SNP Genotyping Techniques

There are several high throughput techniques available now to genotype thousands to millions of SNPs simultaneously in a cost effective manner. Some of the commonly used techniques include:

Microarray Based Genotyping: Microarrays have been a workhorse platform for large scale SNP genotyping for over a decade. It uses DNA probes immobilized on a solid surface to assay for SNPs through hybridization. Several microarray chips like Affymetrix and Illumina arrays can genotype up to million SNPs in one go.

Sequencing Based Genotyping: Recent advances in next generation sequencing technologies have enabled direct low cost sequencing of whole genomes and exomes for SNP discovery and genotype calling. Platforms like Illumina NovaSeq and BGISEQ provide accurate SNP calling from sequencing data at very high throughput.

Luminex Based Genotyping: The Luminex xTAG system uses unique dye labeled microspheres to multiplex SNP Genotyping and Analysis. It provides medium throughput genotyping of hundred to thousands of SNPs simultaneously.

Other Techniques: Methods like SNaPshot, MassARRAY, pyrosequencing are also commonly used for targeted lower throughput genotyping of few hundred SNPs.

SNP Data Analysis

Several bioinformatics tools and statistical methods are applied to genotype data to gain meaningful biological insights:

Quality Control: Rigorous quality control is performed to filter out poor quality samples and SNPs based on criteria like call rate, heterozygosity and Hardy-Weinberg equilibrium.

Population Genetics Analysis: Tools like PLINK, EIGENSTRAT help analyze population structure, ancestry, linkage disequilibrium patterns, ancient migrations etc. in large reference populations.

Heritability & Genome Wide Association: GCTA, GEMMA, PLINK/SEQ are used to estimate trait heritability and identify genome wide significant trait associated SNPs through case control studies.

Functional Annotation: Plugins in ANNOVAR, VEP help annotating SNPs to their location, effect on genes, evolutionary conservation, regulatory regions etc. to prioritize potential functional SNPs.

Pharmacogenomics Analysis: Important pharmacogenes affecting drug response are interrogated for variants tied to drug efficacy, safety, dosage requirements in diverse populations.

Get More Insights on SNP Genotyping and Analysis