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.

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: 16.   
     
     
         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 , wherein the quantifying comprises reverse transcribing RNA from the individual into cDNA and determining the amount of RNA based upon the quantity of allele-specific IGF2 cDNA resulting from the reverse transcribing. 
     
     
         5 . The method of  claim 4 , wherein the quantifying comprises amplifying the IGF2 cDNA or a portion thereof comprising at least one of the polymorphic options. 
     
     
         6 . The method of  claim 4 , wherein the quantifying comprises nucleotide sequencing the IGF2 cDNA, or a portion thereof comprising at least one of the polymorphic options, from the individual. 
     
     
         7 . The method of  claim 4 , wherein the quantifying comprises contacting the IGF2 cDNA, or a portion thereof comprising at least one of the polymorphic options, from the individual with an oligonucleotide that distinguishes between polymorphic options of the SNP. 
     
     
         8 . The method of  claim 7 , wherein the penultimate or ultimate 3′ nucleotide of the oligonucleotide hybridizes to the polymorphic nucleotide of the SNP. 
     
     
         9 . The method of  claim 4 , wherein the quantifying comprises contacting the IGF2 cDNA, or a portion thereof comprising at least one of the polymorphic options, from the individual with an oligonucleotide that is complementary to the nucleotide immediately upstream of the polymorphic nucleotide of the SNP. 
     
     
         10 . The method of  claim 1 , wherein the quantifying comprises nucleotide sequencing the RNA, or a portion thereof comprising at least one of the polymorphic options, from the individual. 
     
     
         11 . The method of  claim 1 , wherein the quantifying comprises contacting the RNA from the individual with an oligonucleotide that distinguishes between polymorphic options of the SNP. 
     
     
         12 . The method of  claim 11 , wherein the penultimate or ultimate 3′ nucleotide of the oligonucleotide hybridizes to the polymorphic nucleotide of the SNP. 
     
     
         13 . The method of  claim 1 , wherein the quantifying comprises contacting the RNA, or a portion thereof comprising at least one of the polymorphic options, from the individual with an oligonucleotide that is complementary to the nucleotide immediately upstream of the polymorphic nucleotide of the SNP. 
     
     
         14 . 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. 
     
     
         15 . 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. 
     
     
         16 . 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. 
     
     
         17 . 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.