Genetic alterations associated with autism and the autistic phenotype and methods of use thereof for the diagnosis and treatment of autism

Abstract

Compositions and methods for the detection and treatment of autism and autistic spectrum disorder are provided.

1 - 32 . (canceled) 
     
     
         33 . A method for detecting a subset of single-nucleotide polymorphisms (SNPs) identifying copy number variant (CNV) deletions consisting of
 rs8185771 on chromosome 8 identifying a deletion between nucleotides 43765570-43776595,   rs4971724 on chromosome 2 identifying a deletion between nucleotides 51120644-51147600,   rs10510221 on chromosome 3 identifying a deletion between nucleotides 1915190-1915922,   rs1444056 on chromosome 3 identifying a deletion between nucleotides 4199731-4236304,   rs12411971 on chromosome 10 identifying a deletion between nucleotides 87941666-87949029,   rs12214788 on chromosome 6 identifying a deletion between nucleotides 162584576-162587001,   rs2164850 on chromosome 2 identifying a deletion between nucleotides 78268199-78311249, and   rs174642 on chromosome 16 identifying a deletion between nucleotides 45834321-45887745   in a human subject comprising obtaining a nucleic acid sample from said subject and contacting the nucleic acid sample with a set of probes or primers to detect each of rs8185771, rs4971724, rs10510221, rs1444056, rs12411971, rs12214788, rs2164850, and rs174642.   
     
     
         34 . A method as claimed in  claim 33 , wherein the target nucleic acid is amplified prior to detection. 
     
     
         35 . The method of  claim 33 , wherein the step of detecting the presence of said subset of SNPs further comprises the step of analyzing a polynucleotide sample to determine the presence of said SNPs by performing a process selected from the group consisting of detection of specific hybridization, measurement of allele size, restriction fragment length polymorphism analysis, allele-specific hybridization analysis, single base primer extension reaction, and sequencing of an amplified polynucleotide. 
     
     
         36 . A method as claimed in  claim 33 , wherein in the target nucleic acid is DNA. 
     
     
         37 . A method as claimed in  claim 33 , wherein in the target sequence is a ribonucleic acid (RNA). 
     
     
         38 . The method of  claim 33 , wherein nucleic acids comprising said SNPs are obtained from an isolated cell of the human subject. 
     
     
         39 . A method for detecting a subset of SNPs identifying CNV duplications consisting of
 rs4346352 on chromosome 2 identifying a deletion between nucleotides 13119667-13165898,   rs7497239 on chromosome 15 identifying a deletion between nucleotides 22393833-22532309,   rs617372 on chromosome 12 identifying a deletion between nucleotides 31300846-31302088,   rs9342717 on chromosome 6 identifying a deletion between nucleotides 69291821-69294028,   rs17015816 on chromosome 3 identifying a deletion between nucleotides 2548148-2548531,   rs9860992 on chromosome 3 identifying a deletion between nucleotides 174754378-174771975,   rs7681914 on chromosome 4 identifying a deletion between nucleotides 144847402-144854579,   rs12408178 on chromosome 1 identifying a deletion between nucleotides 145658465-145807358,   rs1107194 on chromosome 2 identifying a deletion between nucleotides 237486328-237497105,   rs9346649 on chromosome 6 identifying a deletion between nucleotides 168091860-168339100,   rs1230300 on chromosome 19 identifying a deletion between nucleotides 22431189-22431397,   rs674478 on chromosome 22 identifying a deletion between nucleotides 19351264-19358946,   rs13225132 on chromosome 7 identifying a deletion between nucleotides 32667087-32770713,   rs6025553 on chromosome 20 identifying a deletion between nucleotides 55426961-55430874,   rs10798450 on chromosome 1 identifying a deletion between nucleotides 174500555-174543675,   rs10435634 on chromosome 8 identifying a deletion between nucleotides 55021047-55070134, and   rs2070180 on chromosome 3 identifying a deletion between nucleotides 122826190-122870474   in a human subject comprising obtaining a nucleic acid sample from said subject and contacting the nucleic acid sample with a set of probes or primers to detect each of rs4346352, rs7497239, rs617372, rs9342717, rs17015816, rs9860992, rs7681914, rs12408178, rs1107194, rs9346649, rs1230300, rs674478, rs13225132, rs6025553, rs10798450, rs10435634, and rs2070180.   
     
     
         40 . The method of  claim 39  further comprising detecting an allele of at least one additional SNP identifying a copy number variant (CNV) duplication on chromosome 5, said additional SNP selected from the group consisting of rs4307059, rs7704909, rs12518194, rs4327572, rs1896731, and rs10038113. 
     
     
         41 . A method as claimed in  claim 39 , wherein the target nucleic acid is amplified prior to detection. 
     
     
         42 . The method of  claim 39 , wherein the step of detecting the presence of said subset of SNPs further comprises the step of analyzing a polynucleotide sample to determine the presence of said SNPs by performing a process selected from the group consisting of detection of specific hybridization, measurement of allele size, restriction fragment length polymorphism analysis, allele-specific hybridization analysis, single base primer extension reaction, and sequencing of an amplified polynucleotide. 
     
     
         43 . A method as claimed in  claim 39 , wherein in the target nucleic acid is DNA. 
     
     
         44 . A method as claimed in  claim 39 , wherein in the target sequence is a ribonucleic acid (RNA). 
     
     
         45 . The method of  claim 39 , wherein nucleic acids comprising said SNPs are obtained from an isolated cell of the human subject.