Methods for the diagnosis of fetal disease
View Patent ↗Methods are provided for detecting an aneuploidy in a fetus. These methods can be used to detect trisomy 13, 8 or 21, amongst other aneupoloidies. In some embodiments, the methods include selectively purifying fetal DNA from a maternal biological sample using the methylation status of a CpG containing genomic sequence and genotyping the fetus using the purified fetal DNA, thereby detecting aneuploidy in the fetus.
1. A method of detecting aneuploidy of chromosome 21 in human fetal genomic DNA from a human fetus, comprising:
(a) obtaining purified human fetal genomic DNA from a human maternal biological sample comprising fetal genomic DNA and maternal DNA, comprising separating a fetal CpG-containing genomic sequence from chromosome 21 comprising at least 15 consecutive nucleotides of SEQ ID NO: 1 comprising the CpG at position 153-154 from said maternal DNA, wherein the CpG at position 153-154 is not methylated on said maternal DNA and is methylated on said fetal DNA; and
(b) detecting an aneuploid copy number of the CpG-containing genomic sequence from chromosome 21 in the purified human fetal genomic DNA obtained in step (a).
2. The method of claim 1 , wherein detecting the aneuploid copy number of the CpG-containing genomic sequence comprises detecting an allelic ratio of a bi-allelic single nucleotide polymorphism in the purified human fetal genomic DNA, wherein an allelic ratio of 1:2 or 2:1 is detected.
3. The method of claim 2 , wherein SEQ ID NO: 1 comprises the single nucleotide polymorphism.
4. The method of claim 1 , wherein detecting the aneuploid copy number of the CpG-containing genomic sequence comprises detecting an allelic ratio of a biallelic short tandem repeat polymorphism in the purified human fetal genomic DNA, wherein an allelic ratio of other than 1:1 is detected.
5. The method of claim 1 , wherein obtaining purified human fetal genomic DNA from a human maternal biological sample comprises the use of a microarray.
6. The method of claim 1 , wherein obtaining purified human fetal genomic DNA from a human maternal biological sample comprises the use of a restriction enzyme that differentially cleaves methylated or unmethylated DNA.
7. The method of claim 6 , wherein the restriction enzyme is Hpa II.
8. The method of claim 1 , wherein obtaining purified human fetal genomic DNA from a human maternal biological sample comprises the use of bisulfite.
9. The method of claim 1 , further comprising amplifying the purified human fetal genomic DNA.
10. The method of claim 1 , wherein obtaining purified human fetal genomic DNA from a human maternal biological sample comprises separating a fetal CpG-containing genomic sequence from chromosome 21 comprising SEQ ID NO: 1.
11. The method of claim 1 , wherein detecting an aneuploid copy number comprises at least one of 1) DNA amplification; 2) detecting a fluorescent signal; 3) detecting hybridization of a probe; and 4) DNA sequencing.
12. The method of claim 1 , wherein the aneuploidy is trisomy 21.
13. The method of claim 1 , wherein the human maternal biological sample is a maternal blood sample.
14. The method of claim 1 , wherein the human fetus is between 11 and 13 weeks of age.
15. The method of claim 1 , further comprising karyotyping the human fetus.