Strategies for high throughput identification and detection of polymorphisms

• US 9,023,768 B2
• Filed: 04/15/2014
• Issued: 05/05/2015
• Est. Priority Date: 06/23/2005
• Status: Active Grant

• Current Assignee: Keygene N.V.
• Original Assignee: Keygene N.V.
• Inventors: Van Eijk, Michael Josephus Theresia, Van Der Poel, Henricus Johannes Adam
• Primary Examiner(s): BOESEN, CHRISTIAN C
• Application Number:
  US14/253,806
• Publication Number:
  US 20140274744A1
• Time in Patent Office: 385 Days
• Field of Search: None
• US Class Current: 506/9
• 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: C12Q 1/6806 Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 1/6809 Methods for determination or identification of nucleic acids involving differential detection
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6858 Allele-specific amplification
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 2525/191 incorporating an adaptor
• CPC Class Codes: C12Q 2531/113 PCR
• CPC Class Codes: C12Q 2539/107 Representational Difference Analysis [RDA]
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: C40B 30/04 by measuring the ability to specifically bind a target molecule, e.g. antibody-antigen binding, receptor-ligand binding
• CPC Class Codes: C40B 30/10 by measuring physical properties, e.g. mass
• CPC Class Codes: G16B 20/20 Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• 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

The invention relates to a method for the high throughput identification of single nucleotide polymorphisms by performing a complexity reduction on two or more samples to yield two or more libraries, sequencing at least part of the libraries, aligning the identified sequences and determining any putative single nucleotide polymorphisms, confirming any putative single nucleotide polymorphism, generating detection probes for the confirmed single nucleotide polymorphisms, subjection a test sample to the same complexity reduction to provide a test library and screen the test library for the presence or absence of the single nucleotide polymorphisms using the detection probe.

Claims

1. A method for identifying one or more polymorphisms, comprising the steps of:

(a) providing a first nucleic acid sample of interest;

(b) performing a complexity reduction on the first nucleic acid sample to provide a first library of the first nucleic acid sample, which comprises;

(i) digesting the nucleic acid sample with at least one restriction endonuclease to fragment it into restriction fragments;

(ii) ligating the restriction fragments obtained with at least one double-stranded synthetic oligonucleotide adaptor having one end compatible with one or both ends of the restriction fragments to produce adapter-ligated restriction fragments (ALRFs);

(iii) contacting said ALRFs with one or more oligonucleotide primers under hybridizing conditions; and

(iv) amplifying said ALRFs by elongation of the one or more oligonucleotide primers,

wherein at least one of the one or more oligonucleotide primers includes at least part of the nucleotides present in the adapters,

wherein the adaptor and/or the primer comprises an identifier sequence,

(c) consecutively or simultaneously performing steps (a) and (b) with a second or further nucleic acid sample of interest to obtain a second or further library of the second or further nucleic acid sample;

(d) sequencing at least a portion of the first library and the second or further library;

(e) aligning the sequences obtained in step (d) to obtain an alignment; and

(f) determining one or more polymorphisms between the first nucleic acid sample and second or further nucleic acid sample in the alignment of step (e).

2. The method according to claim 1, wherein at least one of the primers is phosphorylated.

3. The method according to claim 1, wherein the sequencing step (d) is performed on a solid support such as a bead.

4. The method according to claim 1, wherein sequencing is based on dideoxy chain-terminating sequencing.

5. The method according to claim 3, wherein the sequencing step (d) comprises the steps of:

(i) annealing adapter-ligated fragments to beads, each bead annealing with a single adapter-ligated fragment;

(ii) emulsifying the beads in water-in-oil microreactors, each water-in-oil microreactor comprising a single bead;

(iii) loading the beads in wells, each well comprising a single bead; and

(iv) generating a pyrophosphate signal.

6. The method according to claim 5, wherein, preceding the annealing step, sequencing adaptors are ligated to fragments within the first library and the second library or combination library.

7. The method according to claim 6, wherein the sequencing adaptors carry a 3′

-T overhang.

8. The method according to claim 1, comprising after step (f), a further step of using the one or more polymorphisms determined in step (f) to design detection probes, and wherein high-throughput screening is performed by immobilizing said probes onto an array, followed by contacting of the array comprising the probes with a test library under hybridizing conditions.

9. A method comprising carrying out the steps of the method of claim 1 for screening enriched microsatellite libraries, performing transcript profiling cDNA-AFLP (digital Northern), sequencing of complex genomes, Expressed Sequence Tag library sequencing on whole cDNA or cDNA-AFLP, microRNA discovery, Bacterial Artificial Chromosome contig sequencing, Bulked Segregant analysis in combination with AFLP/cDNA-AFLP, and routine detection of AFLP.

10. The method of claim 1, further comprising the steps of :

(g) using the one or more polymorphisms determined in step (f) to design detection probes;

(h) providing a test sample nucleic acid of interest;

(i) performing the complexity reduction of step (b) on the test sample nucleic acid to provide a test library of the test sample; and

(j) subjecting the test library to high-throughput screening to identify the presence, absence or amount of the polymorphisms determined in step (f) using the detection probes designed in step (g).

11. The method of claim 1, wherein at least one of said primers includes at its 3′

end a selected sequence comprising at least one nucleotide located immediately adjacent to the nucleotides involved in the formation of the target sequence for said restriction endonuclease.