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US 2013/0184165 A1Published application
Genotyping by next-generation sequencing
AssigneeData2Bio
InventorsPatrick S. Schnable, Sanzhen Liu, Wei Wu
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Abstract
Provided herein is technology relating to genotyping and particularly, but not exclusively, to methods for genotyping one or more organisms by genome sequencing.
Claims14
A method for genotyping by sequencing, the method comprising:
- 1) digesting a nucleic acid with a restriction enzyme to produce a fragment;
- 2) ligating a single-stranded barcode oligonucleotide to the fragment to produce a template;
- 3) amplifying the template to produce an amplicon;
- and
- 4) sequencing the amplicon to produce a sequence read.
2 more elements
A method for genotyping by sequencing, the method comprising:
- 1) providing a first plurality of nucleic acids from a first subject;
- 2) providing a second plurality of nucleic acids from a second subject;
- 3) digesting the first plurality of nucleic acids with a restriction enzyme to produce a first plurality of fragments;
- 4) digesting the second plurality of nucleic acids with the restriction enzyme to produce a second plurality of fragments;
- 5) ligating a first single-stranded barcode oligonucleotide to each fragment of the first plurality of fragments to produce a first plurality of templates;
- 6) ligating a second single-stranded barcode oligonucleotide to each fragment of the second plurality of fragments to produce a second plurality of templates;
- 7) mixing the first plurality of templates and the second plurality of templates to produce a template pool;
- 8) amplifying a subset of the template pool using a target specific primer to produce a plurality of amplicons;
- and
- 9) sequencing the plurality of amplicons to produce a plurality of sequence reads;
- 10) deconvoluting the sequence reads using a first sequence of the first barcode oligonucleotide and a second sequence of the second barcode oligonucleotide.
8 more elements
A composition comprising a single-stranded barcode oligonucleotide.
A composition comprising a nucleic acid, wherein the nucleic acid sequence comprises a sequence of a single-stranded barcode oligonucleotide, a sequence of a target site, and a sequence of a second single-stranded oligonucleotide.
Dependencies are inferred from the claim text.