Methods and Compositions For Detecting Autoimmune Disorders

a technology for detecting autoimmune disorders and compositions, applied in the field of molecular determination of autoimmune diseases, can solve the problem that the definition of the interferon response gene expression profile is still not compl

Inactive Publication Date: 2010-10-21
GENENTECH INC
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  • Abstract
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Problems solved by technology

The most comprehensive of these studies have been performed with oligonucleotide microarrays, but definitions of interferon response gene expression profiles are still not complete, at least in part because until recently microarrays have not contained a very complete set of reporters for the genes of the human genome, and also because a variety of technical difficulties prevented identification of broadly applicable yet simple sets of marker genes that reliably correlate with pathological conditions of interest.
One of the most difficult challenges in clinical management of autoimmune diseases is the accurate and early identification of the diseases in a patient.

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  • Methods and Compositions For Detecting Autoimmune Disorders
  • Methods and Compositions For Detecting Autoimmune Disorders
  • Methods and Compositions For Detecting Autoimmune Disorders

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example 1

[0154]Materials and Methods

[0155]Expression of IFN-alpha responsive genes (IRG's) was analyzed in data from blood-peripheral blood mononuclear cells (PBMC) from SLE patients (with active or inactive disease) and normal donors from the University Of Minnesota (Minneapolis, Minn.).

[0156]Data was produced as follows: 92 blood samples were collected on different dates from 18 patients with active SLE, 19 blood samples were collected on different dates from 5 patients with inactive SLE, and 4 blood samples were collected from 4 healthy donors. PBMC was isolated from whole blood by standard Ficoll gradient centrifugation. RNA was prepared from PBMC samples using RNA Isolation Kit from Qiagen (Valencia, Calif.) and hybridized to WHG oligonucleotide microarray chips from Agilent (Palo Alto, Calif.). Raw data was processed by standard Agilent Feature Extraction to yield Agilent log ratio data. Normal expression of genes in response to IFN-alpha was examined by isolating PBMC from healthy don...

example 2

[0177]Materials and Methods

[0178]Expression of IFN-alpha responsive genes (IRG's) was analyzed in data from white blood cells (WBC) from SLE patients and healthy donors obtained by Gene Logic Inc. (Gaithersburg, Md.).

[0179]Data was produced as follows: 72 blood samples were collected from patients with active SLE, 46 blood samples were collected from healthy donors. RNA was prepared from WBC samples using RNA Isolation Kit from Qiagen (Valencia, Calif.) and hybridized to HGU133 oligonucleotide microarray chips from Affymetrix, Inc. (Santa Clara, Calif.). Raw data was processed by Affymetrix MAS5.0 feature extraction to yield Signal data.

[0180]Microarray data was clustered hierarchically in two dimensions (samples and probes) using the xcluster software program (pearson on log2 signal) on probes with both mean signal in the top 70% ile and coefficient of variability in the top 70% ile. Cluster data was viewed with the Java Treeview software program. Numerical analysis was performed w...

example 3

[0187]To further assess the extent to which gene combinations comprising one or more of the genes that have been identified herein correlate with an interferon response gene signature, the Pearson correlation of all possible three-gene combinations of 24 selected genes (Table 4A) were assessed. Data are shown in Table 4B.

[0188]Materials and Methods

[0189]PAXgene tubes from Qiagen / PreAnalytix (Valencia, Calif.) were used to collect whole blood from 35 SLE samples and 10 healthy donors. RNA was prepared by using a blood RNA isolation kit from Qiagen / PreAnalytix (Valencia, Calif.) and the expression of twenty-four interferon-alpha (IFN α) responsive genes was assayed using routine methods, e.g., by using primers / probes with TaqMan reagents from ABI (Foster City, Calif.). Relative abundance was determined by normalizing expression to RPL19. One “healthy” donor sample was removed from the analysis due to abnormally high expression of IFN responsive genes probably due to a recent viral inf...

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Abstract

The invention provides methods and compositions useful for detecting autoimmune disorders.

Description

RELATED APPLICATION[0001]This application is a continuation of U.S. patent application Ser. No. 11 / 739,606 filed on Apr. 24, 2007, claiming priority under 35 USC 119(e) to U.S. Provisional Application Ser. No. 60 / 794,393 filed on Apr. 24, 2006, all of which are hereby incorporated herein in their entirety.TECHNICAL FIELD[0002]The present invention relates generally to the fields of molecular determination of autoimmune diseases. More specifically, the invention concerns methods and compositions based on unique molecular signatures associated with various aspects of autoimmune disorders.BACKGROUND[0003]A number of autoimmune disorders are now believed to be characterized by the production of autoantibodies against a variety of self antigens. For example, systemic lupus erythematous (SLE) is an autoimmune disease in which autoantibodies cause organ damage by binding to host cells and tissues and by forming immune complexes that deposit in vascular tissues and activate immune cells. Sj...

Claims

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Application Information

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Patent Type & Authority Applications(United States)
IPC IPC(8): C12Q1/68C07H21/04C40B40/06C40B40/08G16B20/00
CPCC12Q1/6883C12Q2600/112G06F19/18C12Q2600/158G16B20/00A61P37/02Y02A90/10C12Q1/6837C12Q2600/106
Inventor ABBAS, ALEXANDERMODREK, BARMAKTOWNSEND, MICHAEL J.
Owner GENENTECH INC
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