Inexpensive, high-throughput genotyping methods are needed for analyzing human genetic variations. We have successfully applied the regular bioluminometric assay coupled with modified primer extension reactions (BAMPER) method to single-nucleotide polymorphism (SNP) typing as well as the allele frequency determination for various SNPs. This method includes the production of single-strand target...

Of a number of DNA marker typing techniques for personal identification in the field of forensic medicine, polymorphic short tandem repeat (STR) typing is currently the most frequently used technique. However, the multiplex STR method is time consuming. In contrast, single nucleotide polymorphism (SNP) detection methods are relatively rapid and amenable to high throughput. The discrimination po...

Legionella pneumophila is an important human pathogen causing Legionnaires' disease. In this study, whole genome sequencing (WGS) was used to study the characteristics and population structure of L. pneumophila strains. We sequenced and compared 53 isolates of L. pneumophila covering different serogroups and sequence-based typing (SBT) types (STs). We found that 1,896 single-copy orthologous ge...

BACKGROUND Trypanosoma cruzi is the causative agent of Chagas' Disease. The parasite has a complex population structure, with six major evolutionary lineages, some of which have apparently resulted from ancestral hybridization events. Because there are important biological differences between these lineages, strain typing methods are essential to study the T. cruzi species. Currently, there are...

Here we report a single nucleotide polymorphism (SNP) based genotyping method for Klebsiella pneumoniae utilising high-resolution melting (HRM) analysis of fragments within the multilocus sequence typing (MLST) loci. The approach is termed mini-MLST or Minim typing and it has previously been applied to Streptococcus pyogenes, Staphylococcus aureus and Enterococcus faecium. Six SNPs were derived...

OBJECTIVE To identify type 1 diabetes-susceptible HLA DR-DQ haplotypes using tag single nucleotide polymorphisms (SNPs) and to estimate the disease risk using these tag SNPs. RESEARCH DESIGN AND METHODS Five tag SNPs were typed in a total of 211 Japanese subjects including 201 patients with type 1 diabetes who had already been typed for HLA-DRB1, -DQA1, and -DQB1 alleles and 300 control subje...

BACKGROUND Infants in the neonatal intensive care unit (NICU) are at increased risk for methicillin-resistant Staphylococcus aureus (MRSA) acquisition. Outbreaks may be difficult to identify due in part to limitations in current molecular genotyping available in clinical practice. Comparison of genome-wide single nucleotide polymorphisms (SNPs) may identify epidemiologically distinct isolates a...

Streptococcus suis, an important zoonotic pathogen, is a highly diverse species with only a subset of strains that cause disease in humans. Our previous study proposed a minimum core genome (MCG) sequence typing method and defined seven MCG groups, with MCG group 1 as the prevalent group causing human infections. In this study, we identified a set of 10 single nucleotide polymorphisms (SNPs) di...

We have developed a single nucleotide polymorphism (SNP) nucleated high-resolution melting (HRM) technique to genotype Enterococcus faecium. Eight SNPs were derived from the E. faecium multilocus sequence typing (MLST) database and amplified fragments containing these SNPs were interrogated by HRM. We tested the HRM genotyping scheme on 85 E. faecium bloodstream isolates and compared the result...

On typing a large number of SNPs within a small genomic region in European populations it is commonly found that there is rather little haplotype diversity — the observed haplotypes fall into rather few major groups with only minor differences between haplotypes within groups. Johnson et al. [1] suggested that linkage disequilibrium and haplotype diversity within the region can be captured by a...