How do Genotyping Systems work?
Genotyping always compares a measured signal with a known allele pattern. Allele-specific real-time PCR uses two probes labelled with different fluorophores that match each allele, and the ratio of signal from the two channels, plotted against a reference, classifies the sample as homozygous, heterozygous or no call. SNP arrays work by hybridising fragmented, amplified DNA to immobilised probes and reading fluorescence intensity for each allele. Capillary fragment analysis amplifies short tandem repeats or microsatellites and sizes the products, so allele lengths are scored from the electropherogram. Targeted sequencing reads the variant positions directly, which allows discovery of unexpected variants and detection of low-frequency alleles. Across all methods, the quality metrics of cluster separation or coverage depth determine which calls are accepted, and laboratories usually include positive and negative controls in each batch.
Which Genotyping Systems variants are available?
- Real-Time PCR Genotyping System — A real-time PCR genotyping system scores known alleles with fluorescently labelled allele-specific probes across 96 or 384 wells, delivering results in about two hours with minimal set-up.
- SNP Array Genotyping System — An SNP array genotyping system hybridises amplified DNA to arrays carrying thousands to millions of allele-specific probes and reads the fluorescence with a scanner, giving genome-wide coverage per sample at high call rates for population and breeding studies.
- Capillary Fragment Analysis Genotyper — A capillary fragment analysis genotyper sizes fluorescently labelled PCR products to score short tandem repeat and microsatellite markers, and is the reference method for cell line authentication and forensic profiling.
- Targeted Sequencing Genotyping System — A targeted sequencing genotyping system reads defined genomic regions at high depth and scores variants from the alignment, covering thousands of loci per sample while also revealing unexpected variants and low-frequency alleles that probe-based methods cannot detect.
- Automated High-Throughput Genotyping Platform — An automated high-throughput genotyping platform integrates liquid handling, PCR set-up and detection so that thousands of samples are genotyped per day with minimal operator intervention.
How do I choose the right variant?
Start with the number of variants and samples. If you score a few known markers in many samples, real-time PCR with allele-specific probes gives the lowest cost per data point and a simple workflow. For hundreds of thousands of markers across a population, arrays provide the highest call rate per sample but need a scanner, and custom arrays have long lead times. Capillary fragment analysis remains the reference for short tandem repeat markers in cell line authentication, forensic work and plant breeding. Targeted sequencing suits panels where you want both known and unexpected variants, or where alleles occur at low frequency in mixed samples. Check multiplexing limits, DNA input, turnaround time, analysis software, genotype-calling algorithm transparency and the ability to re-analyse raw data under your own rules.
Where are Genotyping Systems used?
Genotyping Systems are specified in clinical variant and pharmacogenomic testing, crop and livestock marker-assisted selection, cell line authentication and STR profiling, microbial strain typing and outbreak tracing and seed purity and variety verification.
Which standards and certifications apply?
Work with Genotyping Systems is commonly governed by ISO 20395, ISO 15189, CLSI MM01, ISO 17025 and IEC 61010-1. Instrument certifications such as CE marking are confirmed per configuration and never assumed.
What are the key considerations before purchase?
Genotyping results depend heavily on DNA quality, so extract samples with a consistent method and check concentration and purity before starting. Real-time PCR genotyping needs validated primers and probes and a thermocycler with calibrated optics; arrays and sequencers need controlled temperature and humidity plus a scanner with consistent gain settings. Run positive controls for each genotype and a no-template control in every batch, and re-run ambiguous calls on an independent method rather than re-reading the same data. Cell line authentication should be repeated whenever a line is re-established or a stock is replaced. In clinical use, genotyping assays fall under ISO 15189 and require documented validation of limit of detection, precision and specificity for each reported genotype.
