Assay systems for genetic analysis

1. A method for simultaneous detection of the presence or absence of a fetal copy number variation (CNV) of a genomic region and presence or absence of one or more fetal polymorphisms in a maternal plasma or serum sample comprising fetal and maternal cell-free DNA using a single assay, comprising the steps of:

(a) hybridizing at least 200 and less than 2000 first sets of two fixed sequence oligonucleotides to the fetal and maternal cell-free DNA in the maternal plasma or serum sample in a first reaction, wherein the first sets of two fixed sequence oligonucleotides are complementary to a locus in a first maternal and fetal genomic region from a first chromosome or a portion of the first chromosome without regard to polymorphisms in the locus, wherein at least one of the fixed sequence oligonucleotides comprises a universal primer region, wherein the two fixed sequence oligonucleotides of each first set hybridize immediately adjacent to each other, wherein the maternal plasma or serum sample comprises at least 5% and less than 25% fetal DNA, and wherein the melting temperatures (T m s) of first fixed sequence oligonucleotides of each of the first sets of two fixed sequence oligonucleotides vary in range of two degrees centigrade;

(b) hybridizing at least 200 and less than 2000 second sets of two fixed sequence oligonucleotides to the fetal and maternal cell-free DNA in the first reaction, wherein the second sets of two fixed sequence oligonucleotides are complementary to a locus in a second maternal and fetal genomic region from a second chromosome or a portion of the second chromosome without regard to polymorphisms in the locus, wherein at least one of the fixed sequence oligonucleotides comprises a universal primer region, wherein the two fixed sequence oligonucleotides of each second set hybridize immediately adjacent to each other and wherein the T m s of first fixed sequence oligonucleotides of each of the second sets of two fixed sequence oligonucleotides vary in a range of two degrees centigrade;

(c) hybridizing a third set of two fixed sequence oligonucleotides to the fetal and maternal cell-free DNA in the first reaction, wherein the third set of two fixed sequence oligonucleotides is complementary to regions on a maternal and fetal locus in a polymorphic region, wherein at least one of the fixed sequence oligonucleotides comprises a universal primer region, and wherein the fixed sequence oligonucleotides of the third set hybridize immediately adjacent to each other;

(d) ligating in a multiplexed manner the hybridized oligonucleotides of the first, second and third sets of two fixed sequence oligonucleotides to create contiguous ligation products complementary to the loci in the first genomic region, the second genomic region, and the polymorphic region;

(e) amplifying in a multiplexed manner the contiguous ligation products using primers complementary to the universal primer regions of the first, second and third sets of two fixed sequence oligonucleotides to create amplification products;

(f) isolating the amplification products to create isolated amplification products;

(g) sequencing in a multiplexed, high throughput manner the isolated amplification products an average of at least 100 times, wherein the sequenced isolated amplification products are representative of the DNA content of the genomic regions in the maternal sample;

(h) detecting the presence or absence of a fetal polymorphism in the polymorphic region; and

(i) detecting the presence or absence of a fetal CNV by observing a statistical variation in the quantity of total sequence reads from isolated amplification products of the first genomic region and the quantity of total sequence reads from isolated amplification products of the second genomic region.

2. The method of claim 1 , wherein the universal primer regions are used in sequence determination of the amplification products.

3. The method of claim 1 , wherein one or more of the sets of fixed sequence oligonucleotides comprise precircle probes.

4. The method of claim 1 , wherein the isolated amplification products are further amplified to create identical copies of all or a portion of the amplification products prior to high throughput sequence determination.

5. The method of claim 1 , wherein the isolated amplification products are further amplified to create identical copies of molecules complementary to all or a portion of the amplification products prior to high throughput sequence determination.

6. The method of claim 1 , wherein the loci interrogated for copy number are different from the loci interrogated for polymorphisms.

7. The method of claim 1 , wherein the first and second genomic regions are each single genes.

8. A method for determining the likelihood of a fetal copy number variation (CNV) of a genomic region and presence or absence of one or more fetal polymorphisms in a maternal plasma or serum sample comprising fetal and maternal cell-free DNA using a single assay, comprising the steps of:

(a) hybridizing at least 200 and less than 2000 first sets of two fixed sequence oligonucleotides to the fetal and maternal cell-free DNA in the maternal plasma or serum sample in a first reaction, wherein the first sets of two fixed sequence oligonucleotides are complementary to a region on a locus in a first maternal and fetal genomic region from a first chromosome or a portion of the first chromosome without regard to polymorphisms in the locus, wherein at least one of the fixed sequence oligonucleotides comprises a universal primer region, wherein the two fixed sequence oligonucleotides of each first set hybridize immediately adjacent to each other, wherein the maternal plasma or serum sample comprises at least 5% and less than 25% fetal DNA, and wherein the melting temperatures (T m s) of first fixed sequence oligonucleotides of each of the first sets of two fixed sequence oligonucleotides vary in range of two degrees centigrade;

(b) hybridizing at least 200 and less than 2000 second sets of two fixed sequence oligonucleotides to the fetal and maternal cell-free DNA in the first reaction, wherein the second sets of fixed sequence oligonucleotides are complementary to a region on a locus in a second maternal and fetal genomic region from a second chromosome or a portion of the second chromosome without regard to polymorphisms in the locus, wherein at least one of the fixed sequence oligonucleotides comprises a universal primer region, wherein the two fixed sequence oligonucleotides of each second set hybridize immediately adjacent to each other, and wherein the T m s of first fixed sequence oligonucleotides of each of the second sets of two fixed sequence oligonucleotides vary in a range of two degrees centigrade;

(c) hybridizing a third set of two fixed sequence oligonucleotides to the fetal and maternal cell-free DNA in the first reaction, wherein the third set of fixed sequence oligonucleotides is complementary to regions on a maternal and fetal locus in a polymorphic region, wherein at least one of the fixed sequence oligonucleotides comprises a universal primer region, and wherein the fixed sequence oligonucleotides of the third set hybridize immediately adjacent to each other;

(d) ligating in a multiplexed manner the hybridized oligonucleotides to create contiguous ligation products complementary to the loci in the first genomic region, the second genomic region, and the polymorphic region;

(e) amplifying in a multiplexed manner the contiguous ligation products using primers complementary to the universal primer regions to create amplification products;

(f) isolating the amplification products to create isolated amplification products;

(g) sequencing in a multiplexed high throughput manner the isolated amplification products an average at least 100 times producing total sequence reads;

(h) detecting a likelihood of a fetal CNV using the quantified total sequence reads corresponding to the first genomic region and the quantified total sequence reads corresponding to the second genomic region; wherein a likelihood of a fetal CNV is indicated if the quantified total sequence reads from the loci of first and second genomic regions statistically vary; and

(i) detecting the presence or absence of a fetal polymorphism in the polymorphic region from the sequence reads of the isolated amplification products from the locus of the polymorphic region.

9. The method of claim 8 , wherein the universal primer regions are used in high throughput sequence determination of the isolated amplification products.

10. The method of claim 8 , wherein one or more of the sets of fixed sequence oligonucleotides comprise a precircle probe.

11. The method of claim 8 , wherein the isolated amplification products are isolated as individual molecules prior to high throughput sequence determination.

12. The method of claim 11 , 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 high throughput sequence determination.

13. The method of claim 11 , wherein the individual isolated amplification products are further amplified to create identical copies of molecules complementary to all or a portion of the individual amplification products prior to high throughput sequence determination.

14. The method of claim 8 , wherein the loci interrogated for copy number are different from the loci interrogated for polymorphisms.

15. The method of claim 8 , wherein the first and second genomic regions are each single genes.