Methods for targeted genomic analysis

1. A method for determining copy number of a specific genomic target region comprising:

(a) hybridizing a tagged genomic library with a multifunctional capture probe module to form a complex,

(i) wherein the multifunctional capture probe module selectively hybridizes to a specific genomic target region in the genomic library and wherein the multifunctional capture probe module comprises a tail portion comprising a PCR binding site,

(ii) wherein the tagged genomic library comprises genomic DNA ligated to a multifunctional adaptor module comprising a first region comprising a random nucleic acid tag sequence; a second region comprising a sample code sequence; and a third region comprising a tail portion comprising a PCR primer sequence, and

(iii) wherein the sample code sequence identifies the sample;

(b) isolating the tagged genomic library-multifunctional capture probe module complex from a);

(c) performing 3′-5′ exonuclease enzymatic processing on the isolated tagged genomic library-multifunctional capture probe module complex from b) using an enzyme with 3′-5′ exonuclease activity to remove the single stranded 3′ ends;

(d) performing a PCR reaction on the enzymatically processed complex from c) wherein a tail portion of the multifunctional capture probe module is replicated to generate a hybrid nucleic acid molecule, wherein the hybrid nucleic acid molecule comprises the genomic target region capable of hybridizing to the multifunctional capture probe module and a complement of the multifunctional capture probe module tail sequence;

(e) performing PCR amplification of the hybrid nucleic acid molecule in d); and

(f) quantitating the PCR reaction in e), wherein the quantitation comprises determination of copy number of the specific genomic target region.

2. The method of claim 1 , wherein steps a) through d) are repeated at least about twice and a sequence alignment is performed using the hybrid nucleic acid molecule sequences obtained from the at least two e) steps.

3. The method of claim 2 , wherein at least two different multifunctional capture probe modules are used in the at least two a) steps, wherein the at least two a) steps employ one multifunctional capture probe module each.

4. The method of claim 3 , wherein at least one multifunctional capture probe module hybridizes downstream of the genomic target region and at least one multifunctional capture probe module hybridizes upstream of the genomic target region.

5. A method for determining copy number of a specific genomic target region comprising:

(a) hybridizing a tagged genomic library with a multifunctional capture probe module to form a complex,

(i) wherein the multifunctional capture probe module selectively hybridizes to a specific genomic target region in the genomic library,

(ii) wherein the tagged genomic library comprises genomic DNA ligated to a multifunctional adaptor module comprising a first region comprising a random nucleic acid tag sequence; a second region comprising a sample code sequence; and

(iii) wherein the sample code sequence identifies the sample;

(b) isolating the tagged genomic library-multifunctional capture probe hybrid module complex from a);

(c) performing 5′ to 3′ DNA polymerase extension of the multifunctional capture probe on the complex from b) to replicate a region of the captured, tagged genomic target region that is 3′ of the multifunctional capture probe to generate a hybrid nucleic acid molecule, wherein the hybrid nucleic acid molecule comprises the multifunctional capture probe hybrid module and a complement of the region of the tagged genomic target region that is located in the 3′ direction from the location where the multifunctional capture probe hybrid module hybridizes to the genomic target region; and

(d) performing PCR amplification of the hybrid nucleic acid molecule in c); and

(e) quantitating the PCR reaction in d), wherein the quantitation comprises determination of copy number of the specific genomic target region.

6. The method of claim 5 , wherein steps a) through c) are repeated at least about twice and a sequence alignment of the hybrid nucleic acid molecules from the at least two d) steps.

7. The method of claim 6 , wherein at least two different multifunctional capture probe modules are used in the at least two a) steps, wherein the at least two a) steps employ one multifunctional capture probe module each.

8. The method of claim 7 , wherein at least one multifunctional capture probe module hybridizes downstream of the genomic target region and at least one multifunctional capture probe module hybridizes upstream of the genomic target region.

9. The method of claim 1 , wherein the random nucleic acid tag sequence is randomly selected from a pool of known nucleic acid tags.

10. The method of claim 5 , wherein the random nucleic acid tag sequence is randomly selected from a pool of known nucleic acid tags.