Methods and materials for identifying polymorphic variants, diagnosing susceptibilities, and treating disease

Abstract

The invention is directed to materials and methods associated with polymorphic variants in two enzymes involved in folate-dependent and one-carbon metabolic pathways: MTHFD1 (5,10-methylenetetrahydrofolate dehydrogenase, 5,10-methenyltetrahydrofolate cyclohydrolase, 10-formyltetrahydrofolate synthetase) and methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1-like (MTHFD1L). Diagnostic and therapeutic methods are provided involving the correlation of polymorphic variants in MTHFD1, MTHFD1, and other genes with relative susceptibility for various pregnancy-related and other complications.

1 .- 2 . (canceled) 
     
     
         3 . A method of testing for an increased susceptibility for a complication related to a defect in a one-carbon metabolic pathway, the method comprising:
 (a) screening a sample from a subject to detect the presence or absence of a polymorphic variant of a polymorphism in at least one chromosomal copy of the MTHFD1L gene, wherein the polymorphic variant is associated with an increased susceptibility for a complication related to a defect in a one-carbon metabolic pathway; and   (b) diagnosing the susceptibility of the subject for a complication related to a defect in a one-carbon metabolic pathway based on the presence or absence of the polymorphic variant of at least one chromosomal copy of the MTHFD1L gene.   
     
     
         4 . The method of  claim 3 , wherein the complication is related to administration of a drug. 
     
     
         5 . The method of  claim 4 , wherein the drug is selected from the group consisting of a chemotherapeutic drug, a cardiovascular drug, and a central nervous system (CNS) drug. 
     
     
         6 . The method of  claim 3 , wherein the complication is selected from the group consisting of a pregnancy-related complication, miscarriage, second trimester miscarriage, placental abruption, severe placental abruption, neural tube defect, and cardiovascular disease. 
     
     
         7 . The method of  claim 6 , wherein the complication is a neural tube defect, and wherein the neural tube defect is in a child of the subject screened. 
     
     
         8 . The method of  claim 7 , wherein the neural tube defect is selected from the group consisting of anencephaly, encephalocele, iniencephaly, and spina bifida. 
     
     
         9 . The method of  claim 3 , wherein the subject is selected from the group consisting of a female, a female of child-bearing age, a pregnant female, a female that has had complications during a previous pregnancy, a female that has had complication becoming pregnant, a male, and a gestating child. 
     
     
         10 . The method of  claim 3 , wherein the sample comprises an egg, a sperm, a somatic cell, or blood. 
     
     
         11 . The method of  claim 3 , wherein the polymorphism variant is selected from the group consisting of a single nucleotide polymorphism (SNP) and a short tandem repeat polymorphism (STRP). 
     
     
         12 . The method of  claim 3 , wherein the polymorphic variant is present in a single chromosomal copy of the gene, and wherein heterozygosity is associated with an increased risk for the complication. 
     
     
         13 . The method of  claim 3 , wherein the sample comprises two chromosomal copies of the gene, wherein the polymorphic variant is present in both chromosomal copies of the gene, wherein homozygosity of the polymorphic variant is associated with an increased risk for the complication, and wherein the complication is diagnosed if homozygosity of the polymorphic variant is detected. 
     
     
         14 . The method of  claim 3 , wherein the sample comprises a nucleic acid selected from the group consisting of (a) a nucleic acid encoding MTHFD1L, (b) a fragment of (a) comprising at least 30 contiguous nucleotides of SEQ ID NO: 12 wherein the 30 contiguous nucleotides comprise the polymorphism, (c) a complement of (a) or (b), and (d) a combination of two or more of (a), (b), and (c). 
     
     
         15 . The method of  claim 3 , wherein the screening comprises assaying a sample comprising a nucleic acid selected from the group consisting of (a) a nucleic acid encoding MTHFD1L, (b) a fragment of (a) comprising at least 30 contiguous nucleotides of SEQ ID NO: 12 wherein the 30 contiguous nucleotides comprise the tandem repeated “ATT” sequence of the rs3832406 polymorphism of MTHFD1L, (c) a complement of (a) or (b), and (d) a combination of two or more of (a), (b), and (c). 
     
     
         16 . The method of  claim 15 , wherein the polymorphic variant is an “ATT” tandem repeat of rs3832406, and the diagnosis is for an increased susceptibility for the condition if the tandem repeat comprises seven or fewer “ATT” repeats. 
     
     
         17 . The method of  claim 15 , wherein the polymorphic variant causes an alternative splicing of a mRNA derived from the MTHFD1 L gene or a decrease in the synthetase activity of the MTHFD1 L gene product. 
     
     
         18 . The method of  claim 3 , wherein the sample is further screened for a polymorphic variant of a polymorphism in a gene selected from the group consisting of the MTHFR gene, the coagulation factor II gene, the coagulation factor V gene, and the transcobabalamin II gene, and wherein the polymorphic variant is associated with the complication. 
     
     
         19 . The method of  claim 3 , wherein the sample is screened using a method selected from the group consisting of a nucleic acid array, allele-specific-oligonucleotide (ASO) hybridization, PCR-RFLP analysis, PCR, single-strand conformation polymorphic variant (SSCP) technique, an amplification refractory mutation system (ARMS) technique, nucleotide sequencing, an antibody specific to the protein encoded by the polymorphic variant containing gene, and mass spectrometry. 
     
     
         20 .- 23 . (canceled)