Method and apparatus for diagnosing age-related macular degeneration

Abstract

Disclosed is a method for identifying an individual who has an altered risk for developing age-related macular degeneration comprising detecting an insertion/deletion polymorphism in the ARMS2 gene

1 . A method comprising the steps of:
 amplifying a nucleic acid sequence containing position 3143 of SEQ ID NO: 1 using a first primer that binds upstream of said position and a second primer that binds downstream of said position;   detecting an insertion/deletion polymorphism starting at position 3143 of SEQ ID NO: 1; and   determining the genotype of the subject at position 3143 of SEQ ID NO: 1,   wherein a homozygote for the insertion/deletion polymorphism is predictive of susceptibility to age-related macular degeneration and a heterozygote for the insertion/deletion polymorphism is predictive of a carrier for susceptibility to age-related macular degeneration wherein the insertion/deletion comprises deletion of a nucleic acid sequence from position 3143 of SEQ ID NO: 1 to position 3585 of SEQ ID NO: 1 and insertion of a sequence from position 104 of SEQ ID NO: 2 to position 157 of SEQ ID NO: 2 in place of the deleted sequence.   
     
     
         2 . The method of  claim 1 , wherein the insertion/deletion polymorphism is detected by hybridization, chemical cleavage, direct DNA sequencing, use of restriction enzymes or Southern blotting. 
     
     
         3 . The method of  claim 1 , further comprising the step of obtaining a biological sample containing nucleic acid from the human subject prior to amplifying the insertion/deletion polymorphism. 
     
     
         4 . A method for diagnosing a susceptibility to age-related macular degeneration in a human subject, the method comprising the steps of:
 detecting the presence of mRNA corresponding to the age-related maculopathy susceptibility 2 (ARMS2) gene in a sample obtained from the human subject, wherein the absence of mRNA corresponding to the ARMS2 gene is predictive of susceptibility to age-related macular degeneration.   
     
     
         5 . The method of  claim 4 , wherein the mRNA is detected by Northern blot analysis, nuclease protection assays, in situ hybridization or reverse-transcriptase polymerase chain reaction. 
     
     
         6 . An apparatus for detecting a nucleotide in a nucleic acid sequence, the apparatus comprising:
 a substrate; and   a first oligonucleotide bound to the substrate, the first oligonucleotide comprising a contiguous nucleic acid sequence complementary to SEQ ID NO: 1 containing position 3143 of the sequence.   
     
     
         7 . The apparatus of  claim 6 , further comprising a second oligonucleotide bound to the substrate, the second oligonucleotide comprising a contiguous nucleic acid sequence complementary to SEQ ID NO: 2 containing position 104 of the sequence. 
     
     
         8 . The apparatus of  claim 7 , wherein the first oligonucleotide comprises a 25-mer contiguous nucleic acid sequence. 
     
     
         9 . The apparatus of  claim 8 , wherein the second oligonucleotide comprises a 25-mer contiguous nucleic acid sequence. 
     
     
         10 . The apparatus of  claim 7 , wherein the first oligonucleotide comprises a 60-mer contiguous nucleic acid sequence. 
     
     
         11 . The apparatus of  claim 8 , wherein the second oligonucletide comprises a 60-mer contiguous nucleic acid sequence. 
     
     
         12 . A nucleic acid comprising a sequence selected from the group consisting of:
 a) a nucleic acid sequence comprising SEQ ID NO: 3 or 4;   b) a complement of a nucleic acid sequence comprising SEQ ID NO: 3 or 4;   c) a fragment of either a) or b);   d) a nucleic acid sequence capable of hybridizing to any one of a), b) or c); and   e) a nucleic acid sequence that exhibits greater than about 70% sequence identity with the nucleic acids defined in a), b) or c).   
     
     
         13 . A method of predicting susceptibility to age-related macular degeneration in a human subject, comprising the steps of:
 obtaining a biological sample from the human subject;   exposing the biological sample to an antibody that recognizes a polypeptide corresponding to the age-related macular degeneration susceptibility 2 (ARMS2) gene; and   detecting the presence of the antibody/polypeptide complex,   wherein the absence of binding between the antibody and the polypeptide is predictive of susceptibility to age-related macular degeneration.   
     
     
         14 . The method of  claim 13 , wherein the polypeptide is VLDPGVG (SEQ ID NO: 5). 
     
     
         15 . The method of  claim 13 , wherein the presence of the antibody/polypeptide complex is detected by immunoblotting, immunoprecipitation, enzyme-linked immunosorbent assay (ELISA) or NMR spectrometry. 
     
     
         16 . An antibody or fragment thereof that specifically binds the polypeptide VLDPGVG (SEQ ID NO: 5). 
     
     
         17 . A system for analyzing a biological sample comprising:
 a) a determination module configured to receive a biological sample and to determine sequence information, wherein the sequence information comprises: expression of age-related maculopathy susceptibility 2 (ARMS2) gene or an insertion/deletion polymorphism starting at position 3143 of SEQ ID NO: 1;   b) a storage device configured to store sequence information from the determination module;   c) a comparison module adapted to compare the sequence information stored on the storage device with reference data, and to provide a comparison result, wherein the comparison result is a level of ARMS2 gene expression compared to the reference data or is the presence or absence of the insertion/deletion polymorphism starting at position 3143 of SEQ ID NO:1; and   d) a display module for displaying a content based in part on the comparison result for the user, wherein the content is a signal indicative of age-related macular degeneration.   
     
     
         18 . A computer readable medium having computer readable instructions recorded thereon to define software modules including a comparison module and a display module for implementing a method on a computer, said method comprising:
 a) comparing with the comparison module the data stored on a storage device with reference data to provide a comparison result, wherein the comparison result is a level of ARMS2 gene expression compared to the reference data or is the presence or absence of the insertion/deletion polymorphism starting at position 3143 of SEQ ID NO: 1; and   b) displaying a content based in part on the comparison result for the user, wherein the content is a signal indicative of age-related macular degeneration.