PROCESSES AND COMPOSITIONS FOR METHYLATION-BASED ENRICHMENT OF FETAL NUCLEIC ACID FROM A MATERNAL SAMPLE USEFUL FOR NON-INVASIVE PRENATAL DIAGNOSES
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.
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.