Method and kit for diagnosing Autism using gene expression profiling

Abstract

This invention relates to DNA microarray technology, and more specifically to methods and kits for identifying autism and autism spectrum disorders in humans.

1 . A method for screening of an Autism Spectrum Disorder in a subject comprising the steps of:
 i) obtaining a sample of peripheral cells from the subject   ii) determining a gene expression profile of one or more ASD biomarker genes in the sample; and   iii) comparing the gene expression profile of the one or more ASD indicative genes in the sample to a positive control comprising an average gene expression level of the ASD indicative genes in a plurality of reference samples that are derived from subjects displaying symptoms of Autistic Spectrum Disorder to determine differential gene expression between the sample and the positive control, wherein presence of the Autistic Spectrum Disorder is indicated if there is no statistically significant differential gene expression between the gene expression profile of one or more ASD biomarker genes in the sample and the positive control, wherein the ASD biomarker genes comprise one or more genes of Table 1, Table 3, Table 4, Table 5, or a combination thereof.   
     
     
         2 . The method of  claim 1 , wherein the differential gene expression distinguishes among phenotypic variants of the Autism Spectrum Disorder. 
     
     
         3 . The method of  claim 1 , wherein the phenotypic variants of the Autism Spectrum Disorder comprises, verbal and non-verbal language abilities, social skills, repetitive behavior, restricted interest, savant skills, or a combination thereof. 
     
     
         4 . The method of  claim 1 , wherein the peripheral cells-comprise white blood cells. 
     
     
         5 . The method of  claim 4 , wherein the lymphoblasts the white blood cells comprise lymphoblasts. 
     
     
         6 . The method of  claim 1 , wherein the peripheral cells are mucosal epithelial cells. 
     
     
         7 . The method of  claim 1 , wherein the gene expression profile is obtained by using DNA microarray analysis comprising, oligonucleotide microarray, c-DNA microarray, and focused gene chip analysis, or a combination thereof. 
     
     
         8 . The method of  claim 1 , wherein the one or more genes of Table 1 comprise ASS, ALOX5AP (FLAP), DAPK1, F13A1, IL6ST, NAGLU, and ROBO1. 
     
     
         9 . The method of  claim 8 , wherein the one or more genes of Table 1 comprise genes involved in neuroinflammation comprising ASS, ALOX5AP (FLAP), DAPK1, and IL6ST. 
     
     
         10 . The method of  claim 1 , wherein the Autism Spectrum Disorder comprises autism, Asperger's Syndrome, and pervasive developmental disorder-not otherwise specified (PDD-NOS). 
     
     
         11 . An assay for screening an agent for its ability to treat or prevent one or more symptoms of Autism Spectrum Disorder comprising the steps of:
 i) isolating a nucleic acid control sample from a peripheral cell of an autistic individual that produces a differential gene expression profile representative of an autism spectrum disorder and determining the level of gene expression in the control sample;   ii) subjecting the peripheral cell to the agent;   iii) isolating a nucleic acid test sample from the peripheral cell after subjection of the peripheral cell to the agent of step (ii) and determining the level of gene expression in the test sample;   iv) comparing production, stability, degradation and/or activation of gene expression between the control sample and the test sample to find differential gene expression profile between the test sample and the control sample;   
       wherein a differential gene expression profile between the test sample as compared with the control sample is indicative of the ability of the agent to prevent or treat one or more symptoms of Autism Spectrum Disorder. 
     
     
         12 . The assay of  claim 11 , wherein Autism Spectrum Disorder is indicated upon observing statistically significant differential gene expression in an ensemble of genes comprising a gene ensemble according to Table 1, a gene ensemble according to Table 3, a gene ensemble according to Table 4, and a gene ensemble according to Table 5, or a combination thereof. 
     
     
         13 . The assay of  claim 11 , wherein the Autism Spectrum Disorder is selected from the group consisting of autism, Asperger's Syndrome, and pervasive developmental disorder-not otherwise specified (PDD-NOS). 
     
     
         14 . A test kit to facilitate diagnosis and treatment of Autism Spectrum Disorders; comprising one or more nucleic acid samples derived from an autistic individual as a positive control; reagents and equipment for isolating and analyzing a nucleic acid sample of peripheral cells of a subject in order to compare gene expression profile of the subject with the positive control; and directions for use of the kit, wherein the one or more nucleic acid sample comprise an ensemble of genes comprising a gene ensemble according to Table 1, a gene ensemble according to Table 3, a gene ensemble according to Table 4, and a gene ensemble according to Table 5, or a combination thereof. 
     
     
         15 . The kit of  claim 14 , wherein Autism Spectrum Disorders comprise autism, Asperger's Syndrome, and pervasive developmental disorder-not otherwise specified (PDD-NOS). 
     
     
         16 . The kit of  claim 14 , wherein the sample of peripheral cells comprises white blood cells or their lymphoblast derivatives. 
     
     
         17 . The kit of  claim 14 , wherein the sample of peripheral cells comprises buccal mucosal epithelial cells. 
     
     
         18 . The kit of  claim 14 , wherein the reagents and equipment comprise DNA microarray analysis materials including oligonucleotide microarray, c-DNA microarray, and focused gene chip, or a combination thereof. 
     
     
         19 . A computer-implemented method for analyzing gene expression to screen for an Autism Spectrum Disorder comprising the steps of:
 i) compiling data comprising a plurality of measured gene expression signals derived from cDNA microarray analysis of peripheral cells into a form suitable for computer-based analysis: and   ii) analyzing the compiled data, wherein the analyzing comprises identifying gene networks from a number of upregulated biomarker genes and downregulated biomarker genes, wherein the biomarker genes are genes that have been identified as associating with presence or severity of autism or autism spectrum disorder, said genes comprising genes listed in Table 1, genes listed in Table 3, genes listed in Table 4, and genes listed in Table 5, or a combination thereof.   
     
     
         20 . The computer-implemented method of  claim 19 , wherein the biomarker genes comprise genes involved in nervous system development and/or function. 
     
     
         21 . A computer-readable medium encoding a programming code for analyzing Autism Spectrum Disorder gene expression from a plurality of data points which comprises a gene ensemble which is filtered using a log 2(ratio) as a criterion for differential expression, said gene ensemble comprising a gene ensemble according to Table 1, a gene ensemble according to Table 3, a gene ensemble according to Table 4, and a gene ensemble according to Table 5, or a combination thereof.