Patent DE-20121978-U1 (DE)
Title: Novel chemically modified genomic DNA sequences, useful in the characterization, classification, differentiation, grading, staging, treatment and/or diagnosis of astrocytomas or predisposition to astrocytomas
IPC: C07K14/47
Filed: 2001-07-02
Abstract: A nucleic acid (I) comprising a sequence of at least 18 bases in length of a segment of chemically pretreated genomic DNA which has any one of the sequences of (S1)-(S120) or its complement, is new. Sequence listing of (S1)-(S120) not provided in the specification. Independent claims are also included for the following: (1) an oligomer (II), in particular an oligonucleotide or peptide nucleic acid (PNA)-oligomer comprising at least one base sequence having a length of at least 9 nucleotides which hybridizes to or is identical to (I); (2) a set of oligomers (III) comprising at least two (II); (3) a set of at least two oligonucleotides used as primer oligonucleotides for amplification of DNA (S1)-(S120) and/or chemically pretreated DNA of gene sequences or complementary to it; (4) use of the set of oligomer probes of at least 10 oligomers to detect the cytosine methylation state and/or single nucleotide polymorphisms (SNPs) in a chemically pretreated genomic DNA; (5) manufacturing (M1) an arrangement of different oligomers (array) fixed to a carrier material for analyzing diseases associated with the methylation state of the CpG dinucleotides of any one of (S1)-(S120) or sequences complementary to it, where at least one (II) is coupled to a solid phase; (6) an arrangement (IV) of different oligomers (array) obtained according to (M1); (7) a DNA- and/or peptide nucleic acid (PNA)-array (V) for analyzing diseases associated with the methylation state of genes, comprising at least one nucleic acid as described above; (8) a kit (VI) comprising a bisulfite (=disulfite, hydrogen sulfite) as well as (II); and (9) (III) for determining genetic and/or epigenetic parameters, classification, differentiation, grading, staging, treatment and/or diagnosis of astrocytomas, or the predisposition to astrocytomas by analyzing cytosine methylations, involves obtaining a biological sample containing genomic DNA e.g., cells or cellular components which contain DNA, sources of DNA comprising, e.g., cell lines, histological slides, biopsies, cerebrospinal fluid, lymphatic fluid, tissue embedded in paraffin; brain or lymphatic tissue and all possible combinations; extracting the genomic DNA; converting cytosine bases which are unmethylated at the 5-position, in the genomic DNA sample, to uracil or another base which is dissimilar to cytosine in terms of hybridization behavior, by chemical treatment; and amplifying chemically pretreated genomic DNA fragments using (III) (preferably comprising two (II) of which at least one oligonucleotide is bound to a solid phase) and a polymerase, where the amplificates carry a detectable label. The method further involves identifying methylation status of one or more cytosine positions, and analyzing methylation status of the cytosine positions by reference to one or more data sets. ACTIVITY : Cytostatic. No supporting data is given. MECHANISM OF ACTION : Gene therapy. No supporting data is given.