Processes and compositions for methylation-based enrichment of fetal nucleic acid from a maternal sample useful for non-invasive prenatal diagnoses

Abstract

Provided are compositions and processes that utilize genomic regions differentially methylated between a mother and her fetus to separate, isolate or enrich fetal nucleic acid from a maternal sample. The compositions and processes described herein are useful for non-invasive prenatal diagnostics, including the detection of chromosomal aneuploidies.

What is claimed is: 
     
         1 . A method for enriching for fetal nucleic acid, comprising
 a) digesting nucleic acid from a pregnant female, which nucleic acid comprises fetal nucleic acid and maternal nucleic acid, with a methylation sensitive restriction enzyme that specifically digests the fetal nucleic acid at one or more loci that are hypomethylated in fetal nucleic acid; and   b) separating the fetal nucleic acid from the maternal nucleic acid, thereby enriching for fetal nucleic acid.   
     
     
         2 . The method of  claim 1 , wherein the one or more loci are selected from loci of SEQ ID NOs: 60-85. 
     
     
         3 . The method of  claim 1 , wherein one or more loci are on a target chromosome. 
     
     
         4 . The method of  claim 2 , further comprising determining the amount of fetal nucleic acid for the target chromosome. 
     
     
         5 . The method of  claim 4 , wherein one or more loci are on a reference chromosome. 
     
     
         6 . The method of  claim 5 , further comprising determining the amount of fetal nucleic acid for the reference chromosome. 
     
     
         7 . The method of  claim 3 , further comprising determining the presence or absence of a fetal aneuploidy according to the amount of fetal nucleic acid for the target chromosome. 
     
     
         8 . The method of  claim 6 , further comprising comparing the amount of fetal nucleic acid for the target chromosome to the amount of fetal nucleic acid for the reference chromosome, whereby a statistically significant difference between the amount of fetal nucleic acid for the target chromosome and the amount of fetal nucleic acid for the reference chromosome determines the presence of a fetal aneuploidy. 
     
     
         9 . The method of  claim 6 , wherein the amount of fetal nucleic acid at about 3 to about 15 loci on each of the target chromosome and the reference chromosome is determined. 
     
     
         10 . The method of  claim 6 , wherein the amount of fetal nucleic acid at about 16 or more loci on each of the target chromosome and the reference chromosome is determined. 
     
     
         11 . The method of  claim 1 , wherein enriching for fetal nucleic comprises use of an amplification reaction. 
     
     
         12 . The method of  claim 4 , wherein determining the amount of fetal nucleic acid comprises use of a mass spectrometry method. 
     
     
         13 . The method of  claim 6 , wherein determining the amount of fetal nucleic acid comprises use of a mass spectrometry method. 
     
     
         14 . The method of  claim 4 , wherein determining the amount of fetal nucleic acid comprises use of a sequencing method. 
     
     
         15 . The method of  claim 6 , wherein determining the amount of fetal nucleic acid comprises use of a sequencing method. 
     
     
         16 . The method of  claim 14 , wherein the sequencing method comprises sequencing by synthesis. 
     
     
         17 . The method of  claim 15 , wherein the sequencing method comprises sequencing by synthesis.