GENEMAP OF THE HUMAN GENES ASSOCIATED WITH LONGEVITY

• US 20090305900A1
• Filed: 06/19/2006
• Published: 12/10/2009
• Est. Priority Date: 06/17/2005
• Status: Abandoned Application

• Current Assignee: Abdelmajid Belouchi, Bruno Paquin, Johanne Cousineau, John Verner Raelson, Jonathan Segal, Nouzha Paquin, Pascal Croteau, Paul Van Eerdewegh, Quynh Nguyen-Huu, Randall David Little, Rene Allard, Tim Keith, Walter Edward Bradley
• Original Assignee: Abdelmajid Belouchi, Bruno Paquin, Johanne Cousineau, John Verner Raelson, Jonathan Segal, Nouzha Paquin, Pascal Croteau, Paul Van Eerdewegh, Quynh Nguyen-Huu, Randall David Little, Rene Allard, Tim Keith, Walter Edward Bradley
• Inventors: Paquin, Bruno, Nguyen-Huu, Quynh, Paquin, Nouzha, Van Eerdewegh, Paul, Keith, Tim, Belouchi, Abdelmajid, Cousineau, Johanne, Bradley, Walter Edward, Raelson, John Verner, Allard, Rene, Croteau, Pascal, Segal, Jonathan, Little, Randall David
• Application Number:
  US11/917,896
• Publication Number:
  US 20090305900A1
• Time in Patent Office: Days
• US Class Current: 506/7
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: C12Q 2600/158 Expression markers
• CPC Class Codes: C12Q 2600/172 Haplotypes

Abstract

The present invention relates to the selection of a set of SNP markers for use in genome wide association studies based on linkage disequilibrium mapping. In particular, the invention relates to the fields of pharmacogenomics, diagnostics, patient therapy and the use of genetic haplotype information to predict an individual'"'"'s longevity, their protection against age-related diseases and/or their response to a particular drug or drugs.

Claims

1. A method of constructing a longevity trait GeneMap in a human population, comprising screening for the expression level of or presence or absence of at least one allele of (i) at least one gene from Tables 4, 5 and 6 or (ii) at least one single nucleotide polymorphism (SNP) from Tables 2, 3 and 7 in at least one sample.

2. A method of claim 1, wherein said population is a general population.

3. A method of claim 1, wherein said population is a founder population.

4. A method of claim 3, wherein said founder population is the population of Quebec.

5-21. -21. (canceled)

22. A set of genetic markers comprising at least two SNPs of Tables 2, 3 and 7.

23. A set of nucleic acid probes that specifically detect said SNPs of claim 22.

24. A solid support or collection of solid supports comprising the nucleic acid probes of claim 23.

25. A solid support of claim 24, wherein the support is selected from the group consisting of at least one microarray and a set of beads.

26. A method for predicting the efficacy of a drug for treating an age-associated disorder in a human patient, comprising:

a) obtaining a sample of cells from the patient;

b) obtaining (i) a gene expression profile or (ii) a set of genotype from the sample in the absence and presence of in vitro modulation of the cells with specific mediators;

the gene expression profile comprising one or more genes from Tables 4, 5 and 6;

the set of genotypes comprising one or more polymorphic loci from Tables 2, 3 and 7 and c) comparing the gene expression profile or the set of genotypes of the sample with a reference gene expression profile or a reference set of genotypes associated with efficacy of the drug, wherein similarity between the sample expression profile and the reference expression profile or between the set of genotypes and the reference set of genotypes predicts the efficacy of the drug for treating age-associated disorder in the patient.

27. The method of claim 26, further comprising exposing the sample to the drug for treating an age-associated disorder prior to obtaining the gene expression profile of the sample.

28. The method of claim 26, wherein the sample of cells is derived from a tissue selected from the group consisting of:

any parts of the body such as the scalp, blood, dermis, epidermis and other skin cells, cutaneous surfaces, intertrigious areas, genitalia, vessels and endothelium.

29. The method of claim 28, wherein the cells are selected from the group consisting of:

red blood cells, muscle cells, heart cells, nerve cells, insulin-producing cells, pancreatic cells, brain cells, germ cells, keratinocytes, monocytes, neutrophils, Langerhans cells, CD4+ and CD8+ T cells, B and T lymphocytes, leukocytes, hormonal cells, bone marrow cells, skin cells, buccal cells, spinal cord cells, bone cells, adipose cells, cartilage cells, dendritic cells, intestinal cells, hepatic cells, mucous cells, olfactory cells, retinal cells, somatic cells and arterial cells.

30. The method of claim 26, wherein the sample is obtained via biopsy.

31. The method of claim 26, wherein the gene expression profile comprises expression values for at least two of the genes listed in Tables 4, 5 and 6.

32. The method of claim 31, wherein the gene expression profile of the sample is obtained by detecting the protein products of said genes.

33. The method of claim 26, wherein the gene expression profile of the sample is obtained using a hybridization assay to oligonucleotides contained in a microarray.

34. The method of claim 26, wherein the oligonucleotides comprises nucleic acid molecules at least 95% identical to SEQ ID from Tables 2, 3, 4, 5 or 7.

35. The method of claim 26, wherein the reference expression profile is that of cells derived from patients that have the longevity trait.

36. The method of claim 26, wherein the drug is selected from the group consisting of symptom relievers and drugs for an age-associated condition.

132. The method of claim 26, wherein the set of genotypes from the sample comprises genotypes of at least two of the polymorphic loci listed in Tables 2, 3 and 7.

133. The method of claim 26, wherein the set of genotypes from the sample is obtained by hybridization to allele-specific oligonucleotides complementary to the polymorphic loci from Tables 2, 3 and 7, wherein said allele-specific oligonucleotides are contained on a microarray.

134. The method of claim 133, wherein the oligonucleotides comprise nucleic acid molecules at least 95% identical to SEQ ID from Tables 1, 2 or 3.

135. The method of claim 26, wherein the set of genotypes from the sample is obtained by sequencing said polymorphic loci in said sample.

136. The method of claim 26, wherein the drug is selected from the group consisting of symptom relievers and drugs for an age-associated condition.

37. A method for inducing a longevity-like state in a resident tissue or cell, comprising contacting the tissue or cell with at least one gene from Tables 4, 5 and 6 that induces a longevity-like state.

38. The method of claim 37, wherein the resident tissue cell is selected from the group consisting of red blood cells, muscle cells, heart cells, nerve cells, insulin-producing cells, pancreatic cells, brain cells, germ cells, keratinocytes, monocytes, neutrophils, Langerhans cells, CD4+ and CD8+ T cells, B and T lymphocytes, leukocytes, hormonal cells, bone marrow cells, skin cells, buccal cells, spinal cord cells, bone cells, adipose cells, cartilage cells, dendritic cells, intestinal cells, hepatic cells, mucous cells, olfactory cells, retinal cells, somatic cells and arterial cells.

39. A method for screening drug candidates for treating age-associated disorders, comprising:

a) contacting a resident cell induced by the method of claim 37 with a drug candidate for treating age-associated disorders; and

b) assaying for a longevity-like state, such that an absence of the longevity-like state is indicative of the drug candidate being effective in treating age-associate disorders.

40-43. -43. (canceled)

44. A drug screening assay comprising:

a) administering a test compound to an animal having an age-associated disorder, or related phenotype, or a cell composition isolated therefrom; and

b) comparing the level of gene expression of at least one gene from Tables 4, 5 and 6 in the presence of the test compound with one or both of the level of said gene expression in the absence of the test compound or in normal cells;

wherein test compounds which cause the level of expression of one or more genes from Tables 4, 5 and 6 to approach normal are candidates for drugs to treat age-associated disorders.

45-46. -46. (canceled)

47. A method for identifying a gene that regulates drug response in an age-associated disorder, comprising:

a) obtaining a gene expression profile for at least one gene from Tables 4, 5 and 6 in a resident tissue cell induced for a longevity-like state in the presence of the candidate drug; and

b) comparing the expression profile of said gene to a reference expression profile for said gene in a cell induced for the longevity-like state in the absence of the candidate drug, wherein genes whose expression relative to the reference expression profile is altered by the drug may identifies the gene as a gene that regulates drug response in the longevity trait.

48. An expression profile indicative of the presence of longevity trait in a patient, comprising the level of expression of at least one gene of Tables 4, 5 and 6.

49. A microarray comprising probes that hybridize to one or more genes of Tables 4, 5 and 6.

50-51. -51. (canceled)

52. A method of diagnosing susceptibility to an age-associated disorder in an individual, comprising screening for an at-risk haplotype of at least one gene from Tables 4, 5 and 6, or comprising at least one SNP from Tables 2, 3 and 7, that is more frequently present in an individual susceptible to an age-associated disorder, compared to the frequency of its presence in a control individual, wherein the presence of the at-risk haplotype is indicative of a susceptibility to an age-associated disorder.

53. The method of claim 52, wherein the at-risk haplotype is characterized by the presence of at least one single nucleotide polymorphism from Tables 2, 3 and 7.

54. The method of claim 52, wherein screening for the presence of an at-risk haplotype in at least one gene from Tables 4, 5 and 6, or comprising at least one SNP from Tables 2, 3 and 7, comprises enzymatic amplification of nucleic acid from said individual or amplification using universal oligos on elongation/ligation products.

55. The method of claim 54, wherein the nucleic acid is DNA.

56. The method of claim 55, wherein the DNA is human DNA.

57. The method of claim 52, wherein screening for the presence of an at-risk haplotype in at least one gene from Tables 4, 5 and 6 or comprising at least one SNP from Tables 2, 3 and 7 comprises:

a) obtaining material containing nucleic acid from the individual;

(b) amplifying said nucleic acid as for claim 54; and

c) determining the presence or absence of an at-risk haplotype in said amplified nucleic acid.

58. The method of claim 57, wherein determining the presence of an at-risk haplotype is performed by electrophoretic analysis, restriction length polymorphism analysis, sequence analysis or hybridization analysis.

59-95. -95. (canceled)

96. A method for determining the phenotype of a cell comprising detecting the differential expression, relative to a normal cell, of at least one gene from Tables 4, 5 and 6.

97. The method of claim 96, wherein said difference in the level of expression of said gene, is of at least a factor of about two.

98. The method of claim 96, including the further step of cloning said genes which are up- or down-regulated.

99. The method of claim 96, including the further step of generating nucleic acid probes for detecting the level of expression of said genes which are up- or down-regulated.

100. A kit for assessing a patient'"'"'s risk of having or developing an age-associated disorder, comprising:

a) detection means for detecting the differential expression, relative to a normal cell, of at least one gene shown in Tables 4, 5 and 6 or the gene product thereof; and

b) instructions for correlating the differential expression of said gene or gene product with a patient'"'"'s risk of having or developing an age-associated disorder.

101. The kit of claim 100, wherein the detection means includes nucleic acid probes for detecting the level of mRNA of said genes.

102. A kit for assessing a patient'"'"'s risk of having or developing an age-associated disorder, comprising:

(a) at least one means for amplifying or detecting a sequence of at least one gene in Tables 4, 5 and 6, or at least one sequence comprising a SNP in Tables 2, 3 and 7, wherein the detection means includes nucleic acid probes or primers for detecting the presence or absence of an associated allele, a particular allele of a polymorphic locus, or the like or changes to at least one sequence of Tables 4, 5 and 6 or Tables 2, 3 and 7, and (b) instructions for correlating the presence or absence of at least one sequence of Tables 4, 5 and 6 or Tables 2, 3 and 7 with a patient'"'"'s risk of having age-associated disorder.

103. The kit of claim 102, wherein the detection means includes an immunoassay for detecting the level of at least one gene product from Tables 4, 5 and 6.

104. A method of assessing a patient'"'"'s risk of having or developing an age-associated disorder, comprising:

a) determining the level of expression of at least one gene from Tables 4, 5 and 6 or gene products thereof, and comparing the level of expression to a normal cell; and

b) assessing a patient'"'"'s risk of having or developing an age-associated disorder, if any, by determining the correlation between the differential expression of said genes or gene products with known changes in expression of said genes measured in at least one parent suffering from an age-associated disorder.

105. A nucleic acid array comprising a solid support comprising nucleic acid probes which selectively hybridize to at least 5 different genes from Tables 4, 5 and 6 or at least 5 different SNPs of Tables 2, 3 and 7.

106. The array of claim 105, wherein the solid support is selected from the group consisting of paper, membranes, filters, chips, pins, and glass.

107. A method of diagnosing the longevity trait in a patient, comprising detecting a nucleic acid molecule encoding at least one protein from Tables 4, 5 and 6 in a fluid or tissue sample from the patient.

108. A method of claim 107, wherein the detecting comprises detecting at least one associated allele, particular allele of a polymorphic locus, or the like in the nucleic acid molecule encoding said protein.

109. A method of claim 107, wherein said method comprises hybridizing a probe to said patient'"'"'s sample of DNA or RNA under stringent conditions which allow hybridization of said probe to nucleic acid comprising said associated allele, a particular allele of a polymorphic locus, or the like, wherein the presence of a hybridization signal indicates the presence of said associated allele, particular allele of a polymorphic locus, or the like, in at least one gene from Tables 4, 5 and 6.

110. A method of claim 109, wherein the patient'"'"'s DNA or RNA has been amplified and said amplified DNA or RNA is hybridized.

111. A method of claim 109, wherein said method comprises using a single-stranded conformation polymorphism technique to assay for said associated allele, particular allele of a polymorphic locus, or the like.

113. A method of claim 109, wherein said patient'"'"'s sample of DNA has been amplified or cloned.

114. A method of claim 109, wherein said method comprises sequencing at least one gene from Tables 4, 5 and 6 in a sample of RNA or DNA from a patient.

115. A method of claim 109, wherein said method comprises determining the sequence of at least one gene from Tables 4, 5 and 6 by preparing cDNA from RNA taken from said patient and sequencing said cDNA to determine the presence or absence of an associated allele, a particular allele of a polymorphic locus, or the like.

116. A method of claim 109, wherein said method comprises performing an RNAse assay.

117. A method of claim 109, wherein said probe is attached to a microarray or a bead.

118. A method of claim 109, wherein said probes are oligonucleotides.

119. A method of claim 109, wherein said sample is selected from the group consisting of blood, normal tissue and tumor tissue.

120. A method of claim 109, wherein the associated allele, particular allele of a polymorphic locus, or the like is selected from the group consisting of at least one of the SNPs from Tables 2, 3 and 7, alone or in combination.

112. (canceled)

121-123. -123. (canceled)

124. A method for diagnosing or prognosticating longevity comprising comparing the level of expression or activity of a polypeptide encoded by a gene of Tables 4, 5 and 6 in a test sample from a patient with the level of expression or activity of the same polypeptide in a control sample wherein a difference in the level of expression or activity between the test sample and control sample is indicative of the longevity trait.

125-131. -131. (canceled)

137-145. -145. (canceled)

146. A kit for assessing a patient'"'"'s risk of having or developing an age-associated disorder, comprising:

a) detection means for detecting the genotype of at least one polymorphic locus shown in Tables 2, 3 and 7; and

b) instructions for correlating the genotype of said at least one polymorphic locus with a patient'"'"'s risk of having or developing an age-associated disorder.

147. The kit of claim 146, wherein the detection means includes nucleic acid probes for detecting the genotype of said at least one polymorphic locus.

148. A method of assessing a patient'"'"'s risk of having or developing an age-associated disorder, comprising:

a) selecting at least one polymorphic locus from Tables 2, 3 and 7;

b) determining a genotype for said at least one polymorphic locus from Table 1 in a patient;

c) comparing said genotype of b) to a genotype for said at least one polymorphic locus from Tables 2, 3 and 7 that is associated with the age-associated disorder; and

d) assessing the patient'"'"'s risk of having or developing the age-associated disorder, wherein said patient has a higher risk of having or developing the age-associated disorder if the genotype for said at least one polymorphic locus from Tables 2, 3 and 7 in said patient is the same as said genotype for said at least one polymorphic locus from Tables 2, 3 and 7 that is associated with the age-associated disorder.