Genotyping is the process of determining the DNA sequence—the genotype—at specific positions within a gene of an individual. Sequence variations can be used as markers in linkage and association studies to determine genes relevant to specific traits or disease.
By comparing sequence variations among individual plants, animals, or humans, researchers can identify heritable genes relevant to specific traits. These unique differences can be used as markers in linkage and association studies to:
As mentioned above, there are also other types of information collected apart from sequence differences, such as copy number variation (CNV).
There are different approaches to SNP genotyping with the number of samples, the number of genotypes to be tested, and the amount of sample material available, all factoring into choice of technology. Methods include whole genome analysis by NGS or microarrays, or more targeted analysis using qPCR, dPCR, or targeted sequencing.
Experimental design can be low throughput vs. highly multiplexed (look at numerous SNPs simultaneously). Common analysis methods include end-point or quantitative PCR (qPCR), targeted sequencing, bead or microarray analysis, and even mass spectrometry.
Learn more about the language used in genotyping studies.
Polymerase chain reaction (PCR) is a commonly used genotyping technique. Often employing a primer-pair and target-specific fluorescent probe, quantitative PCR (qPCR) can be a sensitive and specific way to detect SNPs. IDT offers a complete SNP-typing solution with predesigned assays, as well as complementary easy- and ready-to-use reagent mixes. For other applications, modified probes are available that can be incorporated into custom qPCR assays.
Targeted sequencing uses deep sequencing to detect known and novel variants within your region of interest. Thus, it can be used as a method for SNP and mutation detection, and gene structural analysis.
If you choose to use qPCR technology, the rhAmp SNP Genotyping System provides a fully integrated, high performing solution for out-of-the-box convenience. For user-defined methods, order custom probes with modifications, such as Affinity Plus qPCR locked nucleic acid Probes, that increase probe stability and enable designs within difficult sequences and with selective target identification.
The rhAmp SNP Genotyping System is a fully integrated genotyping solution that includes an extensive predesigned assay collection, a custom design tool, optimized reagent mixes, and optional synthetic control templates. SNP detection may be performed on any commonly available qPCR instrument.
Precise and easy-to-use, the rhAmp SNP Genotyping System offers an out-of-the-box solution for SNP genotyping studies for small discovery or large screening projects.
Use Affinity Plus qPCR Probes for SNP genotyping, transcript variant identification, and more sensitive target detection in challenging samples (FFPE tissue, biofluids). The Affinity Plus bases used in these qPCR probes are locked nucleic acid monomers. When incorporated into a probe, they impart heightened structural stability, leading to increased hybridization melt temperature (Tm).
PACE™ SNP genotyping uses competitive, allele-specific PCR and a simple, easily detected fluorescent readout for bi-allelic genotyping. Obtain primer sets from IDT for cost-effective, high-throughput assays.
The rhAmpSeq system enables highly accurate amplicon sequencing on Illumina next generation sequencing (NGS) platforms. Whether you are investigating thousands of targets or a few, the fast and easy rhAmpSeq workflow generates NGS-ready amplicon libraries for deep, targeted resequencing.