Assays for single molecule detection and use thereof

1. A method of detecting a genetic variation in a fetus comprising:

a) contacting a first and a second probe set to a sample comprising a mixture of genetic material derived from the fetus and from a mother of the fetus, wherein

(i) the first probe set comprises a first labeling probe, and a first tagging probe comprising an affinity tag, wherein the affinity tag comprises a nucleic acid sequence, and the first labeling probe hybridizes adjacent to the first tagging probe on a first nucleic acid region of interest, and

(ii) the second probe set comprises a second labeling probe, and a second tagging probe comprising the affinity tag, wherein the second labeling probe hybridizes adjacent to the second tagging probe on a second nucleic acid region of interest;

b) ligating the first labeling probe to the first tagging probe thereby providing a first ligated probe set, and ligating the second labeling probe to the second tagging probe, thereby providing a second ligated probe set;

c) amplifying the first and second ligated probe sets to form first and second amplified ligated probe sets, respectively, wherein,

(i) the first ligated probe set is amplified using a first primer that hybridizes to the first labeling probe, or to a complement of the first labeling probe, and comprises a first label, and a second primer that hybridizes to the first tagging probe, or to a complement of the first tagging probe, wherein the first amplified probe set comprises the first label and the affinity tag, or a complement of the affinity tag, and

(ii) the second ligated probe set is amplified using a third primer that hybridizes to the second labeling probe, or to a complement of the second labeling probe, and comprises a second label, and the second primer, wherein the second primer hybridizes to the second tagging probe, or to a complement of the second tagging probe, wherein the second amplified probe set comprises the second label and the affinity tag, or a complement of the affinity tag, and the first and second labels are different; and

d) immobilizing the affinity tag or a complement of the affinity tag, of the first and second amplified ligated probe sets to a first member of an array having a pre-defined location on the array;

e) counting a number of individual labeled molecules of the first amplified ligated probe set immobilized on the first member thereby providing a first count, and counting a number of individual labeled molecules of the second amplified ligated probe set immobilized on the first member thereby providing a second count, wherein each of the first and the second labels are individually optically resolvable on the first member; and

f) determining a presence or absence of the genetic variation in the fetus according to at least the first count and the second count.

2. The method of claim 1 , wherein the first labeling probe comprises a first primer binding site, the first and second tagging probes comprise a second primer binding site, and the second labeling probe comprises a third primer binding site.

3. The method of claim 2 , wherein the first primer hybridizes to the first primer binding site, or to a complement of the first primer binding site, the second primer hybridizes to the second primer binding site, or to a complement of the second primer binding site, and the third primer hybridizes to the third primer binding site, or to a complement of the third primer binding site.

4. The method of claim 1 , wherein the first nucleic acid region of interest comprises a locus on a first chromosome and the second nucleic acid region of interest comprises a locus on a second chromosome, different than the first chromosome.

5. The method of claim 4 , wherein the genetic variation is a copy number variation.

6. The method of claim 4 , wherein the genetic variation is an aneuploidy.

7. The method of claim 1 , wherein (d) further comprises immobilizing the affinity tag of a third amplified ligated probe set comprising the first label to the first member of the array, and immobilizing the affinity tag of a fourth amplified ligated probe set comprising the second label to the first member of the array, wherein the third amplified ligated probe set is different than the first amplified ligated probe set and the fourth amplified ligated probe set is different than the second amplified ligated probe set.

8. The method of claim 7 , wherein the third amplified ligated probe set comprises a nucleic acid sequence complementary to a third nucleic acid region of interest, different than the first or the second nucleic acid region of interest, and the fourth amplified ligated probe set comprises a nucleic acid sequence complementary to a fourth nucleic acid region of interest, different than the first, the second or the third nucleic acid region of interest.

9. The method of claim 1 , wherein the array comprises a second member having a different pre-defined location on the array, the second member comprising an immobilized third amplified ligated probe set comprising a second affinity tag and a third label, and an fourth amplified ligated probe set comprising the second affinity tag and a fourth label, different than the third label, wherein the third amplified ligated probe set comprises a nucleic acid sequence complementary to a third nucleic acid region of interest, different than the first or the second nucleic acid region of interest, and the fourth amplified ligated probe set comprises a nucleic acid sequence complementary to a fourth nucleic acid region of interest, different than the first, the second or the third nucleic acid region of interest, and the determining of (e) further comprises counting a number of individual labeled molecules of the third amplified ligated probe set immobilized on the second member thereby providing a third count, and counting a number of individual labeled molecules of the fourth amplified ligated probe set immobilized on the second member thereby providing a first count, and determining the presence or absence of the genetic variation in the fetus is determined according to at least the first, second, third and fourth counts.

10. The method of claim 1 , wherein the method further comprises comparing the first count and the second count to determine a proportion of the genetic material in the sample derived from the fetus relative to the genetic material in the sample derived from the mother.

11. The method of claim 1 , wherein the immobilizing of (d) comprises hybridizing the affinity tag, or a complement of the affinity tag, to a nucleic acid sequence located on the first member of the array.

12. The method of claim 1 , wherein a portion of the first labeling probe does not hybridize to the first nucleic acid region of interest or wherein a portion of the first tagging probe does not hybridize to the first nucleic acid region of interest.

13. The method of claim 1 , wherein a portion of the second labeling probe does not hybridize to the second nucleic acid region of interest or wherein a portion of the second tagging probe does not hybridize to the second nucleic acid region of interest.

14. A method of detecting a genetic variation in a fetus comprising:

a) contacting a first and a second probe set to a sample comprising a mixture of genetic material derived from the fetus and derived from a mother of the fetus, wherein

(i) the first probe set comprises a first labeling probe, and a first tagging probe comprising an affinity tag, wherein the affinity tag comprises a nucleic acid sequence, and the first labeling probe hybridizes adjacent to the first labeling probe at a first allele of a first nucleic acid region of interest, and

(ii) the second probe set comprises a second labeling probe, and a second tagging probe comprising the affinity tag, wherein the second labeling probe hybridizes adjacent to the second labeling probe at a second allele of the first nucleic acid region of interest;

b) ligating the first labeling probe to the first tagging probe, thereby providing a first ligated probe set, and ligating the second labeling probe to the second tagging probe, thereby providing a second ligated probe set;

c) amplifying the first and second ligated probe sets to form first and second amplified ligated probe sets, respectively, wherein,

(i) the first ligated probe set is amplified using a first primer that hybridizes to the first labeling probe, or to a complement of the first labeling probe, and comprises a first label, and a second primer that hybridizes to the first tagging probe, or to a complement of the first tagging probe, wherein the first amplified probe set comprises the first label and the affinity tag, or a complement of the affinity tag, and

(ii) the second ligated probe set is amplified using a third primer that hybridizes to the second labeling probe, or to a complement of the second labeling probe, and comprises a second label, and the second primer, wherein the second primer hybridizes to the second tagging probe, or to a complement of the second tagging probe, wherein the second amplified probe set comprises the second label and the affinity tag, or a complement the affinity tag, and the first and second labels are different; and

d) immobilizing the affinity tag, or a complement of the affinity tag, of the first and second amplified ligated probe sets to a first member of an array having a pre-defined location on the array;

e) counting a number of individual labeled molecules of the first amplified ligated probe set immobilized on the first member thereby providing a first count, and counting a number of individual labeled molecules of the second amplified ligated probe set immobilized on the first member thereby providing a second count, wherein each of the first and the second labels are individually optically resolvable on the first member; and

f) determining a presence or absence of the genetic variation in the fetus according to at least the first count and the second count.

15. The method of claim 14 , wherein the first labeling probe comprises a first primer binding site, the first and second tagging probes comprise a second primer binding site, and the second labeling probe comprises a third primer binding site.

16. The method of claim 15 , wherein the first primer hybridizes to the first primer binding site, or to a complement of the first primer binding site, the second primer hybridizes to the second primer binding site, or to a complement of the second primer binding site, and the third primer hybridizes to the third primer binding site, or to a complement of the third primer binding site.

17. The method of claim 14 , wherein the genetic variation is a single nucleotide polymorphism.

18. The method of claim 14 , wherein the method further comprises comparing the first count and the second count to determine a proportion of the genetic material in the sample derived from the fetus relative to the genetic material in the sample derived from the mother according to at least the first count and the second count.

19. The method of claim 14 , wherein the first tagging probe and the second tagging probe are the same.

20. The method of claim 14 , wherein a portion of the first labeling probe does not hybridize to the first nucleic acid region of interest or wherein a portion of the first tagging probe does not hybridize to the first nucleic acid region of interest.

21. The method of claim 14 , wherein a portion of the second labeling probe does not hybridize to the first nucleic acid region of interest or wherein a portion of the second tagging probe does not hybridize to the second nucleic acid region of interest.