Ded or confirmed independently.Discussion The Multiplex Assay Provides Substantial Advantages

Ded or confirmed independently.Discussion The Multiplex Assay Provides Substantial Advantages Over Alternative MethodsWe aimed to set up a diagnostic protocol that would provide quick and definitive diagnosis for the majority of cases tested in our laboratory. We first evaluated available methodologies taking into account reported accuracy, hands-on time 25033180 and feasibility. We considered several automatable technologies. Array techniques would have been an attractive option except for the need to produce custom arrays, which requires specialized equipment. Melting curve assays substantially reduce analysis time by eliminating post-PCR steps, however, they also rely on the availability of a high-resolution melting instrument and can produce ambivalent results that require additional testing [24]. In comparison, automated sequencing and primer extension reach higher confidence in mutation calling [41]. Sequencing enables a comprehensive investigation of HBB mutations, however, it has its shortcomings. Several reactions have to be run in order to sequence the whole gene. Focusing on key regions can reduce labor and cost but nonetheless, examining the nine mutations requires a minimum of two sequencing reactions per patient, ideally four to sequence both strands and minimize the risk of missing a point mutation in the heterozygous state [11]. The number of reactions can be ASP-015K cost reduced if multiplex minisequencing is used. In our laboratory, the technique has proved to be highly reliable in several applications [42?4]. With that in mind, singlenucleotide extension was deemed to be best suited for our purposes. Well designed primer extension assays provide the desired combination of high accuracy, semi-automation and wideCorrect Interpretation of Assay Results Requires that the Presence of Deletions be DeterminedSamples heterozygous for HBB locus deletions can be genotyped incorrectly by PCR-based assays that fail to amplify the allele carrying the deletion. For example, the sequence hybridizing toGenotyping Mediterranean HBB Gene Mutationsprecision. The test is highly sensitive and specific, rapid and easy to automate offering a high-quality alternative to other methods.Potential Caveats are Carefully CharacterizedAny primer-based test can be affected by the presence of sequence variations in primer-annealing sequences. Such effects need to be assessed when evaluating assay reliability. Firstly, in our assay, the PCR primers used for template amplification prior to primer extension are located in regions of low variability to ensure that they amplify various alleles with equal efficiency (see Materials and Methods). Secondly, we have shown that simple sequence variations located close to the mutations of interest can cause deviations in extension peak profiles, such as lower or missing signals. This applies primarily to normal genotype peaks since the normal sequence for a given nucleotide occurs in a variety of different get GNF-7 genetic backgrounds. In contrast, there is much less variability within individual minor alleles and thus the ability of the primer set to reproducibly detect the mutant genotype in a number of samples is a good indication that the allele of interest is dependably identified by the assay. Furthermore, in our assay the probability of missing a mutation is virtually eliminated by the introduction of two primers per mutation. Finally, we have confirmed that a common deletion spanning primer sequences impacts the assay in a predictable.Ded or confirmed independently.Discussion The Multiplex Assay Provides Substantial Advantages Over Alternative MethodsWe aimed to set up a diagnostic protocol that would provide quick and definitive diagnosis for the majority of cases tested in our laboratory. We first evaluated available methodologies taking into account reported accuracy, hands-on time 25033180 and feasibility. We considered several automatable technologies. Array techniques would have been an attractive option except for the need to produce custom arrays, which requires specialized equipment. Melting curve assays substantially reduce analysis time by eliminating post-PCR steps, however, they also rely on the availability of a high-resolution melting instrument and can produce ambivalent results that require additional testing [24]. In comparison, automated sequencing and primer extension reach higher confidence in mutation calling [41]. Sequencing enables a comprehensive investigation of HBB mutations, however, it has its shortcomings. Several reactions have to be run in order to sequence the whole gene. Focusing on key regions can reduce labor and cost but nonetheless, examining the nine mutations requires a minimum of two sequencing reactions per patient, ideally four to sequence both strands and minimize the risk of missing a point mutation in the heterozygous state [11]. The number of reactions can be reduced if multiplex minisequencing is used. In our laboratory, the technique has proved to be highly reliable in several applications [42?4]. With that in mind, singlenucleotide extension was deemed to be best suited for our purposes. Well designed primer extension assays provide the desired combination of high accuracy, semi-automation and wideCorrect Interpretation of Assay Results Requires that the Presence of Deletions be DeterminedSamples heterozygous for HBB locus deletions can be genotyped incorrectly by PCR-based assays that fail to amplify the allele carrying the deletion. For example, the sequence hybridizing toGenotyping Mediterranean HBB Gene Mutationsprecision. The test is highly sensitive and specific, rapid and easy to automate offering a high-quality alternative to other methods.Potential Caveats are Carefully CharacterizedAny primer-based test can be affected by the presence of sequence variations in primer-annealing sequences. Such effects need to be assessed when evaluating assay reliability. Firstly, in our assay, the PCR primers used for template amplification prior to primer extension are located in regions of low variability to ensure that they amplify various alleles with equal efficiency (see Materials and Methods). Secondly, we have shown that simple sequence variations located close to the mutations of interest can cause deviations in extension peak profiles, such as lower or missing signals. This applies primarily to normal genotype peaks since the normal sequence for a given nucleotide occurs in a variety of different genetic backgrounds. In contrast, there is much less variability within individual minor alleles and thus the ability of the primer set to reproducibly detect the mutant genotype in a number of samples is a good indication that the allele of interest is dependably identified by the assay. Furthermore, in our assay the probability of missing a mutation is virtually eliminated by the introduction of two primers per mutation. Finally, we have confirmed that a common deletion spanning primer sequences impacts the assay in a predictable.