SYSTEMIC LUPUS ERYTHEMATOSUS DIAGNOSTIC ASSAY
The present invention provides compositions and methods for aiding in the diagnosis, monitoring and prognosis of SLE in a subject and for identifying potential therapeutic agents to treat and/or ameliorate the symptoms associated with SLE. Accordingly, embodiments of the invention are directed to methods of identifying the gene expression profile of a suitable sample by screening for the presence of a differentially expressed SLE-associated gene isolated from a sample containing or suspected of containing a cell that can differentially express an SLE-associated gene.
1 - 32 . (canceled)
33 . A systemic lupus erythematosus diagnostic array comprising:
at least 10 probes that hybridize under stringent conditions to one or more polynucleotides listed Table 1A and/or Table 1B;
at least 375 probes that hybridize under stringent conditions to one or more polynucleotides listed in Table 2A and/or Table 2B;
at least 10 probes that hybridize under stringent conditions to one or more polynucleotides listed Table 3A and/or Table 3B; and
at least 2 probes that hybridize under stringent conditions to one or more polynucleotides listed Table 4, mixtures and combinations thereof.
34 . The array of claim 33 , wherein the polynucleotides are probes.
35 . The array of claim 33 , wherein the polynucleotides are amplification primers.
36 . The array of claim 33 , wherein the polynucleotides are attached to an array in a pre-determined location.
37 . A kit comprising:
an array comprising:
at least 10 probes that hybridize under stringent conditions to a polynucleotide of Table 1A and/or Table 1B;
at least 375 probes that hybridize under stringent conditions to a polynucleotide of Table 2A and/or Table 2B;
at least 10 probes that hybridize under stringent conditions to a polynucleotide of Table 3A and/or Table 3B;
at least 2 probes that hybridize under stringent conditions to a polynucleotide of Table 4, mixtures and combinations thereof; and
instructions for determining the identity of each polynucleotide and its location in the array.
38 - 41 . (canceled)
42 . A computer implemented method for determining the genotype of a sample comprising:
obtaining a plurality of sample probe intensities from a patient suspected of having SLE;
diagnosing systemic lupus erythematosus based upon the sample probe intensities; and
calculating linear correlation coefficient between the sample probe intensities and reference probe intensities; and accepting the tentative genotype as the genotype of the sample if the linear correlation coefficient is greater than a threshold value.
43 . The method of claim 42 , wherein the probes comprise:
at least 10 probes that hybridize under stringent conditions to a polynucleotide of Table 1A and/or Table 1B;
at least 375 probes that hybridize under stringent conditions to a polynucleotide of Table 2A and/or Table 2B;
at least 10 probes that hybridize under stringent conditions to a polynucleotide of Table 3A and/or Table 3B;
at least 2 probes that hybridize under stringent conditions to a polynucleotide of Table 4, mixtures and combinations thereof; and
mixtures and combinations thereof.
44 . The method of claim 42 , wherein the probes comprise one or more genes selected from:
Accession No.
Database
Gene
NM_019096
GenBank
GTPBP2
AK002064.1
GenBank
DNAPTP6
AF237762
GenBank
GPR84
NM_004776.1
GenBank
B4GALT5
AB045118.1
GenBank
FRAT2
L13386.1
GenBank
PAFAH1B1.
45 . The method of claim 42 , wherein at least one gene comprises C1 ORF 29 (Affymetrix ID 204439_at).