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. A method for detecting the presence or absence of fetal aneuploidy in a pregnant female with an egg donor pregnancy, comprising
interrogating ten or more nucleic acid regions from a first chromosome from a maternal sample comprising maternal and fetal cell-free DNA, wherein the maternal sample is from the pregnant female;
detecting the interrogated nucleic acid regions from the first chromosome on average at least 100 times;
measuring a relative frequency of alleles from the nucleic acid regions from the first chromosome;
interrogating ten or more selected nucleic acid regions from a second chromosome from the maternal sample;
detecting the interrogated nucleic acid regions from the second chromosome on average at least 100 times;
measuring a relative frequency of alleles from the nucleic acid regions from the second chromosome;
calculating a percent fetal cell-free DNA in the maternal sample by quantifying egg donor informative loci wherein the egg donor informative loci are nucleic acid regions having the following allele patterns: the carrier mother is homozygous and the fetus is heterozygous, the carrier mother is heterozygous and the fetus is homozygous, or the carrier mother is homozygous for one allele and the fetus is homozygous for a different allele;
measuring the relative frequency of the nucleic acid regions from the first chromosome to the relative frequency of the nucleic acid regions from the second chromosome;
providing a statistical likelihood of the presence or absence of a fetal aneuploidy using the relative frequency of the nucleic acid regions from the first chromosome and the relative frequency of the nucleic acid region from the second chromosome in view of an expected statistical presence of a first or second aneuploid chromosome using the percent fetal cell-free DNA in the maternal sample.
2. The method of claim 1 , wherein calculating percent fetal cell-free DNA comprises selecting egg donor informative loci in which the maternal DNA and the fetal DNA differ in both alleles.
3. The method of claim 1 , 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.
4. The method of claim 1 , wherein calculating the percent fetal cell-free DNA comprises:
introducing a first set of fixed sequence oligonucleotides to the maternal sample under conditions that allow the fixed oligonucleotides to specifically hybridize to complementary regions in a first polymorphic nucleic acid region;
introducing a second set of fixed sequence oligonucleotides to the maternal sample under conditions that allow the fixed oligonucleotides to specifically hybridize to complementary regions in a second polymorphic nucleic acid region; and
ligating the hybridized oligonucleotides to create contiguous ligation products complementary to the nucleic acids.
5. The method of claim 4 , wherein the fixed sequence oligonucleotides comprise a universal primer region.
6. The method of claim 4 , wherein the first set of fixed sequence oligonucleotides and the second set of fixed sequence oligonucleotides comprises the same universal primer region.
7. The method of claim 4 , wherein the first set of fixed sequence oligonucleotides comprises a first universal primer region and the second set of fixed sequence oligonucleotides comprises a second universal primer region.
8. The method of claim 4 , and further comprising amplifying the contiguous ligation products using universal primer regions to create amplification products.
9. The method of claim 8 , wherein the amplifying comprises performing polymerase chain reaction (PCR) amplification on the contiguous ligation product templates.
10. The method of claim 1 , wherein the maternal sample is maternal plasma or serum.
11. The method of claim 1 , wherein calculating percent fetal cell-free DNA comprises interrogating twelve or more selected polymorphic nucleic acid regions.
12. The method of claim 11 , wherein interrogating twelve or more selected polymorphic nucleic acid regions comprises interrogating at least 20 or more nucleic acid regions.
13. The method of claim 12 , wherein interrogating 20 or more selected polymorphic nucleic acid regions comprises interrogating at least 24 nucleic acid regions.
14. The method of claim 13 , wherein interrogating 24 or more selected polymorphic nucleic acid regions comprises interrogating at least forty nucleic acid regions.
15. The method of claim 14 , wherein interrogating 40 or more selected polymorphic nucleic acid regions comprises interrogating at least ninety nucleic acid regions.
16. The method of claim 15 , wherein interrogating 90 or more selected polymorphic nucleic acid regions comprises interrogating at least three hundred nucleic acid regions.
17. The method of claim 1 , wherein at least the first chromosome is an autosome.
18. The method of claim 17 , wherein both the first and second chromosomes are autosomes.
19. The method of claim 1 , wherein detecting the interrogated nucleic acid regions from the first and second chromosome is performed using array-based hybridization processes.