Probe set for analyzing a DNA sample and method for using the same
This disclosure provides, inter alia, a probe system probe system for analyzing a nucleic acid sample. In some embodiments, the probe system may comprise: a set of identifier oligonucleotides of sequence B, a set of splint oligonucleotides of formula X′-A′-B′-Z′, wherein sequence A′ is complementary to a genomic fragment and sequence B′ is complementary to at least one member of the set of identifier oligonucleotides, and one or more probe sequences comprising X and Z. Each splint oligonucleotide is capable of hybridizing to the probe sequences, a member of the set of identifier oligonucleotides and a genomic fragment, thereby producing a ligatable complex of formula X-A-B-Z. The probe system can be used to identify a chromosome aneuploidy in cell free DNA, for example.
1. A ligatable nucleic acid complex of formula X-A-B-Z or X-B-A-Z, wherein, in the complex:
sequences A and B are in separate molecules,
sequences X, A, B and Z are ligatably adjacent to one another and held in position by a splint oligonucleotide,
sequence A is a target fragment of a genome,
sequence B identifies the locus from which the adjacent sequence A is derived but is not from the locus, and
the splint oligonucleotide is of formula X′-A′-B′-Z′ or X′-B′-A′-Z′.
2. The ligatable complex of claim 1 , wherein sequence A is a target fragment of the human genome.
3. The ligatable complex of claim 1 , wherein the target fragment is strand of restriction fragment.
4. The ligatable complex of claim 1 , wherein sequence B identifies a region on a chromosome.
5. The ligatable complex of claim 1 , wherein sequence B identifies a particular chromosome arm.
6. The ligatable complex of claim 1 , wherein sequence B identifies a particular chromosome.
7. The ligatable complex of claim 1 , wherein sequence B indicates that the adjacent sequence A is from chromosome 21.
8. The ligatable complex of claim 1 , wherein the complex is a circular ligatable complex of formula X-A-B-Z-Y, where sequence Y joins sequences X and Z.
9. The ligatable complex of claim 1 , wherein the complex is linear.
10. The ligatable complex of claim 1 , wherein the splint oligonucleotide is of formula X′-A′-B′-Z′ or X′-B′-A′-Z′ and wherein sequence A′ is in the range of 8 to 80 nucleotides.
11. The ligatable complex of claim 1 , wherein the splint oligonucleotide is of formula X′-A′-B′-Z′ or X′-B′-A′-Z′ and wherein sequence B′ is in the range of 8 to 30 nucleotides in length.
12. The ligatable complex of claim 1 , wherein, sequences X and Z are independently in the range of 8 to 30 nucleotides in length.