Table 2. Techniques for genotype analysis in pharmacogenetics and genomics.

Methods	Short description and purpose
PCR	PCR, basic technique in almost all current pharmacogenetic and genomic analysis.
PCR-RFLP	The polymorphic genomic region is amplified by PCR and cut by sequence-specific enzymes (restriction endonucleases). The resulting fragments are analyzed by electrophoresis and are indicative of the genotypes.
qPCR (real-time PCR)	Detection of the PCR product formation while PCR reaction proceeds using various fluorescence quenching or fluorescence energy transfer techniques for genotyping of single SNPs in many samples.
qRT-PCR (quantitative reverse transcriptase PCR)	Used to quantify amounts of transcripts in a sample after a reverse transcription reaction. Useful for quantification of RNAs in big numbers of samples.
Denaturing high performance liquid chromatography (DHPLC)	Variant and wild-type DNA forms differently shaped hybrid molecules (homoduplex versus heteroduplex) which can be separated by ion-pair reverse phase HPLC to identify polymorphisms.
Sanger di-deoxy (end terminal) sequencing	Reading of DNA sequences, identification of new polymorphisms.
Single-base (primer) extension (known as mini-sequencing)	Short oligonucleotides are annealed so that their 3’-end directly upstream the polymorphic site. Elongation of only one single base is performed by using a mixture of (fluorescently labeled) ddNTPs without dNTPs. The products can be detected either with sequencing or using MALDI-TOF detection system.
DNA microarrays	Microarray solid-phase bound DNA molecules to simultaneously genotype large numbers of SNPs (up to more than a million) in a single sample. Used in the genome-wide association studies.
Pyrosequencing	A method of DNA sequencing based on the sequencing by synthesis principle. Used in SNP genotyping and DNA methylation analyses. The principle behind this method is also the basis of the current large-scale DNA sequencing known as 454 “next generation” capable of sequencing more than 100 million basepairs per day.