Multiplex nucleic acid detection methods

1. A method for multiplex ligation-dependent probe amplification comprising:

(a) providing a sample tissue to query at least 100 different target nucleic acids;

(b) providing a plurality of different probe sets for each of the at least 100 different target nucleic acids, wherein each probe set comprises:

a first locus specific probe comprising a first adapter sequence and a first target specific portion; and

a second locus specific probe comprising a second adapter sequence, and a second target specific portion adjacent to the first target specific portion;

(c) hybridizing the plurality of different probe sets to the at least 100 different target sequences to form at least 100 different hybridization complexes;

(d) ligating, in a single vessel or tube, the at least 100 different hybridization complexes to form at least 100 different ligated probes;

(e) amplifying the at least 100 different ligated probes to form at least 100 different amplicons, wherein (i) the amplifying step is carried out with a first universal primer comprising a region complementary to the first adapter sequence and a second universal primer comprising a region complementary to the second adapter sequence, and (ii) the amplifying of the at least 100 different ligated probes is carried out in the single vessel or tube; and

(f) detecting the at least 100 different amplicons in a detection system, independently of the length, by sequencing each of the at least 100 different amplicons wherein said at least 100 different ligated probes of step (d) are directly amplified in step (e) without purification.

2. The method of claim 1 , further comprising determining the copy number for each of the at least 100 different target nucleic acids.

3. The method of claim 1 , wherein the at least 100 different target nucleic acids is at least 1000 different target nucleic acids, the at least 100 different hybridization complexes is at least 1000 different hybridization complexes, the at least 100 different ligated probes is at least 1000different ligated probes, and the at least 100 different amplicons is at least 1000 different amplicons.

4. The method of claim 1 , wherein the at least 100 different target nucleic acids is in a range from about 100 to about 500 target nucleic acids, the at least 100 different hybridization complexes is in a range from about 100 to about 500 different hybridization complexes, the at least 100 different ligated probes is in a range from about 100 to about 500 different ligated probes, and the at least 100 different amplicons is in a range from about 100 to about 500 different amplicons.

5. The method of claim 1 , wherein the at least 100 different target nucleic acids is in a range from about 100 to about 1,000 target nucleic acids, the at least 100 different hybridization complexes is in a range from about 100 to about 1,000 different hybridization complexes, the at least 100 different ligated probes is in a range from about 100 to about 1,000 different ligated probes, and the at least 100 different amplicons is in a range from about 100 to about 1,000 different amplicons.

6. The method of claim 1 , wherein the at least 100 different target nucleic acids is in a range from about 100 to about 10 8 target nucleic acids, the at least 100 different hybridization complexes is in a range from about 100 to about 10 8 different hybridization complexes, the at least 100 different ligated probes is in a range from about 100 to about 10 8 different ligated probes, and the at least 100 different amplicons is in a range from about 100 to about 10 8 different amplicons.

7. The method of claim 1 , wherein at least one of the first universal primer and the second universal primer further comprises an indexing sequence.

8. The method of claim 1 , wherein the detection system comprises sequencing by synthesis.

9. The method of claim 8 , wherein the detection system comprises a fluidics handling system configured to perform cycles of sequencing by synthesis on an array comprising the at least 100 different amplicons, the detection system configured to direct radiation from a source to the array and to direct fluorescence emission from the array to a camera, and a system control interface configured to automatically modify the detection system to increase the exposure level of the radiation directed to the array and detect fluorescence emission from the array to the camera at the increased exposure.

10. The method of claim 1 , wherein the method comprises detecting a single nucleotide polymorphism.

11. The method of claim 1 , wherein the method comprises determining a degree of methylation of at least a portion of the at least 100 different target nucleic acids.

12. The method of claim 1 , wherein the method comprises quantifying a target mRNA.

13. The method of claim 1 , wherein the hybridizing of (c), the ligating of (d) and the amplifying of (e) are carried out in the single vessel or tube.

14. A method for multiplex ligation-dependent probe amplification comprising:

(a) contacting at least 100 different target nucleic acids with at least 100 different probe sets for each of the different target nucleic acids, wherein each probe set comprises,

(i) a first locus specific probe comprising a first adapter sequence and a first target specific portion, and

(ii) a second locus specific probe comprising a second adapter sequence, and a second target specific portion adjacent to the first target specific portion,

wherein the probe sets hybridize to the target sequences thereby forming at least 100 different hybridization complexes in a single mixture, wherein the at least 100 different hybridization complexes comprise the at least 100 different target nucleic acids and the at least 100 different probe sets;

(b) ligating the at least 100 different hybridization complexes in the mixture, thereby providing at least 100 different ligated probes comprised in the mixture;

(c) amplifying the at least 100 different ligated probes in the mixture to form at least 100 different amplicons, wherein the amplifying is carried out with a first universal primer comprising a region complementary to the first adapter sequence and a second universal primer comprising a region complementary to the second adapter sequence; and

(d) detecting the at least 100 different amplicons in the mixture in a detection system by sequencing each of the at least 100 different amplicons wherein said at least 100 different ligated probes of step (b) are directly amplified in step (c) without purification.

15. The method of claim 14 , wherein the detection system comprises sequencing by synthesis.