Genotyping is an important tool in the identification of genes associated with a range of inherited traits including:
- Disease susceptibility,
- Response to pathogens and drugs,
- Physical characteristics (for example height), and
- Personality traits (for example associated with mental health).
The most common method of genotyping utilises Single Nucleotide Polymorphisms (SNPs), which are single base DNA sequences known to be variable between members of a species. SNP genotyping studies aim to correlate occurrence of SNP variants with the presence of a given genetic trait; knowing which gene the identified SNP lies within or next to can implicate that gene in the development of the trait. SNPs shown to correlate with traits can therefore be used as markers to predict disease development, response to pathogens & drugs, physical attributes and personality characteristics.
The GoldenGate genotyping assay interrogates up to 1536 SNP loci simultaneously. Briefly, DNA is activated and bound to paramagnetic particles. An oligonucleotide pool is added to the sample; this pool contains two oligos specific to each allele at each SNP site plus one locus specific oligo downstream of each SNP site. All oligos contain regions of genomic complementarity and universal PCR primer sites; the locus specific oligo also contains a bead address sequence. Following an extension and ligation reaction the SNP loci are amplified by PCR, incorporating Cy3 (green) and Cy5 (red) labelled primers specific for each allele. PCR products are hybridised to universal arrays using the bead address sequence of the locus specific oligo. Cy3 and Cy5 signals are detected using the BeadArray Reader scanner.
The GoldenGate assay can be used for:
- Analysis of up to 1536 SNPs, for example in replication studies
- Admixture mapping in African American populations,
- Investigation of 1421 cancer associated SNPs,
- Major histocompatibility (MHC) variant mapping, and
- Mouse linkage studies, at low or medium density.
Figure 1: the GoldenGate assay workflow.