Method of identifying sequence variants using concatenation
Described herein, among other things, is a method of sequencing, comprising: concatenating a plurality of fragments of genomic DNA to produce concatenated DNA; sequencing the concatenated DNA to produce a plurality of sequence reads, wherein at least some of the sequence reads comprise: at least the sequence of the 3′ and/or 5′ ends of a fragment that corresponds to the locus of interest and sequence of one or both of the fragments that flank the fragment in the concatenated DNA; and grouping the sequence reads that corresponds to the locus of interest using, for each of the grouped sequence reads: the 3′ and/or 5′ end sequences; and/or the flanking sequence.
1. A method of sequencing, comprising:
(a) concatenating a plurality of molecules of cfDNA (cell-free DNA) to each other to produce concatenated cfDNA that comprises multiple molecules of the DNA joined together;
(b) fragmenting the concatenated DNA to produce fragments of concatenated DNA; and
(c) sequencing the fragments of concatenated DNA, or amplification products thereof, to produce a plurality of sequence reads.
2. The method of claim 1 , further comprising:
(d) grouping the sequence reads that correspond to a locus of interest using:
one or more end sequences of a fragment of the locus of interest; or
the flanking sequences of the fragment of the locus of interest,
wherein sequence reads that are grouped together have the same 3′ end, the same 5′ end and/or the same flaking sequences.
3. The method of claim 2 , further comprising:
(e) identifying a potential sequence variation in the locus of interest by analysis of a group of sequence reads.
4. The method of claim 2 , wherein:
step (d) further comprises grouping the sequence reads according to their orientation, wherein sequence reads that are derived from the top strand of a double-stranded molecule in the sample (a) are grouped together and sequence reads that are derived from the bottom strand of the same double-stranded molecule are grouped together;
and the method further comprises:
identifying potential sequence variation in a group of sequence reads that correspond to the top strand of a molecule; and
determining if the potential sequence variation is in any of the sequence reads that correspond to the bottom strand of the same molecule.
5. The method of claim 1 , wherein, in (a), the plurality of molecules are concatenated by ligation.
6. The method of claim 1 , wherein, in (a), the plurality of molecules are ligated to an adaptor and then concatenated by an overlap extension reaction that comprises overlapping the ligation products with one another.
7. The method of claim 1 , wherein, in (a) the plurality of molecules of cfDNA are ligated to one another via junction adaptors, to produce the concatenated DNA.
8. The method of claim 7 , wherein the plurality of molecules are A-tailed and the junction adaptors are T-tailed.
9. The method of claim 1 , wherein the method comprises, between steps (a) and (b), amplifying the concatenated DNA.
10. The method of claim 9 , wherein the amplifying is done by a whole genome amplification method.
11. The method of claim 1 , wherein the amplifying is done by fragmenting the concatenated DNA, adding adaptors to the fragments of concatenated DNA, and then amplifying the fragments of concatenated DNA by PCR.
12. The method of claim 11 , wherein the fragmenting and adding adaptors is done by a transposase.
13. The method of claim 1 , wherein the cDNA of (a) is obtained from a cancer patient.
14. The method of claim 1 , wherein the fragmenting of (b) is done by sonication, nebulization, or shearing.