Strategies for high throughput identification and detection of polymorphisms

• US 9,376,716 B2
• Filed: 10/16/2015
• Issued: 06/28/2016
• 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:
  US14/885,063
• Publication Number:
  US 20160060686A1
• Time in Patent Office: 256 Days
• Field of Search: None
• US Class Current: 1/1
• 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 in nucleic acid samples, comprising the steps of:

(a) providing a plurality of nucleic acid samples of interest;

(b) performing a complexity reduction on each of the samples to provide a plurality of libraries of the nucleic acid samples,

(c) ligating sequencing adapters carrying a 3′

-T overhang to the complexity reduced nucleic acid samples in the libraries and combining the libraries;

(d) sequencing at least a portion of the combined libraries to obtain sequences;

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

(f) determining one or more polymorphisms between the plurality of nucleic acid samples in the alignment of step (e).

2. The method according to claim 1, further comprising (g) screening a test sample nucleic acid of interest to identify the presence, absence or amount of the one or more polymorphisms determined in step (f).

3. The method according to claim 2, wherein the screening uses detection probes.

4. The method according to claim 2, wherein the test sample nucleic acid is a complexity reduced nucleic acid sample that has been obtained using the complexity reduction used in step (b).

5. The method according to claim 1, further comprising tagging of the libraries to obtain tagged libraries.

6. The method according to claim 5, wherein the tag is provided in an adaptor or primer.

7. The method according to claim 6, wherein the tag is an identifier sequence.

8. The method according to claim 6, wherein the sequencing step comprises sequencing on a solid support.

9. The method according claim 3, wherein the screening is performed by immobilizing the detection probes onto an array, followed by contacting the array comprising the probes with a test library under hybridizing conditions.

10. The method according to claim 1, wherein the libraries contain amplification products.

11. The method according to claim 10, wherein the amplification products are PCR products.

12. A method for identifying one or more polymorphisms in nucleic acid samples, comprising:

(a) performing a complexity reduction on a plurality of nucleic acid samples of interest to provide a plurality of libraries of the nucleic acid samples,

(b) ligating sequencing adapters carrying a 3′

-T overhang to the complexity reduced nucleic acid samples in the libraries and combining the libraries;

(c) sequencing at least a portion of the combined libraries to obtain sequences, wherein the libraries are each tagged with an identifier sequence, and wherein the sequencing step comprises sequencing on a solid support;

(d) aligning each of the sequences obtained in step (c) to obtain an alignment; and

(e) determining one or more polymorphisms between the plurality of nucleic acid samples in the alignment of step (f).