Method of identifying sequence variants using concatenation
AssigneeOxford Nanopore Technologies PLC
InventorsRobert Osborne, Esther Musgrave-Brown
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Abstract
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.
Claims20
A method of sequencing, comprising:
- (a) concatenating a plurality of fragments of genomic DNA to each other to produce concatenated DNA that comprises multiple fragments of the genomic DNA joined together;
- (b) sequencing fragments of the concatenated DNA, or amplification products thereof, to produce a plurality of sequence reads, wherein at least some of the sequence reads comprise:
- (i) at least the sequence of the 3′ and/or 5′ ends of a fragment of a locus of interest;
- and
- (ii) sequence of one or both of the fragments that flank the fragment of (b)(i) in the concatenated DNA of (a);
- and
- (c) grouping the sequence reads that correspond to the locus of interest using, for each of the grouped sequence reads:
- (i) the 3′ and/or 5′ end sequences of (b)(i);
- and/or
- (ii) the flanking sequence of (b)(ii),
- wherein sequence reads that are grouped together have the same 3′ and/or 5′ end or flanking sequence;
- (d) determining which groups of sequence reads of (c) contain a potential sequence variation for the locus of interest;
- and
- (e) calculating a probability that the potential sequence variation is a genuine mutation or an artifact using:
- (i) the number of reads in the group that contain the potential sequence variation,
- (ii) the number of groups that contain the potential sequence variation, and
- (iii) the total number of groups corresponding to the locus of interest.
Dependencies are inferred from the claim text.