QC steps in the genotyping workflow

Genotyping is the process of using biological assays such as end-point PCR, qPCR or sequencing methods to highlight genetic variations in individuals. Thus, quantity and quality of the DNA or RNA in which the information is encoded are critical to the accurate detection of variants and confident analysis.

Quality control
Genotyping assays require high-quality samples to ensure reliable data and interpretation and confidence in linking a genotype to an observed phenotype. Every technology has different requirements regarding sample quantity and purity. Accurate nucleic acid quantification ensures that experimental conditions are optimized to provide the best results and accurate interpretation.
Detecting and characterizing unique genetic features highlighted by genotyping assays require that initial genetic information remains unaltered from initial sample preparation through final detection. Therefore, the integrity of the DNA or RNA molecules must be ensured prior to processing through end-point PCR, qPCR or sequencing-based genotyping assays.

Capillary electrophoresis instruments such as the QIAxcel Advanced system, can help assess nucleic acid integrity by analyzing a sample's size distribution and informing you of an abundance of short fragments resulting from sample degradation, which can indicate potential loss of genetic information.

Following PCR amplification of cDNA fragments, the specificity of the amplification can be confirmed by agarose gel or capillary electrophoresis. For highly accurate verification and validation, sequencing methods provide deeper insights into the sequence, especially for analysis of SNPs.

Find out more about QC checks in other laboratory workflows:

Huang, J. et al. (2011) Minimum Information about a Genotyping Experiment (MIGEN). Stand. Genomic Sci. 5:2, 224‑229.