Methods and systems for determining haplotypes and phasing of haplotypes
AssigneeIllumina Cambridge Limited
InventorsRoberto Rigatti, Jonathan Mark Boutell
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Abstract
The present disclosure provides methods and systems for determining and/or characterizing one or more haplotypes and/or phasing of haplotypes in a nucleic acid sample. In particular, the disclosure provides methods for determining a haplotype and/or phasing of haplotypes in a nucleic acid sample by incorporating synthetic polymorphisms into fragments of a nucleic acid sample and utilizing the synthetic polymorphisms in determining one or more haplotypes and/or phasing of haplotypes.
Claims20
A method for characterizing one or more haplotypes of a nucleic acid sample comprising:
- a) providing a pool of fragmented nucleic acids,
- b) introducing a plurality of synthetic polymorphisms in the fragmented nucleic acids of said pool to produce fragments comprising a plurality of synthetic polymorphisms,
- c) preparing a library of nucleic acid fragments that are shorter in length than the original pool of fragments comprising a plurality of modified nucleic acids,
- d) sequencing nucleic acid fragments in the library,
- e) aligning the synthetic polymorphisms of the sequenced nucleic acid fragments, and
- f) characterizing one or more haplotypes of the nucleic sample from the aligned synthetic polymorphisms of the sequenced fragments.
A method for determining the sequence of a nucleic acid sample comprising:
- a) providing a nucleic acid molecule having a plurality of nucleotides;
- b) modifying a plurality of the nucleotides in the nucleic acid molecule, thereby producing a modified nucleic acid molecule comprising natural and modified nucleotides, the modified nucleotides introducing a plurality of sequence patterns of the modified nucleotides that are distinguishable from one another into the nucleic acid molecule to produce the modified nucleic acid molecule;
- c) amplifying the modified nucleic acid molecule to produce a plurality of modified nucleic acid copies of a first length;
- d) fragmenting the amplified modified nucleic acid copies under conditions to produce a library of nucleic acid fragments of a second length, wherein individual nucleic acid fragments in the library have a region of sequence overlap with at least one other nucleic acid fragment in the library and wherein the region of sequence overlap comprises at least one individual sequence pattern of the plurality of sequence patterns;
- e) determining a sequence of the nucleic acid fragments of the library, and
- f) aligning the sequence of the nucleic acid fragments based on the locations of the individual patterns of the modified nucleotides in the regions of sequence overlap to determine the sequence of the nucleic acid sample based on said alignment.
A device for determining the sequence of a nucleic acid sample comprising:
- a sequencing instrument configured to sequence individual fragments of a modified nucleic acid molecule to generate sequence data;
- and
- a computer programmed to:
- receive the sequence data of the individual fragments of the modified nucleic acid molecule, the nucleic acid molecule comprising naturally occurring polymorphisms and a plurality of synthetic polymorphisms, the plurality of synthetic polymorphisms forming different patterns on the individual fragments;
- align a subset of the individual fragments having a same pattern of the different patterns;
- and
- assemble a sequence of the nucleic acid molecule based at least in part on the aligning.
Dependencies are inferred from the claim text.