Assay systems for genetic analysis

1. An assay for detecting a presence or absence of a fetal copy number variation (CNV) in a genomic region within a maternal sample comprising fetal and maternal cell-free DNA, the assay comprising the steps of:

(a) hybridizing a first set of fixed sequence oligonucleotides with the maternal and fetal cell-free DNA in the maternal sample, wherein:

(i) the first set of fixed sequence oligonucleotides comprises first and second fixed sequence oligonucleotides complementary to regions of 24 or more loci in a first genomic region,

(ii) the first and second fixed sequence oligonucleotides hybridize directly adjacent to each other at each locus or are separated by a gap of one or more nucleotides, and

(iii) the melting temperatures (T m s) of the first fixed sequence oligonucleotides of the first set of fixed sequence oligonucleotides vary in a range of two degrees centigrade;

(b) hybridizing a second set of fixed sequence oligonucleotides with the maternal and fetal cell-free DNA in the maternal sample, wherein:

(i) the second set of fixed sequence oligonucleotides comprises first and second fixed sequence oligonucleotides complementary to regions of 24 or more loci in a second genomic region,

(ii) the first and second fixed sequence oligonucleotides hybridize directly adjacent to each other at each locus or are separated by a gap of one or more nucleotides, and

(iii) the T m s of the first fixed sequence oligonucleotides of the second set of fixed sequence oligonucleotides vary in a range of two degrees centigrade;

(c) when the first and second fixed sequence oligonucleotides of each set are separated by a gap of one or more nucleotides,

(i) hybridizing bridging oligonucleotides with the maternal and fetal cell-free DNA in the maternal sample, wherein the bridging oligonucleotides are complementary to regions in the loci between the regions complementary to the first and second fixed sequence oligonucleotides of the first and second sets, to create adjacently hybridized oligonucleotides; or

(ii) extending the first and second fixed sequence oligonucleotides of each set with a polymerase to create adjacently hybridized oligonucleotides;

(d) ligating the first set of fixed sequence oligonucleotides, the first set of fixed sequence oligonucleotides and the bridging oligonucleotides, or the first set of extended fixed sequence oligonucleotides to create contiguous ligation products complementary to the loci in the first genomic region, and ligating the second set of fixed sequence oligonucleotides, the second set of fixed sequence oligonucleotides and bridging oligonucleotides, or the second set of extended fixed sequence oligonucleotides to create contiguous ligation products complementary to the loci in the second genomic region;

(e) amplifying each of the contiguous ligation products complementary to the loci in the first genomic region and each of the contiguous ligation products complementary to the loci in the second genomic region to create amplification products;

(f) detecting the amplification products;

(g) determining a relative frequency of the loci measured from the first and second genomic regions; and

(h) detecting the presence or absence of a fetal CNV when the relative frequency of the loci measured from the first genomic region that is different from the relative frequency of the loci measured from the second genomic region.

2. The assay of claim 1 , wherein at least one fixed sequence oligonucleotide of each of the first and second sets of fixed sequence oligonucleotides comprises a universal primer region.

3. The assay of claim 2 , wherein the first and second sets of fixed sequence oligonucleotides are hybridized prior to hybridization of the bridging oligonucleotides.

4. The assay of claim 1 , wherein unhybridized fixed sequence oligonucleotides are removed prior to introduction of the bridging oligonucleotides.

5. The assay of claim 1 , wherein the bridging oligonucleotides are hybridized simultaneously with the first and second sets of fixed sequence oligonucleotides.

6. The assay of claim 1 , wherein the hybridization products of the first and second sets of fixed sequence oligonucleotides and the complementary loci in the first and second genomic regions are isolated prior to hybridization of the bridging oligonucleotides.

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

8. The assay of claim 7 , 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.

9. The assay of claim 7 , 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 detection.

10. The assay of claim 1 , wherein the first or second oligonucleotide of each set of fixed sequence oligonucleotides comprises a sample index.

11. The assay of claim 1 , wherein the amplification products are detected using high throughput sequencing.

12. The assay of claim 11 , wherein the high throughput sequencing is nanopore-based sequencing.

13. The assay of claim 1 , wherein the first and second genomic regions are chromosomes.

14. The assay of claim 13 , wherein the copy number variation is selected from the group consisting of: Down Syndrome (Trisomy 21), Edwards Syndrome (Trisomy 18), Patau Syndrome (Trisomy 13), Klinefelter Syndrome (XXY), Triple X syndrome, XYY syndrome, Trisomy 8, Trisomy 16, Turner Syndrome, Robertsonian translocation, DiGeorge Syndrome, and Wolf-Hirschhorn Syndrome.

15. The assay of claim 13 , wherein the chromosome is selected from the group consisting of: chromosome 13, chromosome 18, chromosome 21, the X chromosome, and the Y chromosome.

16. The assay of claim 1 , wherein the copy number variation is an amplification or a deletion.

17. The assay of claim 16 , wherein the deletion is a deletion of chromosomal region 22q11.

18. The assay of claim 1 , further comprising determination of source contribution by a fetal source.