| CPC C12Q 1/6883 (2013.01) [C12Q 1/686 (2013.01); C12Q 1/6806 (2013.01); C12Q 1/6851 (2013.01); C12Q 2600/112 (2013.01); C12Q 2600/118 (2013.01); C12Q 2600/154 (2013.01); C12Q 2600/16 (2013.01)] | 28 Claims |
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1. A method for detecting a chromosomal aneuploidy in a fetus carried by a pregnant female, said method comprising the steps:
(a) providing a sample taken from said pregnant female, which sample comprises DNA that originates from cells of a fetus and/or the placenta of a fetus in admixture with differently methylated DNA of maternal origin;
(b) treating the DNA present in said sample with a reagent that differentially modifies methylated and non-methylated DNA;
(c) determining an amount of a first target species of DNA, being the chromosome relevant to the chromosomal aneuploidy, in said sample by detecting in said sample the presence of methylation at two or more first target differentially methylated regions (DMRs) located on said chromosome, said first target DMRs differently methylated between DNA that originates from cells of a fetus and/or the placenta of a fetus and DNA of maternal origin, the modification of DNA of the first target DMRs by said reagent is sensitive to methylation of DNA, wherein a detected amount of methylated DNA at one or more of said first target DMRs indicates said amount of first target species of DNA in said sample;
(d) determining an amount of reference species of DNA, being one or more reference chromosomes, in said sample by detecting in said sample the presence of methylation at two or more reference DMRs located on said reference chromosome(s), said reference DMRs differently methylated between DNA that originates from cells of a fetus and/or the placenta of a fetus and DNA of maternal origin, the modification of DNA of such reference DMRs by said reagent is sensitive to methylation of DNA, wherein a detected amount of methylated DNA at one or more of said reference DMRs indicates said amount of reference species of DNA in said sample; and
(e) determining relative amount(s) of an amount determined from step (c) and an amount determined from step (d), wherein one or more of said relative amount(s) indicates the presence or absence of the chromosomal aneuploidy in the fetus,
wherein, said detections in step (c) and step (d) are made using the same aliquot of DNA of said sample, and in the same vessel, and effectively simultaneously for said first target DMRs and said reference DMRs, and using: (x) the same detectable label for at least two of said two or more reference DMRs; and (y) different detectable labels for at least two of said two or more first target DMRs,
optionally, wherein in step (e) said relative amount(s) are compared with threshold(s) and/or reference distribution(s), wherein one or more of said relative amount(s) higher or lower than said threshold(s) and/or reference distribution(s) indicates the presence of the chromosomal aneuploidy in the fetus,
wherein a sensitivity and specificity of the method is 95% or greater,
optionally wherein the relative amount(s) determined in step (e) is a ratio(s); and
optionally further comprising (f) determining an amount of total DNA in said sample by detecting at least one other region (OR) that is not differently methylated between DNA that originates from cells of a fetus and/or the placenta of a fetus and DNA of maternal origin, the modification of which OR(s) by said reagent is insensitive to methylation of DNA.
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