ArticleJournal of clinical microbiology2004
Hairpin primers for simplified single-nucleotide polymorphism analysis of Mycobacterium tuberculosis and other organisms.
Article in Journal of clinical microbiology, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers, 1 of them a synthesis that pooled it.
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Who cites it
26 citing papers in PubMed, 1 synthesis or guideline pooled it, 51 citations in OpenAlex.
- The role of TLR2, TLR4 and CD14 genetic polymorphisms in gastric carcinogenesis: a case-control study and meta-analysis.PloS one · 2013Pooled it
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- A Fast Method for DEFB1 - 44C/G SNP Genotyping in Brazilian Patients with Periodontitis.Acta stomatologica Croatica · 2014Article
- Exquisite allele discrimination by toehold hairpin primers.Nucleic acids research · 2014Article
- Novel DNA chip based on a modified DigiTag2 assay for high-throughput species identification and genotyping of Mycobacterium tuberculosis complex isolates.Journal of clinical microbiology · 2014Article
- Minimum core genome sequence typing of bacterial pathogens: a unified approach for clinical and public health microbiology.Journal of clinical microbiology · 2013Article
- Methodologies for Salmonella enterica subsp. enterica subtyping: gold standards and alternatives.Applied and environmental microbiology · 2011Review
- Application of single-nucleotide polymorphism and mycobacterial interspersed repetitive units-variable number of tandem repeats analyses to clinical Mycobacterium tuberculosis isolates from Korea.The Korean journal of laboratory medicine · 2011Article
- Single nucleotide polymorphism typing of global Salmonella enterica serovar Typhi isolates by use of a hairpin primer real-time PCR assay.Journal of clinical microbiology · 2010Article
- Single nucleotide polymorphism typing of Mycobacterium ulcerans reveals focal transmission of buruli ulcer in a highly endemic region of Ghana.PLoS neglected tropical diseases · 2010Article
- Genomic diversity and evolution of Mycobacterium ulcerans revealed by next-generation sequencing.PLoS pathogens · 2009Article
- Convergent evolutionary analysis identifies significant mutations in drug resistance targets of Mycobacterium tuberculosis.Antimicrobial agents and chemotherapy · 2008Article
- Rifampin resistance, Beijing-W clade-single nucleotide polymorphism cluster group 2 phylogeny, and the Rv2629 191-C allele in Mycobacterium tuberculosis strains.Journal of clinical microbiology · 2008Article
- Genetic differentiation of Escherichia coli O157:H7 clades associated with human disease by real-time PCR.Journal of clinical microbiology · 2008Article
- Variation in virulence among clades of Escherichia coli O157:H7 associated with disease outbreaks.Proceedings of the National Academy of Sciences of the United States of America · 2008Article
- Antibiotic resistance and single-nucleotide polymorphism cluster grouping type in a multinational sample of resistant Mycobacterium tuberculosis isolates.Antimicrobial agents and chemotherapy · 2007Article
- Role of large sequence polymorphisms (LSPs) in generating genomic diversity among clinical isolates of Mycobacterium tuberculosis and the utility of LSPs in phylogenetic analysis.Journal of clinical microbiology · 2007Article
- Population genetics study of isoniazid resistance mutations and evolution of multidrug-resistant Mycobacterium tuberculosis.Antimicrobial agents and chemotherapy · 2006Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
Abstract
We describe a novel, simple, rapid, and highly sensitive method to detect single-nucleotide polymorphisms (SNPs) in Mycobacterium tuberculosis and other organisms. Amplification refractory mutation (ARMS) SNP assays were modified by converting the SNP-detecting linear primers in the ARMS assay to hairpin-shaped primers (HPs) through the addition of a 5' tail complementary to the 3' end of the linear primer. The improved ability of these primers to detect SNPs in M. tuberculosis was compared in a real-time PCR with SYBR-I green dye. Linear primers resulted in incorrect or indeterminate allele designation for 6 of the 13 SNP alleles tested in seven different SNP assays, while HPs determined the correct SNP in all cases. We compared the cycle threshold differences (DeltaC(t)) between the reactions containing primer-template matches and the reactions containing primer-template mismatches (where a larger DeltaC(t) indicates a more robust assay). The use of HPs dramatically improved the mean DeltaC(t) values for the SNP assays (7.6 for linear primers and 11.2 for HPs). We designed 98 different HP assays for SNPs previously associated with resistance to the antibiotic isoniazid to test the large-scale utility of the HP approach. Assay design was successful in 72.4%, 83.7%, 88.8%, and 92.9% of the assays after one to four rounds of assay design, respectively. HP SNP assays are simple, sensitive, robust, and inexpensive. These advantages favor the application of this technique for SNP assays of M. tuberculosis and other organisms.
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