Assay systems for genetic analysis

1. A method of detecting a presence or absence of copy number variation (CNV) in a mixed sample from a single subject, said mixed sample comprising nucleic acids from at least two sources comprising a major source and a minor source, the method comprising:

a) hybridizing at least 24 first sets of two fixed sequence oligonucleotides to the nucleic acids in the mixed sample, wherein each first set of two fixed sequence oligonucleotides is complementary to a locus in a first region of interest, each first set of two fixed sequence oligonucleotides comprising universal primer regions, and wherein melting temperatures (T m s) of first fixed sequence oligonucleotides of each first set of two fixed sequence oligonucleotides vary in a range of two degrees centigrade;

b) hybridizing at least 24 second sets of two fixed sequence oligonucleotides to the nucleic acids in the mixed sample, wherein each second set of two fixed sequence oligonucleotides is complementary to a locus in a second region of interest, each second set of two fixed sequence oligonucleotides comprising universal primer regions, and wherein T m s of first fixed sequence oligonucleotides of each second set of two fixed sequence oligonucleotides vary in a range of two degrees centigrade;

c) extending one of said hybridized fixed sequence oligonucleotides of each first set of two fixed sequence oligonucleotides with a polymerase between the hybridized oligonucleotides of each first set of two fixed sequence oligonucleotides to produce adjacently hybridized fixed sequence oligonucleotides and extending one of said hybridized fixed sequence oligonucleotides of each second set of two fixed sequence oligonucleotides with a polymerase between the hybridized oligonucleotides of each second set of two fixed sequence oligonucleotides to produce adjacently hybridized fixed sequence oligonucleotides;

d) ligating the adjacently hybridized fixed sequence oligonucleotides of each first set of two fixed sequence oligonucleotides to create contiguous ligation products and ligating the adjacently hybridized fixed sequence oligonucleotides of each second set of two fixed sequence oligonucleotides to create contiguous ligation products;

e) amplifying the contiguous ligation products using the universal primer regions on each first and second sets of two fixed sequence oligonucleotides to produce amplification products;

f) detecting the amplification products; and

g) detecting a copy number variation of the first region of interest relative to the second region of interest.

2. The method of claim 1 , wherein the subject comprises a pregnant female such that the nucleic acids of the major source comprise maternal nucleic acids and the nucleic acids of the minor source comprise fetal nucleic acids.

3. The method of claim 1 , wherein the subject comprises an individual having normal cells and cancerous cells such that the nucleic acids of the major source comprise nucleic acids of the normal cells and the nucleic acids of the minor source comprise nucleic acids of the cancerous cells.

4. The method of claim 1 , wherein the subject comprises a transplant patient such that the nucleic acids of the major source comprise nucleic acids of the patient and the nucleic acids of the minor source comprise nucleic acids of a donor organ, and wherein said copy number variation is detected in said major source or said minor source.

5. The method of claim 1 , wherein the subject comprises an individual infected with an organism such that the nucleic acids of the major source comprise nucleic acids of the individual and the nucleic acids of the minor source comprise nucleic acids of the infectious organism, and wherein said copy number variation is detected in said major source or said minor source.

6. The method of claim 1 , wherein each locus in the second region of interest comprises one or more polymorphisms.

7. The method of claim 1 , wherein the first region of interest and the second region of interest are on different chromosomes.

8. The method of claim 1 , wherein at least one locus does not comprise a polymorphism.

9. The method of claim 1 , wherein one or both sets of the fixed sequence oligonucleotides comprises at least one index.

10. The method of claim 9 , wherein the amplification products are detected by sequencing the at least one index.

11. The method of claim 9 , wherein the at least one index comprises a locus index.

12. The method of claim 9 , wherein the at least one index comprises a sample index.

13. The method of claim 1 , wherein the amplification products are detected by high throughput sequencing.

14. The method of claim 1 , wherein the amplification products are detected on an array.

15. The method of claim 1 , wherein one or both sets of fixed sequence oligonucleotides comprises an oligonucleotide 5′ of each locus, an oligonucleotide 3′ of each locus, and a bridging oligonucleotide.

16. The method of claim 1 , wherein one or more bridging oligonucleotides is added prior to the step of extension.

17. The method of claim 1 , wherein the amplification products are isolated as individual molecules prior to detection.

18. The method of claim 17 , wherein the individual isolated amplification products are further amplified to create identical copies of all or a portion of the individual amplification products prior to detection.

19. A method of detecting a presence or absence of genetic variation in a mixed sample from a single subject, said mixed sample comprising nucleic acids from at least two sources comprising a major source and a minor source, the method comprising:

a) hybridizing at least 24 sets of two fixed sequence oligonucleotides to the nucleic acids in the mixed sample, wherein each set of two fixed sequence oligonucleotides is complementary to a polymorphic locus in a region of interest, each set of two fixed sequence oligonucleotides comprising universal primer regions, and each locus in the region of interest having different genotypes in the major source and the minor source, and wherein T m s of first fixed sequence oligonucleotides of each set of two fixed sequence oligonucleotides vary in a range of two degrees centigrade;

b) extending one of said hybridized two fixed sequence oligonucleotides of each set with a polymerase between the hybridized oligonucleotides of the set to produce adjacently hybridized fixed sequence oligonucleotides;

c) ligating the adjacently hybridized oligonucleotides to create contiguous ligation products complementary to the locus;

d) amplifying the contiguous ligation products using the universal primer regions on the two fixed sequence oligonucleotides of each set of fixed sequence oligonucleotides to produce amplification products;

e) detecting the amplification products; and

f) detecting a presence or absence of genetic variation in the locus of interest between the major and minor sources from the detected amplified products.