COLLECTION OF BIOMARKERS FOR DIAGNOSIS AND MONITORING OF ALZHEIMER'S DISEASE IN BODY FLUIDS

• US 20100124756A1
• Filed: 10/09/2009
• Published: 05/20/2010
• Est. Priority Date: 10/10/2008
• Status: Abandoned Application

• Current Assignee: Rules-Based Medicine, Inc., Board of Trustees of the Leland Stanford Junior University (Stanford Management Co.), U.S. Government Represented By The Department Of Veterans Affairs
• Original Assignee: Rules-Based Medicine, Inc.
• Inventors: Ray, Sandip, Wyss-Coray, Anton
• Application Number:
  US12/577,082
• Publication Number:
  US 20100124756A1
• Time in Patent Office: Days
• US Class Current: 435/7.940
• CPC Class Codes: G01N 2800/2821 Alzheimer
• CPC Class Codes: G01N 33/6896 Neurological disorders, e.g. Alzheimer's disease

Abstract

The inventors have discovered sets of proteinaceous biomarkers (“AD biomarkers”) which can be measured in peripheral biological fluid samples to aid in the diagnosis of neurodegenerative disorders, particularly Alzheimer'"'"'s disease. The invention further provides methods of identifying candidate agents for the treatment of Alzheimer'"'"'s disease by testing prospective agents for activity in modulating the levels of the AD biomarkers.

Claims

1. A method of aiding diagnosis of Alzheimer'"'"'s disease (“

AD”

), comprising comparing a measured level of at least sixteen AD diagnosis biomarkers in a biological fluid sample from an individual seeking a diagnosis for AD to a reference level for each biomarker, wherein the at least sixteen AD diagnosis biomarkers comprise;

MCSF (Macrophage Colony Stimulating Factor), RANTES, GCSF (granulocyte-colony stimulating factor), PARC (pulmonary and activation-regulated chemokine), ANG-2 (angiotensin-2), IL-11 (interleukin-11), EGF (epidermal growth factor), MCP-3 (monocyte chemoattractant protein-3), IL-3 (interleukin-3), MIP-1delta (macrophage inflammatory protein-1 delta), ICAM-1 (intercellular adhesion molecule

     1), PDGF-BB (platelet-derived growth factor BB), IL-8 (interleukin

     8), GDNF (glial derived neurotrophic factor), IL-1a (interleukin-1alpha), and TNF-a (tumor necrosis factor alpha).

2. The method of claim 1, wherein said biological fluid sample is a peripheral biological fluid sample.

3. The method of claim 2, wherein said peripheral biological fluid sample is serum or plasma.

4. The method of claim 1, further comprising obtaining a measured level of said AD biomarker in said biological fluid sample.

5. The method of claim 1, wherein the individual is a human.

6. The method of claim 1, wherein the measured levels are normalized.

7. The method of claim 1, wherein the reference levels are obtained from measured values of the at least sixteen biomarkers from samples in the blood of human individuals without AD.

8. The method of claim 1, wherein the reference levels are obtained from measured values of the at least sixteen biomarkers from samples in the blood of human individuals with AD.

9. The method of claim 7, wherein the reference levels are normalized.

10. The method of claim 1, wherein the method comprises comparing the measured level of the at least sixteen AD diagnosis biomarkers to two reference levels for each biomarker.

11. The method of claim 10, wherein the two reference levels for each biomarker comprise:

(a) a reference level obtained from measured values of the at least sixteen biomarkers from samples in the blood of human individuals without AD; and

(b) a reference level obtained from measured values of the at least sixteen biomarkers from samples in the blood of human individuals with AD.

12. The method of claim 7, wherein the group of individuals without AD is a control population selected from an age-matched population, a degenerative control population, a non-AD neurodegenerative control population, a healthy age-matched control population, or a mixed population thereof.

13. The method of claim 1, wherein comparing comprises a method selected from the group consisting of:

Significance Analysis of Microarrays, Tree Harvesting, CART, MARS, Self Organizing Maps, Frequent Item Set, Bayesian networks, Prediction Analysis of Microarray (PAM), SMO, Simple Logistic, Logistic, Multilayer Perceptron, Bayes Net, Naï

ve Bayes, Naï

ve Bayes Simple, Naï

ve Bayes Up, IB1, Ibk, Kstar, LWL, AdaBoost, ClassViaRegression, Decorate, Multiclass Classifier, Random Committee, j48, LMT, NBTree, Part, Random Forest, and Ordinal Classifier.

14. The method of claim 1, wherein comparing comprises a method comprising predication analysis of microarray (PAM).

15. The method of claim 1, further comprising:

formulating a decision tree; and

using the decision tree for classification of the sample from the individual seeking AD diagnosis, wherein the classification aids the diagnosis of AD.

16. The method of claim 15, wherein using the decision tree for classification of the sample is implemented by a computer.

17. The method of claim 1, whereby the diagnosis of AD is aided by determining a difference between the measured levels of the at least sixteen AD diagnosis biomarkers to the reference levels of the at least sixteen biomarkers wherein the difference meets or exceeds a statistically significant difference between normalized measured values of the at least sixteen AD diagnosis biomarkers in the blood samples from individuals without AD and individuals with AD, wherein the statistically significant difference indicates a diagnosis of AD,

wherein the measured levels are normalized, and

wherein the references levels are normalized.

18. The method of claim 17, further comprising:

formulating a decision tree comprising statistically significant differences in normalized measured values of AD diagnosis biomarkers wherein the statistically significant differences are determined from normalized measured values of the plurality of AD diagnosis biomarkers in the blood samples in the group of individuals with AD and the group of individuals without AD; and

using the decision tree for classification of the blood sample from the individual seeking AD diagnosis, wherein the classification aids the diagnosis of AD.

19. The method of claim 1, wherein the method is useful for early detection of conversion of MCI to AD.

20. The method of claim 1, wherein the at least sixteen AD diagnosis biomarkers further comprise:

TRAIL R4, and IGFBP-6.

21. The method of claim 1, further comprising the step of obtaining a value for each comparison of the measured level to the reference level.

22. A computer readable format comprising the values obtained by the method of claim 21.

24. A kit comprising:

at least one reagent specific for each of at least sixteen AD diagnosis biomarkers, said at least sixteen AD diagnosis biomarkers comprising;

MCSF (Macrophage Colony Stimulating Factor), RANTES, GCSF (granulocyte-colony stimulating factor), PARC (pulmonary and activation-regulated chemokine), ANG-2 (angiotensin-2), IL-11 (interleukin-11), EGF (epidermal growth factor), MCP-3 (monocyte chemoattractant protein-3), IL-3 (interleukin-3), MIP-1delta (macrophage inflammatory protein-1 delta), ICAM-1 (intercellular adhesion molecule

     1), PDGF-BB (platelet-derived growth factor BB), IL-8 (interleukin

     8), GDNF (glial derived neurotrophic factor), IL-1a (interleukin-1alpha), and TNF-a (tumor necrosis factor alpha; and

instructions for carrying out the method of claim 1.

23. A method for monitoring progression of Alzheimer'"'"'s disease (AD) in an AD patient, comprising:

comparing a measured level of at least sixteen AD diagnosis biomarkers in a biological fluid sample from an individual seeking a diagnosis for AD to a reference level for each biomarker, wherein the at least sixteen AD diagnosis biomarkers comprise;

MCSF (Macrophage Colony Stimulating Factor), RANTES, GCSF (granulocyte-colony stimulating factor), PARC (pulmonary and activation-regulated chemokine), ANG-2 (angiotensin-2), IL-11 (interleukin-11), EGF (epidermal growth factor), MCP-3 (monocyte chemoattractant protein-3), IL-3 (interleukin-3), MIP-1delta (macrophage inflammatory protein-1 delta), ICAM-1 (intercellular adhesion molecule

     1), PDGF-BB (platelet-derived growth factor BB), IL-8 (interleukin

     8), GDNF (glial derived neurotrophic factor), IL-1a (interleukin-1alpha), and TNF-a (tumor necrosis factor alpha).

25. A surface comprising attached thereto, at least one reagent specific for each of at least sixteen AD diagnosis biomarkers, said at least sixteen AD diagnosis biomarkers comprising:

MCSF (Macrophage Colony Stimulating Factor), RANTES, GCSF (granulocyte-colony stimulating factor), PARC (pulmonary and activation-regulated chemokine), ANG-2 (angiotensin-2), IL-11 (interleukin-11), EGF (epidermal growth factor), MCP-3 (monocyte chemoattractant protein-3), IL-3 (interleukin-3), MIP-1delta (macrophage inflammatory protein-1 delta), ICAM-1 (intercellular adhesion molecule

     1), PDGF-BB (platelet-derived growth factor BB), IL-8 (interleukin

     8), GDNF (glial derived neurotrophic factor), IL-1a (interleukin-1alpha), and TNF-a (tumor necrosis factor alpha.