Direct molecular diagnosis of fetal aneuploidy

• US 9,719,140 B2
• Filed: 11/04/2013
• Issued: 08/01/2017
• Est. Priority Date: 12/22/2009
• 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: Fan, Hei-Mun Christina, Quake, Stephen R.
• Primary Examiner(s): MYERS, CARLA J
• Application Number:
  US14/071,279
• Publication Number:
  US 20140134613A1
• Time in Patent Office: 1,366 Days
• Field of Search: None
• CPC Class Codes: C12Q 1/6851 Quantitative amplification
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 2537/157 A reaction step characterised by the number of molecules incorporated or released
• CPC Class Codes: C12Q 2545/101 with an internal standard/control
• CPC Class Codes: C12Q 2561/113 Real time assay
• CPC Class Codes: C12Q 2565/629 being a microfluidic device
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: C12Q 2600/16 Primer sets for multiplex assays

Abstract

Methods and materials for detection of aneuploidy and other chromosomal abnormalities using fetal tissue are disclosed. Results can be obtained rapidly, without cell culture. The method uses digital PCR for amplification and detection of single target sequences, allowing an accurate count of a specific chromosome or chromosomal region. Specific polynucleic acid primers and probes are disclosed for chromosomes 1, 13, 18, 21, X and Y. These polynucleic acid sequences are chosen to be essentially invariant between individuals, so the test is not dependent on sequence differences between fetus and mother.

Claims

1. A method for detecting an abnormal copy number of a target fetal chromosome, comprising the steps of:

(a) obtaining a fetal sample containing genomic DNA including a target chromosome sequence and a reference chromosome sequence, said fetal sample being at least one of amniotic fluid, uncultured amniocytes and chorionic villus tissue;

(b) distributing said fetal sample into a plurality of reaction areas, each reaction area containing on average not more than one target chromosome sequence and not more than one reference chromosome sequence;

(c) detecting whether said target chromosome sequence is present in each of said plurality of reaction areas by;

(1) using primers to amplify a first ultraconserved element unique to said target chromosome sequence;

(2) binding a first detection probe to said amplified first ultraconserved element; and

(3) counting the number of reaction areas containing a bound first detection probe, to produce a target count;

(d) detecting whether said reference chromosome sequence is present in each of said plurality of reaction areas by;

(1) using primers to amplify a second ultraconserved element unique to said reference chromosome sequence;

(2) binding a second detection probe to said amplified second ultraconserved element; and

(3) counting the number of reaction areas containing a bound second detection probe, to produce a reference count; and

(e) obtaining sufficient numbers in said target count and said reference count to achieve statistical significance, wherein a statistically significant difference between said target count and said reference count indicates an abnormal number of the target fetal chromosome.

2. The method of claim 1 wherein said primers comprise sequences according to SEQ ID NO:

1 and SEQ ID NO;

2 and hybridize to reference chromosome 1.

3. The method of claim 1 wherein said primers comprise sequences according to SEQ ID NO:

3 and SEQ ID NO;

4 and hybridize to target chromosome 13.

4. The method of claim 1 wherein said primers comprise sequences according to SEQ ID NO:

19 and SEQ ID NO;

20 and hybridize to target chromosome 18.

5. The method of claim 1 wherein said primers comprise sequences according to SEQ ID NO:

7 and SEQ ID NO;

8 and hybridize to target chromosome 21.

6. The method of claim 5 wherein said primers comprise sequences according to SEQ ID NO:

1 and SEQ ID NO;

2 and hybridize to reference chromosome 1.

7. The method of claim 1 wherein said primers comprise sequences according to SEQ ID NO:

9 and SEQ ID NO;

10 and hybridize to target chromosome X.

8. The method of claim 1 wherein said primers comprise sequences according to SEQ ID NO:

11 and SEQ ID NO;

12 and hybridize to target chromosome Y.

9. The method of claim 1 wherein said detecting is detecting chromosomes 13, 18, and 21, and said reference chromosome is chromosome 1.

10. The method of claim 1 wherein the difference between said target count and said reference count further requires a confidence interval of at least 99% in order to achieve statistical significance.

11. A method for detecting an abnormal copy number of a target fetal chromosome, comprising the steps of:

(a) directly extracting genomic DNA from a sample, said DNA including target chromosome sequence and reference chromosome sequence, said sample being a fetal sample of at least one of amniotic fluid, uncultured amniocytes and chorionic villus tissue;

(b) distributing said fetal sample from step (a), concurrently into a plurality of reaction areas, each reaction area comprised in a microfluidic device and containing on average not more than one target chromosome sequence and not more than one reference chromosome sequence;

(c) adding amplification primers, wherein a first amplification primer set amplifies an ultraconserved element on a reference chromosome and a second amplification primer set amplifies an ultraconserved element on the target chromosome, and carrying out a plurality of amplification reactions concurrently in the plurality of reaction areas;

(d) adding a first probe having a first detectable label and allowing said first probe to bind to the ultraconserved element on said target chromosome sequence and a second probe having a second detectable label and allowing said second probe to bind to the ultraconserved element on said reference chromosome sequence;

(e) counting a number of reaction areas in the plurality of reaction areas that contain said target chromosome by detecting the first detectable label to produce a target count, and counting a number of reaction areas in the plurality of reaction areas that contain said reference chromosome by measuring the second detectable label to produce a reference count; and

(f) obtaining sufficient numbers in said target count and said reference count to achieve a predetermined statistical significance in any difference between said target count and said reference count;

wherein a statistically significant difference between said target count and said reference count indicates an abnormal number of the target fetal chromosome.

12. The method of claim 11 wherein said amplification reactions comprise heating and denaturing primers in the presence of a DNA polymerase.

13. The method of claim 11 wherein said amplification primers amplify regions of similar size in both the target chromosome sequence and reference chromosome sequence.

14. The method of claim 11 wherein the detectable label is fluorescent.

15. The method of claim 14 wherein a first probe having a first fluorescent label is used for detecting amplified target sequence and a second probe having a second fluorescent label is used for detecting amplified reference sequence.

16. The method of claim 15 wherein said primers hybridize to invariant sequences in the target chromosome and the reference chromosome.

17. The method of claim 15 wherein said first amplification primer set comprises multiple primers directed to a first single chromosome and said second amplification primer set comprises multiple primers directed to a second single chromosome.