Associating sequence variation to specific traits
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:
- Map gene function and genetic variation
- Identify gene variants associated with a unique phenotype or disease; where SNPs serve as genetic markers (biomarkers)
- Match effective medical treatments to populations with specific genotypes (personalized medicine)
- Facilitate animal breeding, such as the selection of a desired genotype from a cross hybrid
- Trace ancestry or the origins of disease; map evolution, such as phylogenetic relationships between species; or test for family relationship for inheritance or paternity
- Carry out population association studies, such as genome-wide linkage analysis, which use SNPs as markers
- Perform forensics, using genotyping to identify a specific individual
- Do pathogen typing and resistance screening
- Monitor biodiversity
As mentioned above, there are also other types of information collected apart from sequence differences, such as copy number variation (CNV).
Technologies used to study genotyping
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.