Single nucleotide polymorphisms and use of same in predicting male-specific prenatal loss

Abstract

The present invention is directed to a panel of single nucleotide polymorphisms (SNPs) in specific genes that serve as biomarkers for sex-specific prenatal loss of a conceptus or embryo. There is provided herein methods and reagents for assessing the specific SNPs in those genes. The method useful in applying these SNPs in predicting an increased risk of prenatal loss is also disclosed.

What is claimed is: 
     
         1 . A method for predicting prenatal loss of a conceptus or embryo, comprising the steps of:
 (a) providing a biological sample from a pregnant woman;   (b) isolating a nucleic acid from said biological sample;   (c) performing a polymerase chain reaction (PCR) on said isolated nucleic acid to produce an amplicon;   (d) assessing said amplicon for the presence of a combination of SNPs, said SNP combination consisting of HLA-DQA1 rs1142316, HLA-DRA rs7192, and HSPA1B rs1061581; and   (e) predicting an increased risk of prenatal loss of said male conceptus or embryo in said pregnant woman by said presence of said SNP combination,   wherein the presence of said SNP combination is indicative of an increased risk of prenatal loss for male conceptus or embryo.   
     
     
         2 . The method of  claim 1 , wherein said biological sample is derived from a conceptus or amniocentesis. 
     
     
         3 . The method of  claim 1 , wherein said nucleic acid is selected from the group consisting of genomic DNA, mRNA and isolated DNA. 
     
     
         4 . The method of  claim 1 , wherein said assessing step is performed by polymerase chain reaction-restriction fragment length polymorphism assay or TaqMan allelic discrimination assay. 
     
     
         5 . The method of  claim 4 , wherein said assessing step is performed by polymerase chain reaction-restriction fragment length polymorphism assay. 
     
     
         6 . The method of  claim 4 , wherein said assessing step is performed by TaqMan allelic discrimination assay. 
     
     
         7 . The method of  claim 4 , wherein said assessing step is performed by a process which comprises subjecting said isolated nucleic acid to a PCR flanking the region of said SNP. 
     
     
         8 . The method of  claim 1 , wherein said assessing step is performed on the presence of a SNP further selected from the group consisting of RXRB rs421446, BRD2 rs635688, HLA-E rs1264456, IRF4 rs12203592, IRF4 rs872071, LIF rs929271, TP53 rs1042522, MDM2 rs2279744, SLC11A2 rs422982, SLC40A1 rs1439814, and RRM2 rs1130609. 
     
     
         9 . A method of predicting prenatal survival probability of a prospective offspring of a couple, comprising the steps of:
 (a) providing a biological sample from a pregnant woman;   (b) isolating a nucleic acid from said biological sample;   (c) performing a polymerase chain reaction (PCR) on said isolated nucleic acid to produce an amplicon;   (d) assessing said amplicon for the presence of a combination of SNPs, said SNP combination consisting of HLA-DQA1 rs1142316, HLA-DRA rs7192, and HSPA1B rs1061581; and   (e) predicting a decreased prenatal survival probability of said prospective male offspring of said couple by said presence of said SNP combination,   wherein the presence of said SNP combination is indicative of a decreased prenatal survival probability of a prospective offspring.   
     
     
         10 . The method of  claim 9 , wherein said biological sample is derived from a conceptus or amniocentesis. 
     
     
         11 . The method of  claim 9 , wherein said nucleic acid is selected from the group consisting of genomic DNA, mRNA and isolated DNA. 
     
     
         12 . The method of  claim 9 , wherein said assessing step is performed by polymerase chain reaction-restriction fragment length polymorphism assay or TaqMan allelic discrimination assay. 
     
     
         13 . The method of  claim 12 , wherein said assessing step is performed by polymerase chain reaction-restriction fragment length polymorphism assay. 
     
     
         14 . The method of  claim 12 , wherein said assessing step is performed by TaqMan allelic discrimination assay. 
     
     
         15 . The method of  claim 12 , wherein said assessing step is performed by a process which comprises subjecting said isolated nucleic acid to a PCR flanking the region of said SNP. 
     
     
         16 . The method of  claim 9 , wherein said assessing step is performed on the presence of a SNP further selected from the group consisting of RXRB rs421446, BRD2 rs635688, HLA-E rs1264456, IRF4 rs12203592, IRF4 rs872071, LIF rs929271, TP53 rs1042522, MDM2 rs2279744, SLC11A2 rs422982, SLC40A1 rs1439814, and RRM2 rs1130609.