Genetic markers associated with age-related macular degeneration, methods of detection and uses thereof

Abstract

Disclosed is a method for identifying an individual who has an altered risk for developing age related macular degeneration comprising detecting a single nucleotide polymorphism (SNP)

1 - 29 . (canceled) 
     
     
         30 . A method for assessing the probability of a therapeutic; or toxic response to a chemical, protein, nucleic acid-based therapeutic or other biological, naturally or synthetic entity in a human subject who has or who may have age-related macular degeneration or any pathological process substantially similar, the method comprising the steps of:
 i) obtaining a biological sample from a human subject;   ii) analyzing the sample to determine whether the subject carries one or more of: a) C or G at rs2230199 of the complement 3 (C3) gene, or b) the amino acid arginine or glycine at position 102 of the C3 protein.   
     
     
         31 . A method according to  claim 30  wherein the biological sample is analyzed by a method comprising assaying DNA in said sample for the presence of at least one allele of the complement component 3 (C3) gene comprising a G nucleotide at the single nucleotide polymorphism (SNP) rs2230199 at the position corresponding to position 366 of SEQ ID NO:1,
 wherein the presence of at least one allele of the C3 gene comprising a G 
 nucleotide at the single nucleotide polymorphism (SNP) rs2230199 at the position 
 corresponding to position 366 of SEQ ID NO:1 is indicative of an increased probability of a therapeutic or toxic response to a chemical, protein, nucleic acid-based therapeutic or other biological, naturally or synthetic entity in the human subject. 
 
     
     
         32 . A method of  claim 31  wherein said assaying comprises;
 amplifying the DNA in the presence of a pair of primers 
 wherein a first of the primers comprises at least 10 consecutive nucleotides selected from the sequence identified as SEQ ID NO 1 and located upstream of the base located at position 366 of the sequence and a second primer comprising at least 10 consecutive nucleotides selected from within the same sequence and located downstream of the base located at position 366; and determining the identity of the base in the amplified genetic material that corresponds to position 366. 
 
     
     
         33 . A method according to  claim 32  wherein the amplified genetic material is between about 16 and about 2000 nucleotides in length, 
     
     
         34 . A method according to  claim 31  wherein said assaying comprises;
 contacting the biological sample with a reagent which specifically hybridizes under stringent hybridization conditions to an allele of the complement component 3 (C3) gene comprising a G nucleotide at the single nucleotide polymorphism (SNP) rs2230199 at the position corresponding to position 366 of SEQ ID NO:1, or a reagent which specifically hybridizes under stringent hybridization conditions to an allele of the complement component 3 (C3) gene comprising a C nucleotide at the single nucleotide polymorphism (SNP) rs2230199 at the position corresponding to position 366 of SEQ ID NO:1, and 
 detecting the formation of a hybridized duplex. 
 
     
     
         35 . A method according to  claim 34  in which detection is carried out by a process which may be selected from the group consisting of: allele-specific probe hybridization, allele-specific primer extension, allele-specific amplification, sequencing, 5′ nuclease digestion, molecular beacon assay, oligonucleotide ligation assay, size analysis, and single-stranded conformation polymorphism. 
     
     
         36 . A method according to  claim 34  wherein the reagent is a polynucleotide probe. 
     
     
         37 . A method according to  claim 36  wherein the polynucleotide probe is contained in a rnicroarray. 
     
     
         38 . A method according to  claim 30  wherein the biological sample is analyzed by a method comprising assaying said sample for the presence of a C3 protein comprising a glycine amino acid at the position corresponding to position 102 of SEQ ID NO:2;
 wherein the presence of a C3 protein comprising a glycine amino acid at the position corresponding to position 102 of SEQ ID N0:2 is indicative of an increased probability of a therapeutic; or toxic response to a chemical, protein, nucleic acid-based therapeutic; or other biological, naturally or synthetic; entity in the human subject. 
 
     
     
         39 . A method according to  claim 38  wherein said assaying comprises; contacting a test sample with a specific binding member which binds to a variant polypeptide encoded by a nucleotide sequence which comprises the nucleotide sequence of SEQ ID NO:1 or SEQ ID NO: 3 with a polymorphic variant sequence at a site of single nucleotide polymorphism (SNP) therein, and
 detecting the binding of the specific binding member to polypeptide in the sample. 
 
     
     
         40 . A method according to  claim 30 , wherein the subject is asymptomatic of macular degeneration. 
     
     
         41 . A method according to  claim 30 , wherein the subject has been diagnosed as having symptoms of macular degeneration. 
     
     
         42 . A method according to  claim 30 , wherein the sample is from blood, saliva, sputum, urine, cell scrapings or biopsy tissue. 
     
     
         43 . The method of  claim 31  further comprising determining whether the subject is homozygous or heterozygous for said polymorphism. 
     
     
         44 . A method comprising the steps of:
 assaying a biological sample from a human and detecting the presence of (i) at least one allele of the complement component 3 (C3) gene comprising a G nucleotide at the single nucleotide polymorphism (SNP) rs2230199 at the position corresponding to position 366 of SEQ ID NO: 1; or (ii) a C3 protein comprising a glycine amino acid at the position corresponding to position 102 of SEQ ID NO: 2;   wherein the presence of at least one allele of the C3 gene comprising a nucleotide at the single nucleotide polymorphism (SNP) rs2230199 at the position corresponding to position 366 of SEQ ID NO: 1 or a C3 protein comprising a glycine amino add at the position corresponding to position 102 of SEQ ID NO:2 is indicative of an increased risk of development of macular degeneration in said human.   
     
     
         45 . The method of  claim 44 , wherein said biological sample is DNA and said assaying comprises: amplifying the DNA in the presence of a pair of primers wherein a first primer comprises at least 10 consecutive nucleotides of one of SEQ ID NO: 1 or the complement of SEQ ID NO:1 and is located upstream of the base located at position 366 of SEQ ID NO:1, and a second primer comprises at least 10 consecutive nucleotides of the other of SEQ ID NO:1 or the complement of SEQ ID NO:1 and is located downstream of the base located at position 366 of SEQ ID NO:1; and
 determining the identity of the base in the amplified genetic material that corresponds to position 366 of SEQ ID NO: 1.   
     
     
         46 . A method comprising the steps of:
 assaying a biological sample from a human and detecting the presence of (i) at least one allele of the complement component 3 (C3) gene comprising a G nucleotide at the single nucleotide polymorphism (SNP) rs2230199 at the position corresponding to position 366 of SEQ ID NO: 1; or (ii) a C3 protein comprising a glycine amino acid at the position corresponding to position 102 of SEQ ID NO: 2;   wherein the presence of at least one allele of the C3 gene comprising a nucleotide at the single nucleotide polymorphism (SNP) rs2230199 at the position corresponding to position 366 of SEQ ID NO: 1 or a C3 protein comprising a glycine amino add at the position corresponding to position 102 of SEQ ID NO:2 is indicative of an increased risk of development of macular degeneration characterized by geographic atrophy or exudative disease in said human.   
     
     
         47 . The method of  claim 44 , wherein said biological sample is DNA and said assaying comprises: amplifying the DNA in the presence of a pair of primers wherein a first primer comprises at least 10 consecutive nucleotides of one of SEQ ID NO: 1 or the complement of SEG ID Nal and is located upstream of the base located at position 366 of SEQ ID NO:1, and a second primer comprises at least 10 consecutive nucleotides of the other of SEQ ID NO:1 or the complement of SEC) ID NO:1 and is located downstream of the base located at position 366 of SEQ ID NO:1; and
 determining the identity of the base in the amplified genetic material that corresponds to position 366 of SEQ ID NO: 1.