Methods for genotyping selected polymorphism

• US 8,114,978 B2
• Filed: 12/02/2008
• Issued: 02/14/2012
• Est. Priority Date: 08/05/2003
• Status: Active Grant

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Jones, Keith W., Shapero, Michael H., Fodor, Stephen P. A.
• Primary Examiner(s): WOOLWINE, SAMUEL C
• Application Number:
  US12/326,596
• Publication Number:
  US 20110009294A1
• Time in Patent Office: 1,169 Days
• Field of Search: None
• US Class Current: 536/24.3
• 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 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 1/6855 Ligating adaptors
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers

Abstract

Methods for genotyping polymorphisms using a locus specific primer that is complementary to a region near a selected polymorphism are described. Methods for synthesizing pools of locus specific primers that incorporate some degenerate positions are also disclosed. A plurality of different sequence capture probes are synthesized simultaneously using degenerate oligonucleotide synthesis. The sequence of the locus specific regions of the capture probes are related in that they have some bases that are identical in each sequence in the plurality of sequences and positions that vary from one locus specific region to another. The sequences are selected based on proximity to a polymorphism of interest and because they conform to a similar sequence pattern.

Claims

1. A kit comprising at least 100 different species of capture probes for genotyping a plurality of polymorphic positions each present on a different target sequence:

wherein each target sequence comprises a common sequence that is within 1000 base pairs of the polymorphic position;

wherein each target sequence comprises a consensus sequence immediately adjacent to the common sequence wherein the consensus sequence comprises at least one base that is identical in all the target sequences and at least one base that is variable between target sequences;

wherein each capture probe comprises a first universal priming sequence and a target specific sequence that comprises a region that is complementary to the consensus sequence from one target sequence and a region that is complementary to the common sequence,

wherein the capture probes are optionally pooled into 1 to 5 containers each containing a plurality of different species of capture probes; and

wherein the kit further comprises an array of allele specific probes, the array comprising at least one allele specific probe for each allele of each polymorphic position in said plurality of polymorphic positions.

2. The kit of claim 1 wherein the array further comprises control probes that are identical to the allele specific probes except for the presence of a single base mismatch at the central position of each probe.

3. The kit of claim 1 wherein the common sequence is between 4 and 10 base pairs.

4. The kit of claim 1 wherein the common sequence is a recognition site for a restriction enzyme.

5. The kit of claim 1 wherein each polymorphism in the plurality is within 1000 base pairs of a recognition site for a selected restriction enzyme and wherein the polymorphic position is between said recognition site and said common and consensus sequences.

6. The kit of claim 5 wherein said selected restriction enzyme is Not 1.

7. The kit of claim 1 wherein said plurality of different species of capture probes are attached to a solid support selected from the group consisting of arrays, beads, microparticles, microtitre dishes and gels.

8. The kit of claim 7 wherein the capture probes are attached to the solid support through a covalent interaction and wherein optionally each species of capture probe is attached to the solid support in a discrete location.

9. The kit of claim 1 wherein the capture probes are synthesized in one or more pools by a series of separate and pooled monomer additions.

10. A kit comprising at least 100 different species of capture probes for genotyping a plurality of polymorphic positions each present on a different target sequence:

wherein each target sequence comprises a common sequence that is within 1000 base pairs of the polymorphic position;

wherein each target sequence comprises a consensus sequence immediately adjacent to the common sequence wherein the consensus sequence comprises at least one base that is identical in all the target sequences and at least one base that is variable between target sequences;

wherein each capture probe comprises a first universal priming sequence and a target specific sequence that comprises a region that is complementary to the consensus sequence from one target sequence and a region that is complementary to the common sequence,

wherein the capture probes are optionally pooled into 1 to 5 containers each containing a plurality of different species of capture probes;

wherein each polymorphism in the plurality is within 1000 base pairs of a recognition site for a selected restriction enzyme and wherein the polymorphic position is between said recognition site and said common and consensus sequences; and

further comprising an adaptor sequence comprising a single strand overhang that is complementary to the overhang generated by digestion with said selected restriction enzyme.

11. The kit of claim 10 further comprising a first primer for the adaptor and a second primer for the universal priming sequence and optionally comprising a polymerase, dNTPs, said selected restriction enzyme, and buffer.

12. A kit comprising at least 100 different species of capture probes for genotyping a plurality of polymorphic positions each present on a different target sequence:

wherein each target sequence comprises a common sequence that is within 1000 base pairs of the polymorphic position;

wherein each target sequence comprises a consensus sequence immediately adjacent to the common sequence wherein the consensus sequence comprises at least one base that is identical in all the target sequences and at least one base that is variable between target sequences;

wherein each capture probe comprises a first universal priming sequence and a target specific sequence that comprises a region that is complementary to the consensus sequence from one target sequence and a region that is complementary to the common sequence,

wherein the capture probes are optionally pooled into 1 to 5 containers each containing a plurality of different species of capture probes;

wherein each polymorphism in the plurality is within 1000 base pairs of a recognition site for a selected restriction enzyme and wherein the polymorphic position is between said recognition site and said common and consensus sequences;

wherein said plurality of different species of capture probes are attached to a solid support selected from the group consisting of arrays, beads, microparticles, microtitre dishes and gels; and

wherein each capture probe further comprises a tag sequence that is unique for each species of capture probe and the capture probes are attached to the solid support by hybridization to a collection of tag probes that are covalently attached to the solid support.