DNA diagnostics by surface-bound melt-curve reactions.
Melting-curve procedures track DNA denaturation in real time and so provide an effective way of assessing sequence variants. Dynamic allele-specific hybridization (DASH) is one such method, based on fluorescence, which uses heat to denature a single allele-specific probe away from one strand of a polymerase chain reaction product attached to a solid support. DASH is a proven system for research genotyping, but here we evaluate it for DNA diagnostics under two scenarios. First, for mutation scanning (resequencing), a human genomic sequence of 97 bp was interrogated with 15 probes tiled with 12-base overlaps, providing up to fourfold redundancy per base. This test sequence spanned three high-frequency single nucleotide polymorphisms, all of which were correctly revealed in 16 individuals. Second, to score multiple different mutations in parallel, 18 alterations in the gyrA gene of Salmonella were assessed in 62 strains by using wild-type- and mutation-specific probes. Both experiments were performed in a blinded manner, and all results were confirmed by sequencing. All DNA variants were unambiguously resolved in every sample, with no false-positive or false-negative signals across all of the investigations. In conclusion, DASH performs accurately and robustly when applied to DNA diagnostic challenges, including mutation scoring and mutation scanning.
Strömqvist Meuzelaar
Linda
L
Department of Genetics, University of Leicester, University Rd., Leicester, LE1 7RH, UK.
Hopkins
Katie
K
Liebana
Ernesto
E
Brookes
Anthony J
AJ
D001483:Base Sequence; D004247:DNA / Q000235:genetics*; D027081:DNA Gyrase / Q000235:genetics; D004252:DNA Mutational Analysis / Q000379:methods*; D017931:DNA Primers; D005069:Evaluation Studies as Topic; D006801:Humans; D025202:Molecular Diagnostic Techniques / Q000379:methods*; D008969:Molecular Sequence Data; D009691:Nucleic Acid Denaturation; D009693:Nucleic Acid Hybridization / Q000379:methods*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D012475:Salmonella / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D044366:Transition Temperature
D017931:DNA Primers; D004247:DNA; D027081:DNA Gyrase