Noninvasive detection of fetal aneuploidy in egg donor pregnancies

Patent metadata

Field	Value
Publication number	US-11441185-B2
Application number	US-201816169458-A
Country	US
Kind code	B2
Filing date	Oct 24, 2018
Priority date	Jan 25, 2011
Publication date	Sep 13, 2022
Grant date	Sep 13, 2022

Abstract

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.

First claim

What is claimed is:

1. A method for determining the percent fetal cell-free DNA in a maternal sample from a pregnant female with an egg donor pregnancy, comprising:
providing a maternal sample comprising maternal and fetal cell-free DNA;
interrogating two or more selected polymorphic nucleic acid regions;
detecting the interrogated nucleic acid regions;
determining a relative frequency of polymorphisms in the interrogated nucleic acid regions to identify egg donor informative loci;
calculating a percent fetal cell-free DNA using the identified egg donor informative loci.

2. The method of claim 1 , wherein the egg donor informative loci include loci in which the maternal DNA and the fetal DNA differ in at least one allele.

3. The method of claim 1 , wherein the egg donor informative loci include loci in which the maternal DNA and the fetal DNA differ in both alleles.

4. 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.

5. The method of claim 1 , wherein the step of interrogating two or more selected polymorphic nucleic acid regions 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 of 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 of a second polymorphic nucleic acid region; and
ligating the hybridized oligonucleotides to create contiguous ligation products complementary to the nucleic acids.

6. The method of claim 5 , wherein the fixed sequence oligonucleotides comprise a universal primer region.

7. The method of claim 6 , wherein the first set of fixed sequence oligonucleotides and the second set of fixed sequence oligonucleotides comprises the same universal primer region.

8. The method of claim 6 , 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.

9. The method of claim 6 , and further comprising amplifying the contiguous ligation products using the universal primer region to create amplification products.

10. The method of claim 9 , wherein the amplifying comprises performing polymerase chain reaction (PCR) amplification on the contiguous ligation product templates.

11. The method of claim 1 , wherein the maternal sample is maternal plasma or serum.

12. The method of claim 1 , wherein interrogating two or more selected polymorphic nucleic acid regions comprises interrogating at least ten nucleic acid regions.

13. The method of claim 12 , wherein interrogating two or more selected polymorphic nucleic acid regions comprises interrogating at least twenty nucleic acid regions.

14. The method of claim 13 , wherein interrogating two or more selected polymorphic nucleic acid regions comprises interrogating at least forty nucleic acid regions.

15. The method of claim 14 , wherein interrogating two or more selected polymorphic nucleic acid regions comprises interrogating at least ninety nucleic acid regions.

16. The method of claim 15 , wherein interrogating two or more selected polymorphic nucleic acid regions comprises interrogating at least 300 nucleic acid regions.

17. 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 identified egg donor informative loci;
demonstrating the sample comprises fetal cell-free DNA above a threshold level;
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.

18. The method of claim 17 , wherein the threshold value is between 1.0 and 5.0 percent.

19. The method of claim 18 , wherein the threshold value is between 1.5 and 4.5 percent.

20. The method of claim 19 , wherein the threshold value is between 2.0 and 4.0 percent.

Assignees

• Ariosa Diagnostics Inc
• Roche Molecular Systems Inc

Inventors

• Oliphant Arnold
• Wang Eric
• Struble Craig

Classifications

• G16B20/00

  ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations · CPC title

• C12Q1/6883 Primary

  for diseases caused by alterations of genetic material · CPC title

• G16B30/00

  ICT specially adapted for sequence analysis involving nucleotides or amino acids · CPC title

• C12Q2600/156

  Polymorphic or mutational markers · CPC title

• C12Q1/6809

  Methods for determination or identification of nucleic acids involving differential detection · CPC title