of quantifying the extent of degradation present in a human DNA sample is described. The process makes use of a real time PCR system to separately quantitate within a sample a first retrotransposon interspersed element and a relatively longer second retrotransposon interspersed element, where the longer element is expected to be disrupted at a faster pace than is the shorter element as the sample degrades. In one embodiment, the process makes use of the appearance of the relatively young (on an evolutionary scale) Alu Yb-lineage subfamily sequences appearing in every human genome and their virtual absence in non-human samples. In a preferred embodiment, the process quantifies longer 290 bp sequences of “SVA” elements and shorter 80 bp sequences of Alu Yb8-lineage. Newly designed primers and TaqMan probes that are useful in the process are presented. A related process additionally quantifies male specific human DNA.
    Type: Application
    Filed: March 13, 2018
    Publication date: August 16, 2018
    Inventor: Sudhir Sinha
  • Patent number: 10004561
    Abstract: By utilizing a Mini-Primer strategy targeting the target site duplication (TSD) sequence of retrotransposons, INNUL markers, which include SINEs, LINEs, and SVAs, can be effectively used as markers for human identification and bio-ancestry studies regardless of the size of the inserted element. The size of the amplicons for INNULs and the difference between allelic states can be reduced substantially such that these markers have utility for analyzing high and low quality human DNA samples. A 15 RE marker and Amelogenin (for sex determination) multiplex for a single tube amplification of DNA, in four color detection was successfully designed. The multiplex provided power of discrimination suitable for forensic and paternity analysis. In addition, sensitivity of detection can enable human identity and bio-ancestry studies on forensic and anthropological samples. Depending on the distribution of the alleles in global populations, INNULs can be selected for human identity testing or for bio-ancestry studies.
    Type: Grant
    Filed: October 15, 2013
    Date of Patent: June 26, 2018
    Assignee: LIFE GENETICS LAB, LLC
    Inventor: Sudhir Sinha
  • Patent number: 9957557
    Abstract: A process of quantifying the extent of degradation present in a human DNA sample is described. The process makes use of a real time PCR system to separately quantitate within a sample a first retrotransposon interspersed element and a relatively longer second retrotransposon interspersed element, where the longer element is expected to be disrupted at a faster pace than is the shorter element as the sample degrades. In one embodiment, the process makes use of the appearance of the relatively young (on an evolutionary scale) Alu Yb-lineage subfamily sequences appearing in every human genome and their virtual absence in non-human samples. In a preferred embodiment, the process quantifies longer 290 bp sequences of “SVA” elements and shorter 80 bp sequences of Alu Yb8-lineage. Newly designed primers and TaqMan probes that are useful in the process are presented. A related process additionally quantifies male specific human DNA.
    Type: Grant
    Filed: August 12, 2013
    Date of Patent: May 1, 2018
    Assignee: LIFE GENETICS LAB, LLC
    Inventor: Sudhir Sinha
  • Publication number: 20160222375
    Abstract: A method for processing forensic samples that include sperm cells from a perpetrator of sexual assault and epithelial cells that are primarily contributed by the victim is provided. The method includes providing a nanofiber filter that is formed of intermingled nanofibers having diameters of about 700 nm or less, selectively digesting the epithelial cells of a forensic sample and separating the sperm cells of the sample from the digested epithelial cells by filtration of the digest mixture through the nanofiber filter, the sperm cells becoming entrapped in the nanofiber filter. The captured sperm cells may then be digested to form a second digest mixture including digested sperm cell DNA. Using the first digest mixture filtrate and the second digest mixture, respectively, DNA samples may be isolated and DNA profiles may be obtained, the DNA profiles being useful for human identification. An apparatus and a kit for processing forensic samples obtained in sexual assault cases are also provided.
    Type: Application
    Filed: February 4, 2016
    Publication date: August 4, 2016
    Inventor: Sudhir SINHA
  • Publication number: 20160186239
    Abstract: A retrotransposable element based multiplexed qPCR assay to robustly quantitate and distinguish cell free DNA integrity and concentration in blood plasma and serum is described. The multiplexed system for characterizing cancer in humans includes a sample of serum, plasma, urine, or other biological fluid, the sample comprising cell free DNA, the cell free DNA comprising long and short retrotransposable element targets and an added internal positive control, the long and short targets being independent of each other, a distinctly labeled TaqMan probe corresponding to each target, a forward primer and a reverse primer corresponding to each target, a DNA standard for generating standard curves, a qPCR system for amplifying the targets and a qPCR data analysis system.
    Type: Application
    Filed: December 29, 2015
    Publication date: June 30, 2016
    Inventor: Sudhir Sinha
  • Publication number: 20160108462
    Abstract: By utilizing a Mini-Primer strategy targeting the target site duplication (TSD) sequence of retrotransposons, insertion and null allele (INNUL) markers, which include short interspersed nuclear elements (SINEs), long interspersed nuclear elements (LINEs), and composite SVA retrotransposons (SINE/VNTR/Alu, where VNTR represents “variable number of tandem repeats” and Alu represents a type of primate specific SINE that has reached a copy number in excess of one million in the human genome), can be effectively used as markers for human identification and bio-ancestry studies regardless of the size of the inserted element. The size of the amplicons for INNULs and the difference between allelic states can be reduced substantially such that these markers have utility for analyzing high and low quality human DNA samples. Multiplexes including either 15 or 20 retrotransposable element (RE) markers plus Amelogenin for single tube amplification of DNA in four color detection were successfully designed.
    Type: Application
    Filed: October 26, 2015
    Publication date: April 21, 2016
    Inventor: Sudhir Sinha
  • Publication number: 20140127696
    Abstract: By utilizing a Mini-Primer strategy targeting the target site duplication (TSD) sequence of retrotransposons, INNUL markers, which include SINEs, LINEs, and SVAs, can be effectively used as markers for human identification and bio-ancestry studies regardless of the size of the inserted element. The size of the amplicons for INNULs and the difference between allelic states can be reduced substantially such that these markers have utility for analyzing high and low quality human DNA samples. A 15 RE marker and Amelogenin (for sex determination) multiplex for a single tube amplification of DNA, in four color detection was successfully designed. The multiplex provided power of discrimination suitable for forensic and paternity analysis. In addition, sensitivity of detection can enable human identity and bio-ancestry studies on forensic and anthropological samples. Depending on the distribution of the alleles in global populations, INNULs can be selected for human identity testing or for bio-ancestry studies.
    Type: Application
    Filed: October 15, 2013
    Publication date: May 8, 2014
    Inventor: Sudhir Sinha
  • Publication number: 20140051075
    Abstract: A process of quantifying the extent of degradation present in a human DNA sample is described. The process makes use of a real time PCR system to separately quantitate within a sample a first retrotransposon interspersed element and a relatively longer second retrotransposon interspersed element, where the longer element is expected to be disrupted at a faster pace than is the shorter element as the sample degrades. In one embodiment, the process makes use of the appearance of the relatively young (on an evolutionary scale) Alu Yb-lineage subfamily sequences appearing in every human genome and their virtual absence in non-human samples. In a preferred embodiment, the process quantifies longer 290 bp sequences of “SVA” elements and shorter 80 bp sequences of Alu Yb8-lineage. Newly designed primers and TaqMan probes that are useful in the process are presented. A related process additionally quantifies male specific human DNA.
    Type: Application
    Filed: August 12, 2013
    Publication date: February 20, 2014
    Inventor: Sudhir Sinha
  • Publication number: 20070003944
    Abstract: The insertion polymorphisms based on interspersed elements including LINEs and SINEs is used for the inference of an individual's geographic origin. SINE polymorphisms are identical-by-descent, essentially homoplasy-free, and inexpensive to genotype using a variety of approaches. Using a Structure analysis of the Alu insertion polymorphism based genotypes, the geographic affiliation of unknown human individuals can be inferred with high levels of confidence. This technique to infer the geographic affiliation of unknown human DNA samples can be a useful tool in forensic genomics.
    Type: Application
    Filed: August 12, 2005
    Publication date: January 4, 2007
    Inventors: Sudhir Sinha, Jaiprakash Shewale, Mark Batzer, Jerilyn Walker, David Ray
  • Publication number: 20060199217
    Abstract: A method for determining gender from a human DNA sample. The loci of Alu element insertion is selected, amplified and evaluated in terms of size of the fragment. The gender assay utilizes AluSTXa for the X chromosome, AluSTYa for the Y chromosome, or both AluSTXa and AluSTYa, to reduce the possibility of error to a negligible quantity. The inserted chromosome yields a large fragment when the homologous region is amplified. The males are distinguished as having two DNA amplicons present, while females have only a single amplicon. The kit adapted for carrying out the method includes a pair of primers to amplify the locus and optionally polymerase chain reaction regents.
    Type: Application
    Filed: May 10, 2006
    Publication date: September 7, 2006
    Inventors: Sudhir Sinha, Dale Hedges, Mark Batzer
  • Publication number: 20060141512
    Abstract: The development of an isolation methodology for separation of human sperm cells from biological samples containing human epithelial cells is provided. Using sperm binding proteins, glycopeptides, lectins, derivatives of N-acetylglucosamine, triazine dyes or inhibitors of glycosyltransferase linked to an insoluble support, our invention enables binding of human sperm cells from biological samples. Bound sperms can be dissociated and used for in vitro analyses or subsequently lysed on the insoluble support for isolation of male specific DNA. Other cell types such as epithelial cells, white blood cells and cell debris present in the biological samples are not bound to the derivatized insoluble support. The sperm cells, thus isolated, can be processed for isolation of nuclear DNA for human identification and forensic DNA analysis.
    Type: Application
    Filed: December 2, 2005
    Publication date: June 29, 2006
    Inventors: Sudhir Sinha, Jaiprakash Shewale
  • Publication number: 20060099620
    Abstract: A comprehensive set of human specific, target specific, multiplex PCR assays for DNA quantitation is provided. Our duplex qPCR for nDNA/mtDNA had a linear quantitation range of 100 ng to 1 pg, and our triplex qPCR assay for nDNA/mtDNA/male Y DNA had a linear range of 100 ng to 0.1 ng. Human-specificity was demonstrated by the accurate detection of 0.05% and 5% human DNA, respectively, from a complex source of starting templates. Target-specificity was confirmed by the lack of cross-amplification among targets. A high throughput alternative for human gender determination was also developed by multiplexing the male Y primer/probe set with an X chromosome based system. Background cross-amplification with DNA templates derived from fourteen other species was negligible aside from the male Y assay which produced spurious amplifications from other non-human primate templates. Mainstream application of these assays will undoubtedly benefit forensic genomics.
    Type: Application
    Filed: October 7, 2005
    Publication date: May 11, 2006
    Inventors: Jerilyn Walker, Dale Hedges, Jaiprakash Shewale, Sudhir Sinha, Mark Batzer