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 aneuplodies.

1 . A method for determining fetal fraction and the presence or absence of a fetal aneuploidy in a sample comprising:
 (a) enriching a sample nucleic acid for a plurality of polymorphic nucleic acid targets, which sample nucleic acid comprises fetal nucleic acid and maternal nucleic acid;   (b) obtaining nucleotide sequences for some or all of the nucleic acid targets by a sequencing process;   (c) analyzing the nucleotide sequences of (b); and   (d) determining fetal fraction and the presence or absence of a fetal aneuploidy based on the analysis in (c).   
     
     
         2 . The method of  claim 1 , wherein the enriching comprises amplifying a plurality of polymorphic nucleic acid targets. 
     
     
         3 . The method of  claim 1 , wherein the enriching comprises cleaving maternal nucleic acid and not cleaving fetal nucleic acid. 
     
     
         4 . The method of  claim 1 , wherein the enriching comprises generating amplification products in an amplification reaction. 
     
     
         5 . The method of  claim 1 , wherein the polymorphic nucleic acid targets each comprise at least one single nucleotide polymorphism (SNP). 
     
     
         6 . The method of  claim 1 , wherein the polymorphic nucleic acid targets each comprise at least one short tandem repeat (STR). 
     
     
         7 . The method of  claim 1 , wherein determining the presence or absence of a fetal aneuploidy comprises (i) quantifying the amount of nucleotide sequences in (b) from a chromosome of interest and a reference chromosome, and (ii) comparing the amount of nucleotide sequences for the chromosome of interest and the reference chromosome. 
     
     
         8 . The method of  claim 1 , wherein determining the fetal fraction comprises (i) identifying at least one informative polymorphic site from the nucleotide sequences in (b), and calculating the fetal fraction from the amount of fetal polymorphic sites and maternal polymorphic sites. 
     
     
         9 . The method of  claim 1 , wherein the sequencing process comprises a sequencing by synthesis method. 
     
     
         10 . The method of  claim 1 , wherein the sequencing process comprises a sequencing by ligation method. 
     
     
         11 . The method of  claim 1 , wherein the sequencing process comprises a single molecule sequencing method. 
     
     
         12 . The method of  claim 1 , wherein the sample nucleic acid is cell-free DNA. 
     
     
         13 . The method of  claim 1 , wherein the sample nucleic acid is obtained from a pregnant female subject. 
     
     
         14 . The method of  claim 13 , wherein the subject is human. 
     
     
         15 . The method of  claim 1 , wherein the sample nucleic acid is from plasma or serum. 
     
     
         16 . The method of  claim 1 , wherein the fetal aneuploidy is trisomy 13. 
     
     
         17 . The method of  claim 1 , wherein the fetal aneuploidy is trisomy 18. 
     
     
         18 . The method of  claim 1 , wherein the fetal aneuploidy is trisomy 21.