End-point polymerase chain reaction (PCR)

Single-nucleotide polymorphisms (SNPs)

A single-nucleotide polymorphism (SNP) is a base pair substitution at a specific locus within a DNA sequence. SNPs are the simplest and most common type of genetic variation and are used to quickly and easily identify heritable differences among individual plants, animals, or humans within a population. Importantly, researchers are building an ever-increasing library of SNPs that are linked to agriculturally and medically important phenotypes including susceptibility to disease or environmental stress as well as response to medication or treatment regimens.

Applications for SNP genotyping

Plant and animal marker-assisted breeding

Following Mendel’s rule of inheritance, single-nucleotide polymorphisms (SNPs) are evolutionarily conserved and therefore, are useful in plant and animal marker-assisted breeding programs. Using SNP genotyping, selective breeding is accelerated by allowing traits to be identified and selected prior to growing the organism to maturity – saving time and money. Large-scale quality control testing also benefits from SNP genotyping, using these simple markers as a 'genetic fingerprint' to trace samples as well as estimate the purity of a population.

Human genetics

SNPs are used in large scale epidemiological studies to identify specific variations in genes that influence susceptibility to disease and response to medication or treatment. Once identified, SNPs may be used to diagnose individuals carrying the gene of interest, which provides critical information necessary to personalize medical care. Human identity testing also may be achieved using the “genetic fingerprint” provided by SNP genotyping.

Cost effective benefits of SNP genotyping

Array Tape™ provides a cost-effective solution for studies designed to identify a moderate number of SNPs in larger population sizes.

	Typical process microplate-based workstations	LCG Biosearch Technologies’ process using Nexar™, Soellex™ and Araya™
Setup	Step 1: Dispense 8 microliters a single 384- microplate at a time Step 2: Seal the microplate Step 3: Stack the microplates	Step 1: The Nexar dispenses 800 nL sample and 800 nL reagent in the equivalent of 200 plates in a continuous strip of Array Tape, seals it, and winds the samples on a dunker reel
Thermal cycling process	Run microplates through water bath PCR 16 or 32 at a time	Entire reel of Array Tape is loaded into the Soellex water bath with shorter cycle time
Scan	Scan Microplate (~ 1.5 – 2.5 minutes)	The Araya scans the entire reel at a rate of 28 seconds per 384-well array
Plates per day	150 microplates (384 wells)	400 arrays (384 wells)
Data points per day	57,600	153,600
Lab processing time	10 hours	8 hours

High-throughput

Streamline workflow: Inline liquid handling (Nexar) and fluorescence scanning (Araya) continuously process reaction wells without the need for robotic or manual handling of microtiter plates.

Batch thermocycling: Up to three reels of Array Tape, 600 microplate equivalents, may be processed simultaneously in the Soellex water bath.

Application flexibility

Modular Nexar and Araya instruments: Customised liquid handling and scanning processes may be achieved for multiple SNP assay technologies.

Scalability: As new modules and attachments are developed, the Platform can be expanded or upgraded to support new applications, increase throughput, reduce cost, etc.

Cost effective

Miniaturised reaction volumes: Reduce reagent and sample consumption up to 80-90% in miniaturized reaction wells – 800 nL or less in Array Tape vs. 5 µL or more in microplates.

Less labour: Highly automated, easy to use design eliminates labour associated with manually moving microplates.