IP Library › Granted Patent US 10,077,474
Granted Patent B2
US 10,077,474 · App. 13/840,142 · Granted Sep 18, 2018

Method of designing primers, method of detecting single nucleotide polymorphisms (SNPs), method of distinguishing SNPs, and related primers, detectable oligonucleotides, and kits

Inventors: Shihai X. Huang (Lincolnshire, IL); Hong X. Su (Evanston, IL); Brian J. Erickson (Kenosha, WI)
Assignee: Abbott Molecular, Inc.
C12Q1/6876C12Q1/6858C12Q1/6886C12Q2600/156
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Quick Facts
Patent No.
US 10,077,474
App. No.
13/840,142
Granted
Sep 18, 2018
Kind
B2
Abstract

A method of designing a primer for detecting a single nucleotide polymorphism (SNP), a method of detecting an SNP, a method of distinguishing SNPs, primers, detectable oligonucleotides, and kits.

Claims (37)

1. A composition comprising: a group of primers for amplification of a mutation (X) of the codon encoding valine at amino acid position 600 (V600X) in exon 15 of the BRAF (B-Raf proto-oncogene, serine/threonine kinase) gene in a sample of nucleic acid from a human,

wherein each primer is labeled and

wherein the group of primers is selected from groups 1-7 wherein:

(i) Group 1 consists of an oligonucleotide consisting of the nucleotide sequence GGTCTAGCTACNGAA [SEQ ID NO: 59] and an oligonucleotide consisting of the nucleotide sequence GGTCTAGCTACNGAG [SEQ ID NO: 60];

(ii) Group 2 consists of an oligonucleotide consisting of the nucleotide sequence GGTCTAGCTACNGAA [SEQ ID NO: 59], an oligonucleotide consisting of the nucleotide sequence GGTCTAGCTACNGAG [SEQ ID NO: 60], an oligonucleotide comprising the nucleotide sequence GGTCTAGCTACNAAA [SEQ ID NO: 46] at its 3′ terminus and an oligonucleotide comprising the nucleotide sequence GGTCTAGCTACNAAG [SEQ ID NO: 47] at its 3′ terminus;

(iii) Group 3 consists of an oligonucleotide consisting of the nucleotide sequence GGTCTAGCTACNGAA [SEQ ID NO: 59], an oligonucleotide consisting of the nucleotide sequence GGTCTAGCTACNGAG [SEQ ID NO: 60], an oligonucleotide comprising the nucleotide sequence GGTCTAGCTACNGAT [SEQ ID NO: 48] at its 3′ terminus and an oligonucleotide comprising the nucleotide sequence GGTCTAGCTACNGAC [SEQ ID NO: 49] at its 3′ terminus;

(iv) Group 4 consists of an oligonucleotide consisting of the nucleotide sequence GGTCTAGCTACNGAA [SEQ ID NO: 59], an oligonucleotide consisting of the nucleotide sequence GGTCTAGCTACNGAG [SEQ ID NO: 60]; an oligonucleotide comprising the nucleotide sequence GGTCTAGCTACNAAA [SEQ ID NO: 46] at its 3′ terminus and an oligonucleotide comprising the nucleotide sequence GGTCTAGCTACNAAG [SEQ ID NO: 47] at its 3′ terminus, an oligonucleotide comprising the nucleotide sequence GGTCTAGCTACNGAT [SEQ ID NO: 48] at its 3′ terminus and an oligonucleotide comprising the nucleotide sequence GGTCTAGCTACNGAC [SEQ ID NO: 49] at its 3′ terminus;

(v) Group 5 consists of an oligonucleotide consisting of the nucleotide sequence GGTCTAGCTACNGAA [SEQ ID NO: 59], an oligonucleotide consisting of the nucleotide sequence GGTCTAGCTACNGAG [SEQ ID NO: 60], an oligonucleotide comprising the nucleotide sequence GGTCTAGCTACNAAT [SEQ ID NO: 50] at its 3′ terminus and an oligonucleotide comprising the nucleotide sequence GGTCTAGCTACNAAC [SEQ ID NO: 51] at its 3′ terminus;

(vi) Group 6 consists of an oligonucleotide consisting of the nucleotide sequence GGTCTAGCTACNGAA [SEQ ID NO: 59], an oligonucleotide consisting of the nucleotide sequence GGTCTAGCTACNGAG [SEQ ID NO: 60], an oligonucleotide comprising the nucleotide sequence GGTCTAGCTACNCGT [SEQ ID NO: 52] at its 3′ terminus, an oligonucleotide comprising the nucleotide sequence GGTCTAGCTACNCGC [SEQ ID NO: 53] at its 3′ terminus, an oligonucleotide comprising the nucleotide sequence GGTCTAGCTACNCGA [SEQ ID NO: 54] at its 3′ terminus, an oligonucleotide comprising the nucleotide sequence GGTCTAGCTACNCGG [SEQ ID NO: 55] at its 3′ terminus, an oligonucleotide comprising the nucleotide sequence GGTCTAGCTACN AGA [SEQ ID NO: 56] at its 3′ terminus, and an oligonucleotide comprising the nucleotide sequence GGTCTAGCTACNAGG [SEQ ID NO: 57] at its 3′ terminus; and

(vii) Group 7 consists of an oligonucleotide consisting of the nucleotide sequence GGTCTAGCTACNGAA [SEQ ID NO: 59], an oligonucleotide consisting of the nucleotide sequence GGTCTAGCTACNGAG [SEQ ID NO: 60], an oligonucleotide comprising the nucleotide sequence GGTCTAGCTACNAAT [SEQ ID NO: 50] at its 3′ terminus, an oligonucleotide comprising the nucleotide sequence GGTCTAGCTACNAAC [SEQ ID NO: 51] at its 3′ terminus, an oligonucleotide comprising the nucleotide sequence GGTCTAGCTACNCGT [SEQ ID NO: 52] at its 3′ terminus, an oligonucleotide comprising the nucleotide sequence GGTCTAGCTACNCGC [SEQ ID NO: 53] at its 3′ terminus, an oligonucleotide comprising the nucleotide sequence GGTCTAGCTACNCGA [SEQ ID NO: 54] at its 3′ terminus, an oligonucleotide comprising the nucleotide sequence GGTCTAGCTACNCGG [SEQ ID NO: 55] at its 3′ terminus, an oligonucleotide comprising the nucleotide sequence GGTCTAGCTACN AGA [SEQ ID NO: 56] at its 3′ terminus, and an oligonucleotide comprising the nucleotide sequence GGTCTAGCTACNAGG [SEQ ID NO: 57] at its 3′ terminus;

wherein N is a nucleotide containing a base other than adenine (A),

wherein the primers of SEQ ID 46-57 comprise a length of from about 15 nucleotides to about 35 nucleotides;

and

wherein said label is selected from the group consisting of dyes, radioactive labels, electron-dense reagents, enzymes, haptens and proteins.

2. A kit comprising:

a group of primers for amplification of a mutation (X) of the codon encoding valine at amino acid position 600 (V600X) in exon 15 of the BRAF (B-Raf proto-oncogene, serine/threonine kinase) gene in a sample of nucleic acid from a human,

wherein each primer is labeled and

wherein the group of primers is selected from groups 1-7 wherein:

(i) Group 1 consists of an oligonucleotide consisting of the nucleotide sequence GGTCTAGCTACNGAA [SEQ ID NO: 59] and an oligonucleotide consisting of the nucleotide sequence GGTCTAGCTACNGAG [SEQ ID NO: 60];

(ii) Group 2 consists of an oligonucleotide consisting of the nucleotide sequence GGTCTAGCTACNGAA [SEQ ID NO: 59], an oligonucleotide consisting of the nucleotide sequence GGTCTAGCTACNGAG [SEQ ID NO: 60], an oligonucleotide comprising the nucleotide sequence GGTCTAGCTACNAAA [SEQ ID NO: 46] at its 3′ terminus and an oligonucleotide comprising the nucleotide sequence GGTCTAGCTACNAAG [SEQ ID NO: 47] at its 3′ terminus;

(iii) Group 3 consists of an oligonucleotide consisting of the nucleotide sequence GGTCTAGCTACNGAA [SEQ ID NO: 59], an oligonucleotide consisting of the nucleotide sequence GGTCTAGCTACNGAG [SEQ ID NO: 60], an oligonucleotide comprising the nucleotide sequence GGTCTAGCTACNGAT [SEQ ID NO: 48] at its 3′ terminus and an oligonucleotide comprising the nucleotide sequence GGTCTAGCTACNGAC [SEQ ID NO: 49] at its 3′ terminus;

(iv) Group 4 consists of an oligonucleotide consisting of the nucleotide sequence GGTCTAGCTACNGAA [SEQ ID NO: 59], an oligonucleotide consisting of the nucleotide sequence GGTCTAGCTACNGAG [SEQ ID NO: 60]; an oligonucleotide comprising the nucleotide sequence GGTCTAGCTACNAAA [SEQ ID NO: 46] at its 3′ terminus and an oligonucleotide comprising the nucleotide sequence GGTCTAGCTACNAAG [SEQ ID NO: 47] at its 3′ terminus, an oligonucleotide comprising the nucleotide sequence GGTCTAGCTACNGAT [SEQ ID NO: 48] at its 3′ terminus and an oligonucleotide comprising the nucleotide sequence GGTCTAGCTACNGAC [SEQ ID NO: 49] at its 3′ terminus;

(v) Group 5 consists of an oligonucleotide consisting of the nucleotide sequence GGTCTAGCTACNGAA [SEQ ID NO: 59], an oligonucleotide consisting of the nucleotide sequence GGTCTAGCTACNGAG [SEQ ID NO: 60], an oligonucleotide comprising the nucleotide sequence GGTCTAGCTACNAAT [SEQ ID NO: 50] at its 3′ terminus and an oligonucleotide comprising the nucleotide sequence GGTCTAGCTACNAAC [SEQ ID NO: 51] at its 3′ terminus;

(vi) Group 6 consists of an oligonucleotide consisting of the nucleotide sequence GGTCTAGCTACNGAA [SEQ ID NO: 59], an oligonucleotide consisting of the nucleotide sequence GGTCTAGCTACNGAG [SEQ ID NO: 60], an oligonucleotide comprising the nucleotide sequence GGTCTAGCTACNCGT [SEQ ID NO: 52] at its 3′ terminus, an oligonucleotide comprising the nucleotide sequence GGTCTAGCTACNCGC [SEQ ID NO: 53] at its 3′ terminus, an oligonucleotide comprising the nucleotide sequence GGTCTAGCTACNCGA [SEQ ID NO: 54] at its 3′ terminus, an oligonucleotide comprising the nucleotide sequence GGTCTAGCTACNCGG [SEQ ID NO: 55] at its 3′ terminus, an oligonucleotide comprising the nucleotide sequence GGTCTAGCTACN AGA [SEQ ID NO: 56] at its 3′ terminus, and an oligonucleotide comprising the nucleotide sequence GGTCTAGCTACNAGG [SEQ ID NO: 57] at its 3′ terminus; and

(vii) Group 7 consists of (an oligonucleotide consisting of the nucleotide sequence GGTCTAGCTACNGAA [SEQ ID NO: 59], an oligonucleotide consisting of the nucleotide sequence GGTCTAGCTACNGAG [SEQ ID NO: 60], an oligonucleotide comprising the nucleotide sequence GGTCTAGCTACNAAT [SEQ ID NO: 50] at its 3′ terminus, an oligonucleotide comprising the nucleotide sequence GGTCTAGCTACNAAC [SEQ ID NO: 51] at its 3′ terminus, an oligonucleotide comprising the nucleotide sequence GGTCTAGCTACNCGT [SEQ ID NO: 52] at its 3′ terminus, an oligonucleotide comprising the nucleotide sequence GGTCTAGCTACNCGC [SEQ ID NO: 53] at its 3′ terminus, an oligonucleotide comprising the nucleotide sequence GGTCTAGCTACNCGA [SEQ ID NO: 54] at its 3′ terminus, an oligonucleotide comprising the nucleotide sequence GGTCTAGCTACNCGG [SEQ ID NO: 55] at its 3′ terminus, an oligonucleotide comprising the nucleotide sequence GGTCTAGCTACN AGA [SEQ ID NO: 56] at its 3′ terminus, and an oligonucleotide comprising the nucleotide sequence GGTCTAGCTACNAGG [SEQ ID NO: 57] at its 3′ terminus;

wherein N is a nucleotide containing a base other than adenine (A),

wherein the primers of SEQ ID 46-57 comprise a length of from about 15 nucleotides to about 35 nucleotides; and

wherein said label is selected from the group consisting of dyes, radioactive labels, electron-dense reagents, enzymes, haptens and proteins, and

instructions for a method of detecting at least one mutation (X) of the codon encoding valine at amino acid position 600 (V600X) in exon 15 of the BRAF gene in a sample of nucleic acid from a human.

3. The kit of claim 2 , wherein X is at least one amino acid selected from the group consisting of E (glutamic acid), K (lysine), D (aspartic acid), R (arginine), and N (asparagine).

4. The kit of claim 2 , wherein X is at least one amino acid selected from the group consisting of E, K, and D.

5. The kit of claim 2 , wherein X is E.

6. The kit of claim 2 , wherein X is E and K, E and D, or K and D.

7. The kit of claim 2 , wherein X is E, K, and D.

8. The Composition of claim 1 , further comprising at least one PNA clamp.

9. The kit of claim 2 , further comprising at least one PNA clamp.

10. The kit of claim 2 , further comprising an internal control primer.

Assignments (1)
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Aug 6, 2013
From: HUANG, SHIHAI X.; SU, HONG X.; ERICKSON, BRIAN J.
To: ABBOTT MOLECULAR INC.
Reel/Frame 030946/0967 →
Continuity (2)
Provisional Application 61652827 · May 29, 2012
Related Publication 20130323727A1 · Dec 5, 2013