Novel single nucleotide polymorphisms and combinations of novel and known polymorphisms for determining the allele-specific expression of the igf2 gene

Abstract

Single nucleotide polymorphisms and uses for determining the imprinting status of the Insulin Growth Factor-2 gene in a clinical specimen are described.

What is claimed is: 
     
         1 . A method of quantifying allelic-specific expression of RNA in a human individual that is a heterozygote for a single nucleotide polymorphism (SNP) in the Insulin Growth Factor-2 (IGF2) gene, the method comprising
 quantifying in a sample from the individual the amount of RNA comprising each polymorphic option of the SNP, wherein the SNP comprises SEQ ID NO: 10, wherein the quantifying comprises   (a) reverse transcribing RNA from the individual into cDNA and (i) amplifying the cDNA or a portion thereof comprising at least one of the polymorphic options or (ii) nucleotide sequencing the cDNA or a portion thereof comprising at least one of the polymorphic options, thereby determining the amount of RNA having each polymorphic option; or   (b) nucleotide sequencing RNA from the individual and determining the amount of RNA having each polymorphic option.   
     
     
         2 . The method of  claim 1 , wherein the sample is a blood sample. 
     
     
         3 . The method of  claim 1 , wherein the sample is a stool or tissue sample. 
     
     
         4 . The method of  claim 1 , further comprising obtaining a sample comprising DNA from the individual and determining from the DNA from the sample that the individual is heterozygous for the SNP. 
     
     
         5 . The method of  claim 1 , wherein the quantifying comprises contacting RNA, or cDNA therefrom, from the individual with an oligonucleotide that distinguishes between polymorphic options of the SNP. 
     
     
         6 . The method of  claim 5 , wherein the penultimate or ultimate 3′ nucleotide of the oligonucleotide hybridizes to the polymorphic nucleotide of the SNP. 
     
     
         7 . The method of  claim 1 , wherein the quantifying comprises contacting RNA, or cDNA therefrom, from the individual with an oligonucleotide that is complementary to the nucleotide immediately upstream of the polymorphic nucleotide of the SNP 
     
     
         8 . The method of  claim 1 , wherein the quantifying comprises performing allele-specific hybridization, allele-specific amplification, restriction fragment length polymorphism analysis, denaturing gradient gel electrophoresis, or single-strand conformation polymorphism analysis. 
     
     
         9 . The method of  claim 1 , wherein the individual is determined to have loss of imprinting of IGF-2, and wherein the method further comprises administering an anti-cancer treatment to the individual. 
     
     
         10 . The method of  claim 1 , wherein the individual is determined to have loss of imprinting of IGF-2, and wherein the method further comprises performing additional cancer diagnostic testing on the individual.