Methods for the diagnosis of fetal disease

Abstract

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 for detecting an aneuploidy in a fetus, comprising:
 (a) selectively purifying fetal DNA from a maternal biological sample using the methylation status of a CpG containing genomic sequence, wherein the CpG-containing genomic sequence is at least 15 nucleotides in length, comprises at least one CpG dinucleotide, and is within a region on chromosome 13, 18 or 21, and wherein the CpG-containing genomic sequence comprises at least 15 nucleotides of one of the nucleic acid sequence set forth as any one of SEQ ID NOs: 2-68 and 83; and   (b) genotyping the fetus using the purified fetal DNA, thereby detecting aneuploidy in the fetus.   
     
     
         2 . The method of  claim 1 , wherein genotyping the fetus comprises determining the allelic ratio of a bi-allelic single nucleotide polymorphism in the fetal DNA, wherein an allelic ratio of 1:2 or 2:1 indicates that the fetus is aneuploid. 
     
     
         3 . The method of  claim 2 , wherein one of SEQ ID NOs: 2-68 or 83, respectively, comprises the single nucleotide polymorphism. 
     
     
         4 . The method of  claim 1 , wherein genotyping the fetus comprises detecting a short tandem repeat polymorphism in the fetal DNA, and a ratio of bi-allelic short tandem repeats of other than 1:1 indicates that the fetus is aneuploid. 
     
     
         5 . The method of  claim 1 , wherein selectively purifying fetal DNA from a maternal biological sample using the methylation status of a CpG containing genomic sequence comprises the use of a microarray. 
     
     
         6 . The method of  claim 1 , wherein selectively purifying fetal DNA from a maternal biological sample using the methylation status of a CpG containing genomic sequence 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 selectively purifying fetal DNA from a maternal biological sample using the methylation status of a CpG containing genomic sequence comprises the use of bisulfite. 
     
     
         9 . The method of  claim 1 , further comprising amplifying the fetal DNA. 
     
     
         10 . The method of  claim 1 , wherein genotyping the fetus comprises detecting the copy number of a nucleic acid comprising at least 15 nucleotides of one of SEQ ID NOs: 2-68 or 83 in the fetal DNA. 
     
     
         11 . The method of  claim 1 , wherein genotyping the fetus comprises detecting the copy number of a nucleic acid comprising at least one of SEQ ID NOs: 2-68 and 83. 
     
     
         12 . The method of  claim 1 , wherein genotyping the fetus comprises detecting the copy number of a bi-allelic single nucleotide polymorphism that is at most 150 nucleotides from one of SEQ ID NOs: 2-68 or 83. 
     
     
         13 . The method of  claim 1 , wherein genotyping the fetus comprises detecting the copy number of a short tandem repeat that is at most 150 nucleotides from one of SEQ ID NOs: 2-68. 
     
     
         14 . The method of  claim 1 , wherein detecting the 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. 
     
     
         15 . The method of  claim 1 , wherein the fetal aneuploidy is a trisomy 18. 
     
     
         16 . The method of  claim 1 , wherein the fetal aneuploidy is trisomy 21. 
     
     
         17 . The method of  claim 1 , wherein the fetal aneuploidy is trisomy 13. 
     
     
         18 . The method of  claim 1 , wherein the first biological sample is a maternal blood sample. 
     
     
         19 . The method of  claim 1 , wherein the fetus is a human fetus. 
     
     
         20 . The method of  claim 19 , wherein the fetus is between 11 and 13 weeks of age. 
     
     
         21 . The method of  claim 1 , further comprising karyotyping the fetus.