Processes and compositions for methylation-based enrichment of fetal nucleic acid from a maternal sample useful for non-invasive prenatal diagnoses
First Claim
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1. A method for determining the amount of fetal nucleic acid in a sample comprising:
- a) contacting nucleic acid from a pregnant female, which nucleic acid comprises fetal nucleic acid and maternal nucleic acid, the combination of the fetal nucleic acid and the maternal nucleic acid comprising total nucleic acid in the sample, with a methylation-sensitive restriction enzyme that digests nucleic acid at non-methylated sites, thereby enriching methylated nucleic acid;
b) amplifying in a single reaction vessel nucleic acid not digested in (a) at loci consisting of a locus comprising a polynucleotide of SEQ ID NO;
42 or a portion thereof and a locus comprising a polynucleotide of SEQ ID NO;
52 or a portion thereof, thereby generating amplification products; and
c) determining the amount of the fetal nucleic acid in the sample based on the amplification products of SEQ ID NO;
42 or a portion thereof and SEQ ID NO;
52 or a portion thereof in (b).
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Abstract
Provided are compositions and processes that utilize genomic regions that are 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 particularly useful for non-invasive prenatal diagnostics, including the detection of chromosomal aneuploidies.
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Citations
20 Claims
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1. A method for determining the amount of fetal nucleic acid in a sample comprising:
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a) contacting nucleic acid from a pregnant female, which nucleic acid comprises fetal nucleic acid and maternal nucleic acid, the combination of the fetal nucleic acid and the maternal nucleic acid comprising total nucleic acid in the sample, with a methylation-sensitive restriction enzyme that digests nucleic acid at non-methylated sites, thereby enriching methylated nucleic acid; b) amplifying in a single reaction vessel nucleic acid not digested in (a) at loci consisting of a locus comprising a polynucleotide of SEQ ID NO;
42 or a portion thereof and a locus comprising a polynucleotide of SEQ ID NO;
52 or a portion thereof, thereby generating amplification products; andc) determining the amount of the fetal nucleic acid in the sample based on the amplification products of SEQ ID NO;
42 or a portion thereof and SEQ ID NO;
52 or a portion thereof in (b). - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10)
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11. A method for determining the amount of fetal nucleic acid in a sample comprising:
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a) contacting nucleic acid from a pregnant female, which nucleic acid comprises fetal nucleic acid and maternal nucleic acid, the combination of the fetal nucleic acid and the maternal nucleic acid comprising total nucleic acid in the sample, with a methylation-sensitive restriction enzyme that digests nucleic acid at non-methylated sites, thereby enriching methylated nucleic acid; b) amplifying in a single reaction vessel nucleic acid not digested in (a) at loci consisting of a locus comprising a polynucleotide of SEQ ID NO;
42 or a portion thereof;
a locus comprising a polynucleotide of SEQ ID NO;
52 or a portion thereof and a locus comprising a polynucleotide of SEQ ID NO;
163 or a portion thereof, thereby generating amplification products; andc) determining the amount of the fetal nucleic acid in the sample based on the amplification products of SEQ ID NO;
42 or a portion thereof, SEQ ID NO;
52 or a portion thereof, and SEQ ID NO;
163 or a portion thereof in (b). - View Dependent Claims (12, 13, 14, 15, 16, 17, 18, 19, 20)
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Specification