Genetic Brain Tumor Markers

• US 20090215055A1
• Filed: 12/13/2005
• Published: 08/27/2009
• Est. Priority Date: 12/13/2005
• Status: Abandoned Application

• Current Assignee: Erasmus University Medical Center Rotterdam
• Original Assignee: Erasmus University Medical Center Rotterdam
• Inventors: French, Peter James, Sillevis Smitt, Petrus Abraham Elisa
• Application Number:
  US12/097,385
• Publication Number:
  US 20090215055A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2600/106 Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
• CPC Class Codes: C12Q 2600/118 Prognosis of disease development
• CPC Class Codes: C12Q 2600/158 Expression markers
• CPC Class Codes: C12Q 2600/172 Haplotypes
• CPC Class Codes: G16B 20/00 ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• CPC Class Codes: G16B 20/20 Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• CPC Class Codes: G16B 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
• CPC Class Codes: G16B 25/10 Gene or protein expression profiling; Expression-ratio estimation or normalisation

Abstract

The invention relates to method of genetic analysis for the prediction of treatment sensitivity and survival prognosis of patients with brain tumors, especially oligodendroglial tumors. The invention provides a method for producing a classification scheme for oligodendroglial tumors comprising the steps of a) providing a plurality of reference samples, said reference samples comprising cell samples from a plurality of reference subjects suffering from oligodendroglial tumors; b) providing reference profiles by establishing a gene expression profile for each of said reference samples individually; c) clustering said individual reference profiles according to similarity; and d) assigning an oligodendroglial tumor class to each cluster.

Claims

1-21. -21. (canceled)

22. A method for producing a classification scheme for oligodendroglial tumors comprising the steps of:

a) providing a plurality of reference samples, said reference samples comprising cell samples from a plurality of reference subjects suffering from oligodendroglial tumors, with known responsiveness to therapy and survival or with known loss of heterozygosity of 1p or 19q;

b) providing reference profiles by establishing a gene expression profile, matched with parameters for treatment sensitivity, survival and loss of heterozygosity for each of said reference samples individually;

c) clustering said individual reference profiles according to a statistical procedure, comprising;

(i) K-means clustering,

(ii) hierarchical clustering, and

(iii) Pearson correlation coefficient analysis; and

d) assigning an oligodendroglial tumor class according to treatment sensitivity, survival or loss of heterozygosity to each cluster.

23. The method according to claim 22, wherein the clustering of said gene expression profiles is performed based on the information of differentially-expressed genes and the treatment sensitivity, survival or loss of heterozygosity of the subject.

24. The method according to claim 22, wherein the clustering of said gene expression profiles with respect to treatment response is performed based on the information of the genes of Table 3.

25. The method according to claim 22, wherein the clustering of said gene expression profiles with respect to survival is performed based on the information of the genes of Table 4.

26. The method according to claim 22, wherein the clustering of said gene expression profiles with respect to loss of heterozygosity of 1p is performed based on the information of the genes of Table 5.

27. The method according to claim 22, wherein the clustering of said gene expression profiles with respect to loss of heterozygosity of 19q is based on the information of the genes of Table 6.

28. The method according to claim 22, wherein the clustering of said gene expression profiles with respect to loss of heterozygosity of 1p and 19q is performed based on the information of the genes of Table 7.

29. A method for classifying an oligodendroglial tumor of a subject suffering from oligodendroglial tumor, comprising the steps of:

a) providing a classification scheme for oligodendroglial tumors according to the method of claim 22;

b) providing a subject profile by establishing a gene expression profile for said subject;

c) clustering the subject profile together with a plurality of reference profiles;

d) determining in said scheme the clustered position of said subject profile among the reference profiles; and

e) assigning an oligodendroglial tumor class that corresponds to said clustered position to said oligodendroglial tumor.

30. The method according to claim 29, wherein said gene expression profile with respect to treatment response comprises a plurality of expression parameters of a set of genes according to Table 3.

31. The method according to claim 29, wherein said gene expression profile with respect to survival comprises a plurality of expression parameters of a set of genes according to Table 4.

32. The method according to claim 29, wherein said gene expression profile with respect to 1p loss of heterozygosity comprises a plurality of expression parameters of a set of genes according to Table 5.

33. The method according to claim 29, wherein said gene expression profile with respect to 19q heterozygosity comprises a plurality of expression parameters of a set of genes according to Table 6.

34. The method according to claim 29, wherein said gene expression profile with respect to 1p and 19q loss of heterozygosity comprises a plurality of expression parameters of a set of genes according to Table 7.

35. A method of determining the prognosis for a subject suffering from an oligodendroglial tumor, said method comprising the steps of:

a) providing a classification scheme for oligodendroglial tumors by the method according to claim 22;

b) determining a prognosis for each olidendroglial tumor class in said classification scheme based on clinical records for the subjects comprised in said class;

c) establishing an oligodendroglial class of a subject suffering from an oligodendroglial tumor by classifying the oligodendroglial tumor in said subject according to the method of claim 29; and

d) assigning to said subject the prognosis corresponding to the established oligodendroglial tumor class of said subject.

36. A method of determining the prognosis for a subject suffering from an oligodendroglial tumor, said method comprising the steps of:

a) isolating an RNA from tumor cells of said subject;

b) preparing an antisense, biotinylated RNA to said RNA of step a);

c) hybridizing said antisense to said RNA;

d) normalizing a plurality of measured values for a gene set of Table 3;

e) clustering the obtained data together with the reference data, obtained from a reference set of patient with known prognosis; and

f) determining the prognosis on basis of the cluster to which the data of the subject are clustering.

37. An oligonucleotide microarray of maximal 500 probesets, comprising at least 1 oligonucleotide probe capable of hybridizing under stringent conditions to a gene of an oligodendroglial tumor-associated genes selected from Tables 3-7.

38. The oligonucleotide microarray of maximal 500 probesets of claim 37, wherein the probesets comprise at least 2 oligonucleotide probes.

39. The oligonucleotide microarray of maximal 500 probesets of claim 37, wherein the probesets comprise at least 25 oligonucleotide probes.

40. The oligonucleotide microarray of maximal 500 probesets of claim 37, wherein the probesets comprise at least 100 oligonucleotide probes.

41. A kit comprising an oligonucleotide microarray according to claim 37 and means for comparing a gene expression profile determined by using said microarray with a database of oligodendroglial tumor reference expression profiles.