Patents by Inventor Kurt Berlin

Kurt Berlin 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).

  • Patent number: 9719131
    Abstract: A method is described for the detection of the degree of methylation of a specific cytosine in the sequence context 5?-CpG-3? of a genomic DNA sample. In the first step, the genomic DNA is chemically treated in such a way that the cytosine bases are converted to uracil, but not the 5-methylcytosine bases. Then segments of the genomic DNA which contain the said specific cytosine are amplified, whereby the amplified products are given a detectable label and in the following steps the extent of hybridization of the amplified products on two classes of oligonucleotides is determined by detection of the label of the amplified products, and a conclusion is made on the extent of methylation of said specific cytosine in the genomic DNA sample from the ratio of the labels detected on the two classes of oligonucleotides as a consequence of the hybridization.
    Type: Grant
    Filed: July 30, 2010
    Date of Patent: August 1, 2017
    Assignee: EPIGENOMICS AG
    Inventors: Alexander Olek, Christian Piepenbrock, Kurt Berlin, David Guetig
  • Publication number: 20150176062
    Abstract: Aspects of the present invention relate to compositions and methods for providing DNA fragments from an archived sample (e.g., paraffin-embedded and/or fixed-tissue biopsies, etc.). Particular aspects provide methods whereby high yields of DNA are isolated as well as a substantial portion of the DNA consists of long DNA fragments, and where the isolated genomic DNA is free of associated or cross-linked contaminants like proteins, peptides, amino acids or RNA. The methods are facile, cost-effective, and are characterized by high reproducibility and reliability. Particular aspects provide methods for providing DNA fragments derived from an archived sample, wherein the yield of DNA before, for example, an amplification step is at least 20%, and amplicons up to a length of about 1,000 base pairs are amplifiable.
    Type: Application
    Filed: February 23, 2015
    Publication date: June 25, 2015
    Inventors: Matthias Ballhause, Kurt Berlin, Dimo Dietrich, Antje Kluth Lukas, Matthias Schuster, Ute Wagner, Reinhold Wasserkort, Heike Ziebarth
  • Publication number: 20150057183
    Abstract: Aspects of the present invention relate to the determination of the DNA methylation level at one or more CpG position within cells of a defined type in a tissue sample. This methylation level is deduced from the total DNA methylation level of all cells of the sample and from the content of said cells of interest. In aspects of the invention, the cell content is determined by means of histopatholoy, staining methods, antibodies, expression analysis or DNA methylation analysis.
    Type: Application
    Filed: November 6, 2014
    Publication date: February 26, 2015
    Inventors: Joern Lewin, Kurt Berlin
  • Patent number: 8962246
    Abstract: Aspects of the present invention relate to compositions and methods for providing DNA fragments from an archived sample (e.g., paraffin-embedded and/or fixed-tissue biopsies, etc.). Particular aspects provide methods whereby high yields of DNA are isolated as well as a substantial portion of the DNA consists of long DNA fragments, and where the isolated genomic DNA is free of associated or cross-linked contaminants like proteins, peptides, amino acids or RNA. The methods are facile, cost-effective, and are characterized by high reproducibility and reliability. Particular aspects provide methods for providing DNA fragments derived from an archived sample, wherein the yield of DNA before, for example, an amplification step is at least 20%, and amplicons up to a length of about 1,000 base pairs are amplifiable.
    Type: Grant
    Filed: December 2, 2013
    Date of Patent: February 24, 2015
    Assignee: Epigenomics AG
    Inventors: Matthias Ballhause, Kurt Berlin, Dimo Dietrich, Antje Kluth Lukas, Matthias Schuster, Ute Wagner, Reinhold Wasserkort, Heike Ziebarth
  • Patent number: 8912129
    Abstract: Aspects of the present invention relate to the determination of the DNA methylation level at one or more CpG position within cells of a defined type in a tissue sample. This methylation level is deduced from the total DNA methylation level of all cells of the sample and from the content of said cells of interest. In aspects of the invention, the cell content is determined by means of histopatholoy, staining methods, antibodies, expression analysis or DNA methylation analysis.
    Type: Grant
    Filed: November 17, 2006
    Date of Patent: December 16, 2014
    Assignee: Epigenomics AG
    Inventors: Joern Lewin, Kurt Berlin
  • Publication number: 20140087449
    Abstract: Aspects of the present invention relate to compositions and methods for providing DNA fragments from an archived sample (e.g., paraffin-embedded and/or fixed-tissue biopsies, etc.). Particular aspects provide methods whereby high yields of DNA are isolated as well as a substantial portion of the DNA consists of long DNA fragments, and where the isolated genomic DNA is free of associated or cross-linked contaminants like proteins, peptides, amino acids or RNA. The methods are facile, cost-effective, and are characterized by high reproducibility and reliability. Particular aspects provide methods for providing DNA fragments derived from an archived sample, wherein the yield of DNA before, for example, an amplification step is at least 20%, and amplicons up to a length of about 1,000 base pairs are amplifiable.
    Type: Application
    Filed: December 2, 2013
    Publication date: March 27, 2014
    Applicant: Epigenomics AG
    Inventors: Matthias Ballhause, Kurt Berlin, Dimo Dietrich, Antje Kluth Lukas, Matthias Schuster, Ute Wagner, Reinhold Wasserkort, Heike Ziebarth
  • Patent number: 8679745
    Abstract: Aspects of the present invention relate to compositions and methods for providing DNA fragments from an archived sample (e.g., paraffin-embedded and/or fixed-tissue biopsies, etc). Particular aspects provide methods whereby high yields of DNA are isolated as well as a substantial portion of the DNA consists of long DNA fragments, and where the isolated genomic DNA is free of associated or cross-linked contaminants like proteins, peptides, amino acids or RNA. The methods are facile, cost-effective, and are characterized by high reproducibility and reliability. Particular aspects provide methods for providing DNA fragments derived from an archived sample, wherein the yield of DNA before, for example, an amplification step is at least 20%, and amplicons up to a length of about 1,000 base pairs are amplifiable.
    Type: Grant
    Filed: September 30, 2005
    Date of Patent: March 25, 2014
    Assignee: Epigenomics AG
    Inventors: Matthias Ballhause, Kurt Berlin, Dimo Dietrich, Antje Kluth Lukas, Matthias Schuster, Ute Wagner, Reinhold Wasserkort, Heike Ziebarth
  • Publication number: 20130190205
    Abstract: Described is a method for detecting 5-methylcytosine in genomic DNA samples. First, a genomic DNA from a DNA sample is chemically converted with a reagent, 5-methylcytosine and cytosine reacting differently, and the pretreated DNA is subsequently amplified using a polymerase and at least one primer. In the next step, the amplified genomic DNA is hybridized to at least one oligonucleotide, forming a duplex, and said oligonucleotide is elongated by at least one nucleotide, the nucleotide carrying a detectable label, and the elongation depending on the methylation status of the specific cytosine in the genomic DNA sample. In the next step, the elongated oligonucleotides are analyzed for the presence of the label.
    Type: Application
    Filed: February 21, 2013
    Publication date: July 25, 2013
    Applicant: Epigenomics AG
    Inventors: Alexander Olek, Kurt Berlin
  • Patent number: 8257950
    Abstract: The present invention provides an improved method for the bisulfite conversion of DNA, and facilitates the analysis of cytosine methylation of genomic DNA. Novel combinations of denaturing solvents, new reaction conditions and new purification methods provide surprisingly efficacious methods for bisulfite conversion of DNA relative to prior art methods. The converted DNA may subsequently be analyzed by many different methods.
    Type: Grant
    Filed: June 13, 2011
    Date of Patent: September 4, 2012
    Assignee: Epigenomics AG
    Inventors: Kurt Berlin, Matthias Ballhause, Karen Cardon
  • Patent number: 8241855
    Abstract: A method is described for the detection of 5-methylcytosine in genomic DNA samples. First, a genomic DNA from a DNA sample is chemically converted with a reagent, whereby 5-methylcytosine and cytosine react differently. Then the pretreated DNA is amplified with the use of a polymerase with primers of different sequence. In the next step, the amplified genomic DNA is hybridized to an oligonucleotide array and PCR products are obtained, which must be provided with a label. Alternatively, the PCR products can be extended in a primer extension reaction, wherein the extension products are also provided with a label. In the last step, the extended oligonucleotides are investigated for the presence of the label.
    Type: Grant
    Filed: October 7, 2006
    Date of Patent: August 14, 2012
    Assignee: Epigenomics AG
    Inventor: Kurt Berlin
  • Publication number: 20120129729
    Abstract: Particular aspects relate to a method for determining the methylation pattern of a polynucleic acid, comprising: a) preparing a solution comprising a mixture of fragments of the polynucleic acid; b) coupling the fragments with a substance being detectable with a detection method; c) contacting a solution comprising the fragments of b) with a DNA microarray having a plurality of different immobilized oligonucleotides, each comprising at least one methylation site, at respectively assigned different locations thereon, the contacting under conditions affording hybridization of fragments with correlated immobilized oligonucleotides under defined stringency, and wherein the immobilized oligonucleotides have a length of less than 200 bases; d) optionally performing a washing step; and e) detecting, using the physical detection method, such immobilized nucleic acids to which solution fragments are hybridized and/or to which solution fragments are not hybridized.
    Type: Application
    Filed: April 4, 2011
    Publication date: May 24, 2012
    Applicant: Epigenomics AG
    Inventors: Anne Fassbender, Ralf Lesche, Juergen Distler, Christian Piepenbrock, Tamas Rujan, Kurt Berlin, Thomas Koenig
  • Publication number: 20120107807
    Abstract: The present invention concerns a method for the detection of cytosine methylation in DNA samples, wherein the following steps are conducted: (a) a genomic DNA sample, which comprises the DNA to be investigated and background DNA, is chemically treated in such a way that all of the unmethylated cytosine bases are converted to uracil, whereas the 5-methylcytosine bases remain unchanged; (b) the chemically treated DNA sample is amplified with the use of at least 1 primer oligonucleotide as well as a polymerase, whereby the DNA to be investigated is preferred as the template over the background DNA, and (c) the amplified products are analyzed and the methylation status in the DNA to be investigated is concluded from the presence of an amplified product and/or from the analysis of additional positions.
    Type: Application
    Filed: June 11, 2007
    Publication date: May 3, 2012
    Inventors: Alexander Olek, Kurt Berlin
  • Publication number: 20110250601
    Abstract: The present invention provides an improved method for the bisulfite conversion of DNA, and facilitates the analysis of cytosine methylation of genomic DNA. Novel combinations of denaturing solvents, new reaction conditions and new purification methods provide surprisingly efficacious methods for bisulfite conversion of DNA relative to prior art methods. The converted DNA may subsequently be analyzed by many different methods.
    Type: Application
    Filed: June 13, 2011
    Publication date: October 13, 2011
    Applicant: Epigenomics AG
    Inventors: Kurt Berlin, Matthias Ballhause, Karen Cardon
  • Patent number: 8029996
    Abstract: A method for the detection of cytosine methylation in DNA samples is described. First, DNA is extracted from a sample and bound to a surface. In the second step, a genomic DNA sample is preferably treated with a bisulfite (=disulfite, hydrogen sulfite), such that all unmethylated cytosine bases are converted to uracil, while the 5-methylcytosine bases remain unchanged. In the third step of the method, one or more oligonucleotides is (are) hybridized to the treated DNA as primers. In the fourth step of the method, the hybridized primer(s) is or are elongated in a polymerase reaction. Here, labeled guanine nucleotides are preferably utilized which are essentially incorporated only if cytosine bases were still present in the treated DNA. Consequently, the extent of incorporation of guanine bases and thus also the number of incorporated labels is proportional to the methylation in the DNA sample under investigation.
    Type: Grant
    Filed: October 4, 2002
    Date of Patent: October 4, 2011
    Assignee: Epigenomics AG
    Inventor: Kurt Berlin
  • Publication number: 20110159491
    Abstract: Described is a method for detecting 5-methylcytosine in genomic DNA samples. First, a genomic DNA from a DNA sample is chemically converted with a reagent, 5-methylcytosine and cytosine reacting differently, and the pretreated DNA is subsequently amplified using a polymerase and at least one primer. In the next step, the amplified genomic DNA is hybridized to at least one oligonucleotide, forming a duplex, and said oligonucleotide is elongated by at least one nucleotide, the nucleotide carrying a detectable label, and the elongation depending on the methylation status of the specific cytosine in the genomic DNA sample. In the next step, the elongated oligonucleotides are analyzed for the presence of the label.
    Type: Application
    Filed: October 29, 2010
    Publication date: June 30, 2011
    Inventors: Alexander Olek, Kurt Berlin
  • Patent number: 7968295
    Abstract: The present invention provides an improved method for the bisulfite conversion of DNA, and facilitates the analysis of cytosine methylation of genomic DNA. Novel combinations of denaturing solvents, new reaction conditions and new purification methods provide surprisingly efficacious methods for bisulfite conversion of DNA relative to prior art methods. The converted DNA may subsequently be analyzed by many different methods.
    Type: Grant
    Filed: March 24, 2009
    Date of Patent: June 28, 2011
    Assignee: Epigenomics AG
    Inventors: Kurt Berlin, Matthias Ballhause, Karen Cardon
  • Publication number: 20110136687
    Abstract: A method is described for the detection of the degree of methylation of a specific cytosine in the sequence context 5?-CpG-3? of a genomic DNA sample. In the first step, the genomic DNA is chemically treated in such a way that the cytosine bases are converted to uracil, but not the 5-methylcytosine bases. Then segments of the genomic DNA which contain the said specific cytosine are amplified, whereby the amplified products are given a detectable label and in the following steps the extent of hybridization of the amplified products on two classes of oligonucleotides is determined by detection of the label of the amplified products, and a conclusion is made on the extent of methylation of said specific cytosine in the genomic DNA sample from the ratio of the labels detected on the two classes of oligonucleotides as a consequence of the hybridization.
    Type: Application
    Filed: July 30, 2010
    Publication date: June 9, 2011
    Applicant: Epigenomics AG
    Inventors: Alexander Olek, Christian Piepenbrock, Kurt Berlin, David Guetig
  • Patent number: 7932027
    Abstract: Particular aspects relate to a method for determining the methylation pattern of a polynucleic acid, comprising: a) preparing a solution comprising a mixture of fragments of the polynucleic acid; b) coupling the fragments with a substance being detectable with a detection method; c) contacting a solution comprising the fragments of b) with a DNA microarray having a plurality of different immobilized oligonucleotides, each comprising at least one methylation site, at respectively assigned different locations thereon, the contacting under conditions affording hybridization of fragments with correlated immobilized oligonucleotides under defined stringency, and wherein the immobilized oligonucleotides have a length of less than 200 bases; d) optionally performing a a washing step; and e) detecting, using the physical detection method, such immobilized nucleic acids to which solution fragments are hybridized and/or to which solution fragments are not hybridized.
    Type: Grant
    Filed: February 16, 2006
    Date of Patent: April 26, 2011
    Assignee: Epigenomics AG
    Inventors: Anne Fassbender, Ralf Lesche, Juergen Distler, Christian Piepenbrock, Tamas Rujan, Kurt Berlin, Thomas Koenig
  • Publication number: 20110059432
    Abstract: Aspects of the present invention relate to compositions and methods for providing DNA fragments from a remote sample. In particular aspects a remote sample comprising DNA is provided, DNA is isolated from the remote sample, and the isolated DNA is treated in a way which allows differentiation of methylated and unmethylated cytosine. Additional, particular embodiments provide compositions and methods for methylation analysis of DNA derived from a remote sample. Other aspects provide for compositions and methods of whole genome amplification of bisulfite treated DNA.
    Type: Application
    Filed: April 17, 2006
    Publication date: March 10, 2011
    Applicant: EPIGENOMICS AG
    Inventors: Matthias Ballhause, Kurt Berlin, Theo De Vos, Dimo Dietrich, Volker Liebenberg, Catherine Lofton-Day, Joe Lograsso, Jennifer Maas, Fabian Model, Matthias Schuster, Andrew Z. Sledziewski, Reimo Tetzner
  • Patent number: 7867701
    Abstract: A method is described for the amplification of nucleic acids, in which the segments to be amplified are first hybridized with at least two primer oligonucleotides that have two domains, wherein the sequence-specific domain found at the 3-end hybridizes to the segment to be amplified, while the generic domain found at the 5-end does not hybridize. Then an amplification reaction is conducted by means of a polymerase and subsequently a labeled primer oligonucleotide, which binds to the generic domain of the first primer, is hybridized to the amplificate which is formed. In the last step, the sequence of the amplificate is investigated.
    Type: Grant
    Filed: December 22, 2001
    Date of Patent: January 11, 2011
    Assignee: Epigenomics AG
    Inventors: J├╝rgen Distler, Kurt Berlin, Alexander Olek