Non-invasive fetal genetic screening by digtal analysis

Patent metadata

Field	Value
Publication number	US-10072295-B2
Application number	US-201414581225-A
Country	US
Kind code	B2
Filing date	Dec 23, 2014
Priority date	Feb 2, 2006
Publication date	Sep 11, 2018
Grant date	Sep 11, 2018

Abstract

The present methods are exemplified by a process in which maternal blood containing fetal DNA is diluted to a nominal value of approximately 0.5 genome equivalent of DNA per reaction sample. Digital analysis is then be used to detect aneuploidy, such as the trisomy that causes Down Syndrome. Since aneuploidies do not present a mutational change in sequence, and are merely a change in the number of chromosomes, it has not been possible to detect them in a fetus without resorting to invasive techniques such as amniocentesis or chorionic villi sampling. Digital amplification allows the detection of aneuploidy using massively parallel amplification and detection methods, examining, e.g., 10,000 genome equivalents.

First claim

What is claimed is:

1. A method for identifying a risk for an aneuploidy on a first chromosome of a fetus carried by mother, the method comprising:
a) providing a sample of nucleic acids derived from a cell-free portion of a maternal blood sample, wherein said sample contains a mixture of maternal and fetal DNA;
b) selectively detecting preselected sequences on at least the first chromosome and preselected sequences on a second chromosome in the sample;
c) determining a first value for an amount of a first preselected sequence representing a first location on the first chromosome, wherein the first value:
i) includes a contribution from detection of the maternal DNA and the fetal DNA, and
ii) is not based on separately determining contributions to the amount at the first location from the maternal DNA and the fetal DNA;

d) determining a second value for an amount of a second preselected sequence representing a second location on the second chromosome, wherein the second value:
i) includes a contribution from detection of the maternal DNA and the fetal DNA; and
ii) is not based on separately determining contributions to the amount at the second location from the maternal DNA and the fetal DNA; and

e) conducting a statistical analysis to analyze for aneuploidy of the first chromosome in the fetus using the first value, the second value, and one or more additional values for additional samples of nucleic acids derived from cell-free portions of additional maternal blood samples that contain mixtures of maternal and fetal DNA.

2. The method of claim 1 , further comprising:
a) determining a third value for an amount of a third preselected sequence at a third location on a third chromosome, wherein the third value:
i) includes a contribution from detection of the maternal DNA and the fetal DNA; and
ii) is not based on separately determining contributions to the amount at the second location from the maternal DNA and the fetal DNA; and

b) conducting the statistical analysis to analyze for aneuploidy of the first chromosome in the fetus using the first value, the second value, and the third value.

3. The method of claim 1 , further comprising:
a) determining multiple values for multiple preselected sequences at multiple different locations on the first chromosome; and
b) determining multiple values for multiple preselected sequences at multiple different locations on the second chromosome,
wherein conducting the statistical analysis comprises analyzing for aneuploidy of the first chromosome in the fetus using the multiple values for the multiple preselected sequences at the multiple different locations on the first chromosome and the multiple values for the multiple preselected sequences at the multiple different locations on the second chromosome.

4. The method of claim 3 , wherein the multiple preselected sequences at multiple different locations on the first chromosome and the multiple preselected sequences at multiple different locations on the second chromosome are detected using probes directed to the locations on the first and second chromosomes.

5. The method of claim 3 , further comprising summing the values for the multiple preselected sequences at multiple different locations on the first chromosome to provide a value for the first chromosome, wherein conducting the statistical analysis comprises analyzing for aneuploidy of the first chromosome in the fetus using the value for the first chromosome.

6. The method of claim 1 , wherein the statistical analysis comprises a t test.

7. The method of claim 1 , wherein the detection method comprises digital PCR.

8. The method of claim 1 , wherein conducting the statistical analysis comprises comparing:
a) a ratio of a value for the first chromosome to a value for one or more chromosomes including the second chromosome, wherein said values are derived from detection reactions on the maternal blood sample being tested; and
b) a value based on multiple ratios of a value for the first chromosome to a value for one or more chromosomes including the second chromosome, wherein said values are derived from analysis of multiple other maternal samples.

9. The method of claim 1 , wherein conducting the statistical analysis further comprises taking into account the fraction level of fetal DNA in the sample of nucleic acids.

10. A method for identifying a risk for an aneuploidy on a first chromosome of a fetus carried by a mother, the method comprising:
a) providing a sample of nucleic acids derived from a cell-free portion of a maternal blood sample, wherein said sample contains a mixture of maternal and fetal DNA;
b) selectively detecting preselected sequences on at least the first chromosome and a second chromosome in the sample using probes to preselected locations on the first chromosome and the second chromosome;
c) determining first multiple values for amounts of multiple preselected sequences at multiple different locations on the first chromosome, wherein the first multiple values:
i) include a contribution from detection of the maternal DNA and the fetal DNA; and
ii) are not based on separately determining contributions to the amounts at the multiple different locations on the first chromosome from the maternal DNA and the fetal DNA; and

d) determining second multiple values for amounts of multiple preselected sequences at multiple different locations on the second chromosome, wherein the second multiple values:
i) include a contribution from detection of the maternal DNA and the fetal DNA; and
ii) are not based on separately determining contributions to the amounts at the multiple different locations on the second chromosome from the maternal DNA and the fetal DNA; and

e) conducting a statistical analysis to analyze for aneuploidy of the first chromosome in the fetus using the first multiple values, the second multiple values, and one or more additional values for additional samples of nucleic acids derived from cell-free portions of additional maternal blood samples that contain mixtures of maternal and fetal DNA.

11. The method of claim 10 , further comprising:
a) determining a third value for an amount of a third preselected sequence at a location on a third chromosome, wherein the third value:
i) includes a contribution from detection of the maternal DNA and the fetal DNA;
ii) is not based on separately determining contributions to the amount at the location on the third chromosome from the maternal DNA and the fetal DNA; and

b) conducting the statistical analysis further comprises conducting the statistical analysis to analyze for aneuploidy of the first chromosome in the fetus using the third value.

12. The method of claim 10 , wherein conducting the statistical analysis comprises comparing:
a) a ratio of a value for the first chromosome to a value for one or more chromosomes, wherein said value includes the second chromosome derived from detection reactions on the sample of nucleic acids; and
b) a value based on multiple ratios of a value for the first chromosome to a value for one or more chromosomes including the second chromosome, wherein said values are derived from analysis of multiple other maternal samples.

13. The method of claim 1 , wherein conducting the statistical analysis further comprises taking into account the fraction level of fetal DNA in the sample of nucleic acids.

14. The method of claim 10 , further comprising summing the first multiple values to provide a value for the first chromosome, wherein conducting the statistical analysis comprises analyzing for aneuploidy of the first chromosome in the fetus using the value f

Assignees

• Univ Leland Stanford Junior

Inventors

• Quake Stephen
• Fan Hei-Mun Christina

Classifications

• C12Q2600/156

  Polymorphic or mutational markers · CPC title

• C12Q1/6809

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

• C12Q1/6851

  Quantitative amplification · CPC title

• C12Q1/6883 Primary

  for diseases caused by alterations of genetic material · CPC title

• Y10T436/143333

  Saccharide [e.g., DNA, etc.] · CPC title