Non-invasive fetal genetic screening by digtal analysis

• US 10,072,295 B2
• Filed: 12/23/2014
• Issued: 09/11/2018
• Est. Priority Date: 02/02/2006
• Status: Active Grant

• Current Assignee: Board of Trustees of the Leland Stanford Junior University (Stanford University)
• Original Assignee: Board of Trustees of the Leland Stanford Junior University (Stanford University)
• Inventors: Quake, Stephen, Fan, Hei-Mun Christina
• Primary Examiner(s): Riggs, II, Larry D
• Application Number:
  US14/581,225
• Publication Number:
  US 20150104793A1
• Time in Patent Office: 1,358 Days
• Field of Search: None
• CPC Class Codes: C12Q 1/6809 Methods for determination or identification of nucleic acids involving differential detection
• CPC Class Codes: C12Q 1/6851 Quantitative amplification
• CPC Class Codes: C12Q 1/6858 Allele-specific amplification
• CPC Class Codes: C12Q 1/6881 for tissue or cell typing, e.g. human leukocyte antigen [HLA] probes
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 2527/125 Specific component of sample, medium or buffer
• CPC Class Codes: C12Q 2527/137 Concentration of a component of medium
• CPC Class Codes: C12Q 2531/113 PCR
• CPC Class Codes: C12Q 2537/143 Multiplexing, i.e. use of multiple primers or probes in a single reaction, usually for simultaneously analyse of multiple analysis
• CPC Class Codes: C12Q 2537/157 A reaction step characterised by the number of molecules incorporated or released
• CPC Class Codes: C12Q 2545/114 involving a quantitation step
• CPC Class Codes: C12Q 2565/629 being a microfluidic device
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: C12Q 2600/158 Expression markers
• CPC Class Codes: Y10T 436/143333 Saccharide [e.g., DNA, etc.]

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.

Claims

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.

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.

24. 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.

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 for the first chromosome.

15. 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 that contains a mixture of maternal and fetal DNA;

b) detecting target sequences on at least the first chromosome and a second chromosome in the sample using probes to target locations on the first chromosome and the second chromosome;

c) determining a first value by counting a number of detected target sequences 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 by counting a number of detected target sequences representing a second location on the second chromosome which is presumed to be euploid, 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) determining a difference between the first value and the second value, wherein a statistically significant difference indicates the presence of aneuploidy on the first chromosome.

16. The method of claim 15, wherein the statistically significant difference is determined using a t test.

17. The method of claim 15, wherein determining the statistically significant difference comprises comparing 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.

18. The method of claim 17, wherein the value for the first chromosome is determined by summing the first value and a one or more values for an amount of additional sequences representing additional locations on the first chromosome.

19. The method of claim 15, wherein determining the statistically significant difference further comprises determining whether the analysis for aneuploidy of the first chromosome meets a confidence interval, and wherein calculation of the confidence interval includes the fraction level of fetal DNA in the sample of nucleic acids.

20. 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 a first preselected sequence of a first location on the first chromosome, wherein the first preselected sequence is common to all copies of the first chromosome in the sample of nucleic acids;

c) selectively detecting a second preselected sequence of a second location on a second chromosome, wherein the second preselected sequence is common to all copies of the second chromosome in the sample of nucleic acids;

d) determining a first value using an amount of the first preselected sequence;

e) determining a second value using an amount of the second preselected sequence, and

f) 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.

21. The method of claim 20, 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.

22. The method of claim 21, 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.

23. The method of claim 21, 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.