Non-invasive fetal genetic screening by digital analysis

• US 7,888,017 B2
• Filed: 02/02/2007
• Issued: 02/15/2011
• Est. Priority Date: 02/02/2006
• Status: Active Grant

• Current Assignee: Board of Trustees of the Leland Stanford Junior University (Stanford Management Co.)
• Original Assignee: Board of Trustees of the Leland Stanford Junior University (Stanford Management Co.)
• Inventors: Quake, Stephen, Fan, Hei-Mun Christina
• Primary Examiner(s): MYERS, CARLA J
• Application Number:
  US11/701,686
• Publication Number:
  US 20070202525A1
• Time in Patent Office: 1,474 Days
• Field of Search: None
• US Class Current: 435/6.12
• 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 PCR 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 of determining a fetal aneuploidy by determining the number of copies of maternal and fetal target chromosomes, having target sequences in a mixture of maternal and fetal genetic material, comprising the steps of:

a) obtaining maternal tissue containing both maternal and fetal genetic material;

b) obtaining a mixture of maternal and fetal genetic material from said maternal tissue;

c) distributing the genetic material obtained in step b) into a plurality of reaction samples, to randomly provide individual reaction samples that contain a target sequence from a target chromosome and individual reaction samples that do not contain a target sequence from a target chromosome;

d) analyzing the target sequences of genetic material present or absent in said individual reaction samples to provide a first number of binary results representing presence or absence of a presumably euploid fetal chromosome in the reaction samples and a second number of binary results representing presence or absence of a presumably aneuploid fetal chromosome in the reaction samples,

e) determining the presence or absence of a fetal aneuploidy by comparing said first number of step (d) with said second number of step (d), wherein a differential between the first number and the second number indicates the presence of a fetal aneuploidy.

2. The method of claim 1 wherein the maternal tissue is maternal peripheral blood or blood plasma.

3. The method of claim 1 wherein the reaction samples are contained in one of:

wells in a microtiter plate, aqueous phases in an emulsion, an area on an array surface, and reaction chambers in a microfluidic device.

4. The method of claim 1 wherein the reaction samples are contacted with a plurality of PCR primers, including at least one primer directed specifically to a target sequence, from a presumably euploid fetal chromosome, and at least one primer directed specifically to a target sequence from a presumably aneuploid fetal chromosome and further including the step of amplifying the target sequence from a presumably euploid fetal chromosome and the target sequence from the presumably aneuploid fetal chromosome.

5. The method of claim 4 wherein said analyzing comprises hybridization with a nucleic acid having a fluorescent label.

6. The method of claim 5 wherein said nucleic acid is in a sample for binding to a target sequence and generating a resulting change in fluorescence.

7. The method of claim 1 wherein the number of reaction samples is at least about 10,000.

8. The method of claim 1 wherein said analyzing comprises the use of nucleic acids specific for human chromosome 21 and specific for another human chromosome presumed to be euploid.

9. The method of claim 1 wherein said analyzing comprises hybridization with nucleic acids which hybridize to a sequence selected from the group consisting of one or more of the genes:

CFTR, Factor VIII (F8 gene), beta globin, hemachromatosis, G6PD, neurofibromatosis, GAPDH, beta amyloid, and pyruvate kinase.

10. The method of claim 1 wherein said analyzing comprises detection of a sequence deleted in a human chromosome deletion, is moved in a translocation or inversion, or is duplicated in a chromosome duplication, wherein said sequence is characterized in a known genetic disorder in the fetal genetic material not present in the maternal genetic material.

11. The method of claim 1 wherein said analyzing comprises detection of a sequence of a known mutated form of a human gene.

12. The method of claim 1 further comprising the step of enriching the mixture for fetal genetic material by size separation, whereby a preparation comprising only DNA fragments less than about 300 bp are used for analyzing in step (d).

13. The method of claim 1 in which the analyzing comprises direct sequencing of the genetic material.

14. The method of claim 1 in which the analyzing comprises sequencing of amplified derivatives of the target sequences.

15. The method of claim 14 where the amplified derivative is selected from the group consisting of an amplicon and a clone.

16. The method of claim 1 in which the genetic material is cDNA derived from RNA in the tissue.

23. The method of claim 1 wherein the reaction samples are formed by partitioning the genetic material into reaction chambers in a microfluidic device.

24. The method of claim 23 wherein the reaction samples are analyzed by PCR.

25. The method of claim 1 wherein the reaction samples are formed by mixing the genetic sample with PCR reagents to form a mixture, flowing the mixture into a microfluidic device with multiple segments, and closing off the multiple segments.

26. The method of claim 1 wherein each reaction sample contains on average not more than about 0.5 genome equivalent of genomic DNA.

27. The method of claim 1 wherein said binary results are obtained by digital PCR of target chromosomes in individual reaction samples.

28. The method of claim 1 wherein said genetic material is genomic DNA.

17. A method for determination of the presence or absence of a fetal aneuploidy in a maternal tissue sample comprising fetal and maternal genomic DNA, wherein the method comprises:

a) obtaining a mixture of fetal and maternal genomic DNA from said maternal tissue sample;

b) distributing random fragments from the mixture of fetal and maternal genomic DNA of step a to provide reaction samples containing a single genomic DNA molecule or amplification products of a single genomic DNA molecule;

c) conducting massively parallel DNA sequencing of the random fragments of genomic DNA in the reaction samples of step b) to determine the sequence of said random fragments;

d) identifying the chromosomes to which the sequences obtained in step c) belong;

e) analyzing the data of step d) to determine i) the number of copies of at least one first target chromosome in said mixture of fetal and maternal genomic DNA, wherein said at least one first target chromosome is presumed to be diploid in both the mother and the fetus, and ii) the number of copies of a second target chromosome in said mixture of fetal and maternal genomic DNA, wherein said second chromosome is suspected to be aneuploid in the fetus;

f) conducting a statistical analysis that compares the number of copies of said at least one first target chromosome to the number of copies of said second target chromosome; and

g) determining the presence or absence of a fetal aneuploidy from the results of the statistical analysis of step f).

18. The method of claim 17 wherein said maternal tissue sample is a maternal plasma sample.

19. The method of claim 17 wherein said reaction samples are contained in one of:

wells in a microtiter plate, aqueous phases in an emulsion, an area on an array surface, and reaction chambers in a microfluidic device.

20. The method of claim 17, wherein the sequences obtained in step c) are at least about 30 bp in length.

21. The method of claim 17 wherein said massively parallel DNA sequencing comprises attachment of said random fragments of genomic DNA to a planar optically transparent surface and solid phase amplification of the attached fragments to create a high density sequencing flow cell.

22. The method of claim 17 wherein said massively parallel sequencing is single molecule sequencing.