A survey of tools for the analysis of quantitative PCR (qPCR) data <s> Genotyping <s> BACKGROUND ::: Real-time (RT) PCR methods for discovering and genotyping single nucleotide polymorphisms (SNPs) are becoming increasingly important in various fields of biological sciences. SNP genotyping is widely used to perform genetic association studies aimed at characterising the genetic factors underlying inherited traits. The detection and quantification of somatic mutations is an important tool for investigating the genetic causes of tumorigenesis. In infectious disease diagnostics there is an increasing emphasis placed on genotyping variation within the genomes of pathogenic organisms in order to distinguish between strains. ::: ::: ::: METHODS ::: There are several platforms and methods available to the researcher wishing to undertake SNP analysis using real-time PCR methods. These use fluorescent technologies for discriminating between the alternate alleles of a polymorphism. There are several real-time PCR platforms currently on the market. Two of the key technical challenges are allele discrimination and allele quantification. ::: ::: ::: CONCLUSIONS ::: Applications of this technology include SNP genotyping, the sensitive detection of somatic mutations and infectious disease subtyping. <s> BIB001 </s> A survey of tools for the analysis of quantitative PCR (qPCR) data <s> Genotyping <s> Genetic analysis is one of the fastest-growing areas of clinical diagnostics. Fortunately, as our knowledge of clinically relevant genetic variants rapidly expands, so does our ability to detect these variants in patient samples. Increasing demand for genetic information may necessitate the use of high throughput diagnostic methods as part of clinically validated testing. Here we provide a general overview of our current and near-future abilities to perform large-scale genetic testing in the clinical laboratory. First we review in detail molecular methods used for high throughput mutation detection, including techniques able to monitor thousands of genetic variants for a single patient or to genotype a single genetic variant for thousands of patients simultaneously. These methods are analyzed in the context of pharmacogenomic testing in the clinical laboratories, with a focus on tests that are currently validated as well as those that hold strong promise for widespread clinical application in the near future. We further discuss the unique economic and clinical challenges posed by pharmacogenomic markers. Our ability to detect genetic variants frequently outstrips our ability to accurately interpret them in a clinical context, carrying implications both for test development and introduction into patient management algorithms. These complexities must be taken into account prior to the introduction of any pharmacogenomic biomarker into routine clinical testing. <s> BIB002
Several methods have been developed that involve different PCR preparation techniques to discover and genotype small DNA sequence variations such as single nucleotide polymorphisms (SNPs) BIB001 . The created assays vary in sample preparation techniques, turnaround time, costs, and multiplexing capabilities BIB002 . Depending on the used protocol, different normalization and quantification strategies need to be applied after Cq value calculation.