SNP Array Genotyping System

What is the 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.

Overview

Array genotyping begins with whole-genome amplification or enzymatic fragmentation of a defined DNA amount, followed by hybridisation to probes immobilised on a bead array or planar array. Each locus has allele-specific probes whose fluorescence intensity indicates which allele is present. A laser scanner images the array, and software converts intensities into genotype calls with quality scores, typically reporting call rates above 99% for good-quality samples. Arrays are available with panels from a few thousand markers for marker-assisted selection up to several million for genome-wide association studies. Turnaround is two to four days including amplification, hybridisation, scanning and calling, and cost per sample falls sharply with higher multiplexing. Custom array content requires design and manufacturing lead time, and the low-frequency variant detection limit is set by probe design.

How does it 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.

What are the key features?

• Panels from a few thousand to several million markers
• Call rates above 99% for good-quality DNA samples
• Bead array or planar array format with allele-specific probes
• Automated scanning and genotype calling with quality scores
• Custom panel design for specific species or traits
• Sample tracking from plate to genotype report

What are the technical specifications?

A typical snp array genotyping system configuration offers markers per sample of approx. 3,000–2,000,000 (panel dependent), call rate of over 99% (typical for good-quality DNA), DNA input of 200 ng–1 µg, samples per array of 1–96 (format dependent), turnaround time of approx. 2–4 days and genotyping accuracy of over 99% versus reference methods (typical). Values are indicative of the product class; the exact figures for each configuration are confirmed on the quotation and the calibration documents supplied with the instrument.

Which applications is it used for?

The SNP Array Genotyping System is used in genome-wide association studies, livestock and crop breeding selection, population genetics and diversity analysis and human ancestry and trait research. Across the wider Genotyping Systems class, laboratories also deploy it for clinical variant and pharmacogenomic testing, crop and livestock marker-assisted selection and cell line authentication and STR profiling.

Which standards and certifications apply?

Relevant standards and methods include ISO 20395, ISO 15189, CLSI MM01, ISO 17025 and IEC 61010-1. Certification candidates for this model are CE, ISO 9001 manufacturing and IEC 61010-1 safety; each is to be confirmed for the specific configuration before shipment, and certificates are supplied only where they have been issued.

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.

How do I select the right SNP Array Genotyping System?

Select an array system when marker density per sample is high and hundreds of samples are processed together. Specify panel size, species or custom content, sample number per array, DNA input, turnaround time, scanner platform compatibility and the bioinformatics support included after scanning.

How does it compare with other Genotyping Systems variants?

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.