High throughput screening of mutagenized populations

• US 8,614,073 B2
• Filed: 04/16/2012
• Issued: 12/24/2013
• Est. Priority Date: 09/29/2005
• Status: Active Grant

• Current Assignee: Keygene N.V.
• Original Assignee: Keygene N.V.
• Inventors: van Eijk, Michael Josephus Theresia, van Tunen, Adrianus Johannes
• Primary Examiner(s): WILDER, CYNTHIA B
• Application Number:
  US13/447,871
• Publication Number:
  US 20120309633A1
• Time in Patent Office: 617 Days
• Field of Search: 435/91.2, 435/6.1
• US Class Current: 435/91.2
• 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 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6846 Common amplification features
• CPC Class Codes: C12Q 1/6851 Quantitative amplification
• CPC Class Codes: C12Q 1/6855 Ligating adaptors
• CPC Class Codes: C12Q 1/6858 Allele-specific amplification
• 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 2525/155 incorporating/generating a new priming site
• CPC Class Codes: C12Q 2537/143 Multiplexing, i.e. use of multiple primers or probes in a single reaction, usually for simultaneously analyse of multiple analysis
• CPC Class Codes: C12Q 2563/155 Particles of a defined size, e.g. nanoparticles
• CPC Class Codes: C12Q 2563/179 the label being a nucleic acid
• CPC Class Codes: C12Q 2600/13 Plant traits
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 30/10 Sequence alignment; Homology search

Abstract

Efficient methods are disclosed for the high throughput identification of mutations in genes in members of mutagenized populations. The methods comprise DNA isolation, pooling, amplification, creation of libraries, high throughput sequencing of libraries, preferably by sequencing-by-synthesis technologies, identification of mutations and identification of the member of the population carrying the mutation and identification of the mutation.

Claims

1. A method for the detection of a mutation in a target sequence in a member of a mutagenized population, comprising the steps of:

(a) isolating genomic DNA of each member of the mutagenized population to provide DNA samples of each population member;

(b) pooling the DNA obtained in step (a);

(c) amplifying the target sequence with a pair of primers from the DNA pools to obtain amplification products;

(d) pooling the amplification products of step (c) to create a library of amplification products;

(e) determining the nucleotide sequence of the amplification products or fragments of step (d) using high throughput sequencing; and

identifying mutations by clustering/aligning the sequences of the amplified products or fragments without the use of an enzyme which recognizes and cuts single nucleotide sequence mismatches and wherein step (d) is immediately followed by step (e) such that no heteroduplex analysis is performed,

(f) screening the identified mutations for a modified function of the target sequence;

(g) designing a primer directed to hybridize to the identified mutation;

(h) amplifying the pooled DNA of step (b) with the primer of step (g) and one of the primers of step (c), and;

(i) identifying the population member or members carrying the mutation.

3. The method according to claim 1, wherein the mutagenized population is obtained by treating the genome with one or more selected from the group consisting of mutation-inducing chemicals, ionizing radiation, targeted nucleotide exchange or region targeted mutagenesis.

4. The method according to claim 1, wherein the population is not mutagenized but comprises sub-populations that contain naturally occurring mutations.

5. The method according claim 1, wherein the pooling is a 3D-pooling strategy.

6. The method according claim 1, wherein the high throughput sequencing is performed by Sequencing-by-Synthesis.

8. The method according to claim 6, wherein sequencing comprises the steps of:

(i) ligating sequencing adaptors to the fragments;

(ii) annealing said adaptor-ligated fragments to beads, each bead annealing with a single fragment;

(iii) emulsifying the beads in water-in-oil microreactors such that each microreactor contains a single bead;

(iv) performing emulsion PCR to amplify adaptor-ligated fragments on the surface of the beads;

(v) selecting/enriching beads to which are attached said amplified adaptorligated fragments;

(vi) placing the beads in wells such that each well comprises a single bead; and

generating a pyrophosphate signal.

9. The method according to claim 1, wherein the primers in steps (c) and/or step (g) contain nucleotides with improved binding affinity.

13. The method according claim 1, wherein the high throughput sequencing is performed by pyrosequeneing.

14. The method according to claim 1, wherein the method further comprises fragmenting the amplification products in the library.

15. The method according to claim 1, wherein the method further confirms the mutation by amplifying the target sequence from the member of step (i) using the primers of step (c) and determining the sequence of the amplified product.

2. A method for the detection of a mutation in a target sequence in a member of a mutagenized population, comprising the steps of:

(a) isolating genomic DNA of each member of the mutagenized population to provide for DNA samples of each population member;

(b) pooling the DNA obtained in step (a);

(c) amplifying part of the target sequence with a pair of primers from the DNA pools to obtain amplification products;

(d) pooling the amplification products of step (c) to create a library of amplification products;

(e) determining the nucleotide sequence of the amplification products of step (d) using high throughput sequencing; and

identifying mutations by clustering/aligning the sequences of the amplified products without the use of an enzyme which recognizes and cuts single nucleotide sequence mismatches and wherein step (d) is immediately followed by step (e) such that no heteroduplex analysis is performed and

(f) identifying members having the mutation.

10. The method according to claim 2, wherein the part of the target sequence that is amplified in step (c) is from about 80 to about 400 bp.

11. The method according to claim 10, wherein the part of the target sequence that is amplified in step (c) is from about 90 to about 300 bp.

12. The method according to claim 10, wherein the part of the target sequence that is amplified in step (c) is from 100 to about 200 bp.

16. The method according to claim 2, wherein the method further confirms the mutation by amplifying the target sequence from the members of step (f) using the primers of step (c) and determining the sequence of the amplified product.

17. The method according to claim 2, wherein at least one of the primers comprises a gene-specific section, a tag and a sequence primer binding site.

7. The method according to claim wherein sequencing is performed on a solid support such as a bead.