Patents by Inventor Matthias Ballhause
Matthias Ballhause 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: 10731215Abstract: 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. Other aspects provide methods for determining the presence or absence of methylation of at least one cytosine, or a series of cytosines in cis, in human DNA of a blood sample, a plasma sample, a serum sample or a urine sample from a human individual.Type: GrantFiled: April 17, 2006Date of Patent: August 4, 2020Assignee: EPIGENOMICS AGInventors: 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
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Publication number: 20150176062Abstract: 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: ApplicationFiled: February 23, 2015Publication date: June 25, 2015Inventors: Matthias Ballhause, Kurt Berlin, Dimo Dietrich, Antje Kluth Lukas, Matthias Schuster, Ute Wagner, Reinhold Wasserkort, Heike Ziebarth
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Patent number: 8962246Abstract: 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: GrantFiled: December 2, 2013Date of Patent: February 24, 2015Assignee: Epigenomics AGInventors: Matthias Ballhause, Kurt Berlin, Dimo Dietrich, Antje Kluth Lukas, Matthias Schuster, Ute Wagner, Reinhold Wasserkort, Heike Ziebarth
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Publication number: 20140087449Abstract: 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: ApplicationFiled: December 2, 2013Publication date: March 27, 2014Applicant: Epigenomics AGInventors: Matthias Ballhause, Kurt Berlin, Dimo Dietrich, Antje Kluth Lukas, Matthias Schuster, Ute Wagner, Reinhold Wasserkort, Heike Ziebarth
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Patent number: 8679745Abstract: 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: GrantFiled: September 30, 2005Date of Patent: March 25, 2014Assignee: Epigenomics AGInventors: Matthias Ballhause, Kurt Berlin, Dimo Dietrich, Antje Kluth Lukas, Matthias Schuster, Ute Wagner, Reinhold Wasserkort, Heike Ziebarth
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Patent number: 8586302Abstract: The present invention relates to an improved method for the bisulfite conversion of DNA. In certain time-temperature ranges the efficacy of the bisulfite conversion is clearly improved. By combination with denaturating solvents, new reaction conditions and new purification methods the efficacy can be further increased The converted DNA can subsequently be analysed by different methods. The present invention facilitates the analysis of cytosine methylation.Type: GrantFiled: February 8, 2012Date of Patent: November 19, 2013Assignee: Epigenomics AGInventors: Ina Fuhrmann, Matthias Ballhause
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Publication number: 20120258454Abstract: The present invention relates to an improved method for the bisulfite conversion of DNA. In certain time-temperature ranges the efficacy of the bisulfite conversion is clearly improved. By combination with denaturating solvents, new reaction conditions and new purification methods the efficacy can be further increased The converted DNA can subsequently be analysed by different methods. The present invention facilitates the analysis of cytosine methylation.Type: ApplicationFiled: February 8, 2012Publication date: October 11, 2012Applicant: EPIGENOMICS AGInventors: Ina Fuhrmann, Matthias Ballhause
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Patent number: 8257950Abstract: 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: GrantFiled: June 13, 2011Date of Patent: September 4, 2012Assignee: Epigenomics AGInventors: Kurt Berlin, Matthias Ballhause, Karen Cardon
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Patent number: 8129107Abstract: The present invention relates to an improved method for the bisulfite conversion of DNA. In certain time-temperature ranges the efficacy of the bisulfite conversion is clearly improved. By combination with denaturating solvents, new reaction conditions and new purification methods the efficacy can be further increased The converted DNA can subsequently be analysed by different methods. The present invention facilitates the analysis of cytosine methylation.Type: GrantFiled: March 31, 2006Date of Patent: March 6, 2012Assignee: Epigenomics AGInventors: Ina Fuhrmann, Matthias Ballhause
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Publication number: 20110250601Abstract: 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: ApplicationFiled: June 13, 2011Publication date: October 13, 2011Applicant: Epigenomics AGInventors: Kurt Berlin, Matthias Ballhause, Karen Cardon
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Patent number: 7968295Abstract: 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: GrantFiled: March 24, 2009Date of Patent: June 28, 2011Assignee: Epigenomics AGInventors: Kurt Berlin, Matthias Ballhause, Karen Cardon
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Publication number: 20110059432Abstract: 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: ApplicationFiled: April 17, 2006Publication date: March 10, 2011Applicant: EPIGENOMICS AGInventors: 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
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Publication number: 20100041024Abstract: The present invention relates to an improved method for the bisulfite conversion of DNA. In certain time-temperature ranges the efficacy of the bisulfite conversion is clearly improved. By combination with denaturating solvents, new reaction conditions and new purification methods the efficacy can be further increased The converted DNA can subsequently be analysed by different methods. The present invention facilitates the analysis of cytosine methylation.Type: ApplicationFiled: March 31, 2006Publication date: February 18, 2010Inventors: Ina Fuhrmann, Matthias Ballhause
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Publication number: 20090280494Abstract: A method is described for the analysis of cytosine methylation patterns in genomic DNA samples. In the first method step, the genomic DNA is isolated from cells or other accompanying materials and bound essentially irreversibly to a surface. Then the DNA bound to the surface is treated, preferably with a bisulfite, in such a way that cytosine is converted into a base that is different in its base pairing behavior in the DNA duplex, while 5-methylcytosine remains unchanged. Then the reagents that were used are removed in a washing step. Finally, selected segments of the immobilized DNA are amplified in a polymerase reaction and the amplified products are investigated with respect to their sequence.Type: ApplicationFiled: May 18, 2009Publication date: November 12, 2009Inventors: Kurt Berlin, Matthias Ballhause, David Gutig
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Publication number: 20090263810Abstract: 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: ApplicationFiled: March 24, 2009Publication date: October 22, 2009Inventors: Kurt Berlin, Matthias Ballhause, Karen Cardon
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Patent number: 7534570Abstract: A method is described for the analysis of cytosine methylation patterns in genomic DNA samples. In the first method step, the genomic DNA is isolated from cells or other accompanying materials and bound essentially irreversibly to a surface. Then the DNA bound to the surface is treated, preferably with a bisulfite, in such a way that cytosine is converted into a base that is different in its base pairing behavior in the DNA duplex, while 5-methylcytosine remains unchanged. Then the reagents that were used are removed in a washing step. Finally, selected segments of the immobilized DNA are amplified in a polymerase reaction and the amplified products are investigated with respect to their sequence.Type: GrantFiled: October 31, 2007Date of Patent: May 19, 2009Assignee: Epigenomics AGInventors: Kurt Berlin, Matthias Ballhause, David Gütig
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Publication number: 20080220418Abstract: 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, an 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: ApplicationFiled: September 30, 2005Publication date: September 11, 2008Inventors: Matthias Ballhause, Kurt Berlin, Dimo Dietrich, Antje Lukas, Matthias Schuster, Ute Wagner, Reinhold Wasserkort, Heike Ziebarth
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Patent number: 7407749Abstract: A method is described for the analysis of cytosine methylation patterns in genomic DNA samples. In the first method step, the genomic DNA is isolated from cells or other accompanying materials and bound essentially irreversibly to a surface. Then the DNA bound to the surface is treated, preferably with a bisulfite, in such a way that cytosine is converted into a base that is different in its base pairing behavior in the DNA duplex, while 5-methylcytosine remains unchanged. Then the reagents that were used are removed in a washing step. Finally, selected segments of the immobilized DNA are amplified in a polymerase reaction and the amplified products are investigated with respect to their sequence.Type: GrantFiled: October 25, 2002Date of Patent: August 5, 2008Assignee: Epigenomics AGInventors: Kurt Berlin, Matthias Ballhause, David Gütig
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Publication number: 20080113379Abstract: A method is described for the analysis of cytosine methylation patterns in genomic DNA samples. In the first method step, the genomic DNA is isolated from cells or other accompanying materials and bound essentially irreversibly to a surface. Then the DNA bound to the surface is treated, preferably with a bisulfite, in such a way that cytosine is converted into a base that is different in its base pairing behavior in the DNA duplex, while 5-methylcytosine remains unchanged. Then the reagents that were used are removed in a washing step. Finally, selected segments of the immobilized DNA are amplified in a polymerase reaction and the amplified products are investigated with respect to their sequence.Type: ApplicationFiled: October 31, 2007Publication date: May 15, 2008Inventors: Kurt Berlin, Matthias Ballhause, David Gutig
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Publication number: 20060134643Abstract: 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: ApplicationFiled: October 12, 2004Publication date: June 22, 2006Inventors: Kurt Berlin, Matthias Ballhause, Karen Cardon