Genotyping by next-generation sequencing

• US 9,951,384 B2
• Filed: 05/28/2015
• Issued: 04/24/2018
• Est. Priority Date: 01/13/2012
• Status: Active Grant

• Current Assignee: Data2Bio
• Original Assignee: Data2Bio
• Inventors: Schnable, Patrick S., Liu, Sanzhen, Wu, Wei
• Primary Examiner(s): Priest, Aaron A
• Application Number:
  US14/723,678
• Publication Number:
  US 20150344947A1
• Time in Patent Office: 1,062 Days
• Field of Search: None
• CPC Class Codes: C12N 15/1065 Preparation or screening of tagged libraries, e.g. tagged microorganisms by STM-mutagenesis, tagged polynucleotides, gene tags
• CPC Class Codes: C12N 15/1093 General methods of preparing gene libraries, not provided for in other subgroups
• CPC Class Codes: C12Q 1/6806 Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/683 involving restriction enzymes, e.g. restriction fragment length polymorphism [RFLP]
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 2521/301 Endonuclease
• CPC Class Codes: C12Q 2525/155 incorporating/generating a new priming site
• CPC Class Codes: C12Q 2525/191 incorporating an adaptor
• CPC Class Codes: C12Q 2535/122 Massive parallel sequencing
• CPC Class Codes: C12Q 2537/159 Reduction of complexity, e.g. amplification of subsets, removing duplicated genomic regions
• CPC Class Codes: C12Q 2565/514 characterised by the use of the arrayed oligonucleotides as identifier tags, e.g. universal addressable array, anti-tag or tag complement array

Abstract

Provided herein is technology relating to genotyping and particularly, but not exclusively, to methods for genotyping one or more organisms by genome sequencing.

Claims

1. A method for genotyping-by-sequencing a sample, the method comprising:

1) providing a first fully single-stranded oligonucleotide comprising a first primer binding site and a second fully single-stranded oligonucleotide comprising a second primer binding site;

2) ligating said first fully single-stranded oligonucleotide to the first ends of nucleic acid fragments produced by digesting nucleic acids from the sample with a restriction enzyme and ligating said second fully single-stranded oligonucleotide to the second ends of the nucleic acid fragments to produce a plurality of templates comprising single-stranded ends;

3) amplifying said templates using a first amplification primer that hybridizes to the first primer binding site or complement thereof and a second amplification primer that hybridizes to the second primer binding site or complement thereof to produce amplicons;

4) acquiring sequence reads from the amplicons; and

5) genotyping-by-sequencing the sample by determining a genotype of the sample using one or more sequence reads, wherein;

a) said first amplification primer comprises a 5′

portion and a 3′

portion, wherein;

1) said 5′

portion of said first amplification primer hybridizes to said first primer binding site or complement thereof; and

2) said 3′

portion of said first amplification primer hybridizes to one or more bases of nucleic acid fragments, said bases being adjacent to the first primer binding site in a subset of the plurality of templates; and

/or

b) said second amplification primer comprises a 5′

portion and a 3′

portion, wherein;

1) said 5′

portion of the second amplification primer hybridizes to said second primer binding site or complement thereof; and

2) said 3′

portion of said second amplification primer hybridizes to one or more bases of nucleic acid fragments, said bases being adjacent to the second primer binding site in a subset of the plurality of templates.

2. The method of claim 1 further comprising mapping one or more sequence reads to a reference sequence.

3. The method of claim 1 wherein the nucleic acids from the sample are digested with two different restriction enzymes.

4. The method of claim 1 wherein the first fully single-stranded oligonucleotide and/or the second fully single-stranded oligonucleotide comprises a common sequence, a unique sequence, and a sequence complementary to the single-stranded end produced by the restriction enzyme.

5. The method of claim 1 further comprising assembling a plurality of overlapping sequence reads.

6. The method of claim 1 wherein the first amplification primer comprises:

a) a 5′

portion that hybridizes to the first primer binding site or complement thereof; and

b) a 3′

portion comprising 1-3 nucleotides, said 3′

portion hybridizing to a subset of the plurality of templates.

7. The method of claim 1 further comprising synthesizing or providing an amplification primer comprising a 5′

portion adjacent to a 3′

portion, the 5′

portion comprising a sequence that hybridizes to the first primer binding site or complement thereof and the 3′

portion comprising 1 to 10 nucleotides appended to the 3′

end of the 5′

portion of the amplification primer.

8. The method of claim 1 wherein the first single-stranded oligonucleotide comprises a barcode and/or the second oligonucleotide comprises a barcode.

9. The method of claim 8 wherein the barcode of the first single-stranded oligonucleotide and/or the barcode of the second oligonucleotide identifies a subject and/or a sample that was the source of the nucleic acid.

10. The method of claim 1 wherein the first single-stranded oligonucleotide and the second oligonucleotide comprise the same nucleotide sequence.

11. The method of claim 1 wherein the first single-stranded oligonucleotide and the second oligonucleotide comprise different nucleotide sequences.

12. The method of claim 1 wherein the 3′

portion of the first amplification primer and/or the 3′

portion of the second amplification primer comprises 1-10 nucleotides.

13. The method of claim 1 wherein the amplifying produces amplicons from a subset of the plurality of templates, wherein each template of the subset comprises a nucleic acid fragment that comprises a portion that hybridizes to the 3′

portion of the first amplification primer and/or a portion that hybridizes to the 3′

portion of the second amplification primer.

14. The method of claim 1 further comprising ligating a third fully single-stranded oligonucleotide comprising the first primer binding site to the first ends of second nucleic acid fragments produced by digesting nucleic acids from a second sample with the restriction enzyme and ligating the second fully single-stranded oligonucleotide to the second ends of the second nucleic acid fragments from the second sample to produce a second plurality of templates;

mixing the second plurality of templates with the first plurality of templates;

genotyping-by-sequencing the first sample by determining a genotype of the first sample using one or more sequence reads, and genotyping-by-sequencing the second sample by determining a genotype of the second sample using one or more sequence reads.

15. A method for genotyping-by-sequencing a plurality of samples, the method comprising:

1) providing a first fully single-stranded oligonucleotide comprising a primer binding site and a first distinct barcode, a second fully single-stranded oligonucleotide comprising said primer binding site and a second distinct barcode, and a fully single-stranded common oligonucleotide;

2) ligating said first fully single-stranded oligonucleotide to the first ends of first nucleic acid fragments produced by digesting nucleic acids from a first sample with a restriction enzyme and ligating said fully single-stranded common oligonucleotide to the second ends of the first nucleic acid fragments from the first sample to produce a first plurality of templates comprising single-stranded ends;

3) ligating said second fully single-stranded oligonucleotide to the first ends of second nucleic acid fragments produced by digesting nucleic acids from a second sample with the restriction enzyme and ligating said fully single-stranded common oligonucleotide to the second ends of the second nucleic acid fragments from the second sample to produce a second plurality of templates comprising single-stranded ends;

4) amplifying said templates from a template mixture comprising the first plurality of templates mixed with the second plurality of templates using a first amplification primer comprising a 5′

portion that hybridizes to the primer binding site or complement thereof and a second amplification primer that hybridizes to the common oligonucleotide or complement thereof to produce amplicons, wherein said 5′

portion of said first amplification primer hybridizes to said primer binding site or complement thereof and a 3′

portion of said first amplification primer hybridizes to one or more bases of nucleic acid fragments, said bases being adjacent to the primer binding site in a subset of the plurality of templates;

5) acquiring sequence reads from the amplicons;

6) associating sequence reads comprising a sequence of the first barcode with the first sample and associating sequence reads comprising a sequence of the second barcode with the second sample; and

7) genotyping-by-sequencing the first sample by determining a genotype of the first sample using one or more sequence reads and genotyping-by-sequencing the second sample by determining a genotype of the second sample using one or more sequence reads.

16. The method of claim 15 wherein the first plurality of nucleic acids from the first sample are from a first subject and the second plurality of nucleic acids from the second sample are from a second subject.