NONINVASIVE DETECTION OF FETAL ANEUPLOIDY IN EGG DONOR PREGNANCIES
The present invention provides assay systems and methods for determining the percent fetal contribution of cell-free DNA in a maternal sample from a pregnant female with an egg donor pregnancy. Further provided, are assay systems and methods for determining a statistical likelihood of the presence or absence of a fetal aneuploidy in a maternal sample using a determined percent fetal cell-free DNA in the sample.
1 .- 44 . (canceled)
45 . A method for identifying the presence or absence of a fetal aneuploidy in sample from a female with an egg donor pregnancy, comprising
providing a maternal sample comprising maternal and fetal cell-free DNA;
calculating a percent fetal cell-free DNA in the sample using a comparison of a relative frequency of low frequency alleles to a relative frequency of both the high and low frequency alleles;
demonstrating the sample comprises fetal cell-free DNA relative to a threshold value;
interrogating two or more nucleic acid regions from a first chromosome;
interrogating two or more nucleic acid regions from at least a second chromosome determining a frequency of the interrogated nucleic acid regions from the first and at least second chromosome;
identifying the presence or absence of a fetal aneuploidy based on the determined relative frequencies of the nucleic acid regions from the first and at least second chromosome.
46 . The method of claim 45 , wherein the threshold value is between 1.0 and 5.0 percent.
47 . The method of claim 46 , wherein the threshold value is between 1.5 and 4.5 percent.
48 . The method of claim 47 , wherein the threshold value is between 2.0 and 4.0 percent.
49 . The method of claim 45 , wherein the threshold value is 3 percent.
50 . The method of claim 45 , wherein the threshold value is 4 percent.
51 . The method of claim 45 , wherein calculating a percent fetal cell-free DNA in the sample comprises:
interrogating two or more polymorphic nucleic acid regions from a first chromosome;
quantifying a relative frequency of alleles from the nucleic acid regions from the first chromosome;
interrogating two or more selected nucleic acid regions from a second chromosome;
quantifying a relative frequency of alleles from the nucleic acid regions from the second chromosome;
comparing the relative frequency of the nucleic acid regions from the first chromosome to the relative frequency of the nucleic acid regions form the second chromosome;
identifying egg donor informative loci based on the frequency of the alleles from the first and second chromosome; and
calculating a percent fetal cell-free DNA in the sample based on the egg donor informative loci.
52 . The method of claim 51 , wherein the egg donor informative loci comprise maternal DNA and the fetal DNA that differ in at least one allele.
53 . The method of claim 51 , wherein the egg donor informative loci comprise maternal DNA and the fetal DNA that differ in both alleles.
54 . The method of claim 45 , wherein calculating the percent fetal cell free DNA comprises comparing a relative frequency of low frequency alleles to a relative frequency of both the high and low frequency alleles.
55 . A method for identifying the presence or absence of a fetal aneuploidy in sample from a female with an egg donor pregnancy, comprising
providing a maternal sample comprising maternal and fetal cell-free DNA;
interrogating two or more polymorphic nucleic acid regions from a first chromosome;
quantifying a relative frequency of alleles from the nucleic acid regions from the first chromosome;
interrogating two or more selected nucleic acid regions from a second chromosome;
quantifying a relative frequency of alleles from the nucleic acid regions from the second chromosome;
comparing the relative frequency of the nucleic acid regions from the first chromosome to the relative frequency of the nucleic acid regions form the second chromosome;
identifying egg donor informative loci based on the frequency of the alleles from the first and second chromosome;
calculating a percent fetal cell-free DNA in the sample based on the egg donor informative loci;
demonstrating the sample comprises fetal cell-free DNA relative to a threshold value;
interrogating two or more nucleic acid regions from a first chromosome;
interrogating two or more nucleic acid regions from at least a second chromosome determining a frequency of the interrogated nucleic acid regions from the first and at least second chromosome; and
identifying the presence or absence of a fetal aneuploidy based on the determined relative frequencies of the nucleic acid regions from the first and at least second chromosome.
56 . The method of claim 55 , wherein the threshold value is between 1.0 and 5.0 percent.
57 . The method of claim 56 , wherein the threshold value is between 1.5 and 4.5 percent.
58 . The method of claim 57 , wherein the threshold value is between 2.0 and 4.0 percent.
59 . The method of claim 55 , wherein the threshold value is 3 percent.
60 . The method of claim 55 , wherein the threshold value is 4 percent.
61 . The method of claim 55 , wherein the egg donor informative loci comprise maternal DNA and the fetal DNA that differ in at least one allele.
62 . The method of claim 55 , wherein the egg donor informative loci comprise maternal DNA and the fetal DNA that differ in both alleles.
63 . The method of claim 55 , wherein calculating the percent fetal cell free DNA comprises comparing a relative frequency of low frequency alleles to a relative frequency of both the high and low frequency alleles.