Locked nucleic acid (LNA) single nucleotide polymorphism (SNP) genotype analysis and validation using real-time PCR

Johnson, M.P., Haupt, L.M., & Griffiths, L.R. (2004) Locked nucleic acid (LNA) single nucleotide polymorphism (SNP) genotype analysis and validation using real-time PCR. Nucleic Acids Research, 32(6), e55.

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Abstract

With an increased emphasis on genotyping of single nucleotide polymorphisms (SNPs) in disease association studies, the genotyping platform of choice is constantly evolving. In addition, the development of more specific SNP assays and appropriate genotype validation applications is becoming increasingly critical to elucidate ambiguous genotypes. In this study, we have used SNP specific Locked Nucleic Acid (LNA) hybridization probes on a real-time PCR platform to genotype an association cohort and propose three criteria to address ambiguous genotypes. Based on the kinetic properties of PCR amplification, the three criteria address PCR amplification efficiency, the net fluorescent difference between maximal and minimal fluorescent signals and the beginning of the exponential growth phase of the reaction. Initially observed SNP allelic discrimination curves were confirmed by DNA sequencing (n = 50) and application of our three genotype criteria corroborated both sequencing and observed real-time PCR results. In addition, the tested Caucasian association cohort was in Hardy-Weinberg equilibrium and observed allele frequencies were very similar to two independently tested Caucasian association cohorts for the same tested SNP. We present here a novel approach to effectively determine ambiguous genotypes generated from a real-time PCR platform. Application of our three novel criteria provides an easy to use semi-automated genotype confirmation protocol.

Impact and interest:

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84 citations in Web of Science®

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ID Code: 63128
Item Type: Journal Article
Refereed: Yes
Additional Information: Articles free to read on journal website
Keywords: antisense oligonucleotide, locked nucleic acid, article, automation, Caucasian, computer simulation, gene frequency, genetics, genotype, human, methodology, migraine, nucleotide sequence, polymerase chain reaction, reproducibility, single nucleotide polymorphism, Automation, Base Sequence, Computer Simulation, DNA Mutational Analysis, European Continental Ancestry Group, Gene Frequency, Genotype, Humans, Migraine Disorders, Oligonucleotides, Antisense, Polymerase Chain Reaction, Polymorphism, Single Nucleotide, Reproducibility of Results
ISSN: 1362-4962
Divisions: Current > Institutes > Institute of Health and Biomedical Innovation
Copyright Owner: Copyright 2004 the authors.
Deposited On: 04 Oct 2013 00:42
Last Modified: 29 Jan 2015 01:35

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