April 17, 2024
SNP Genotyping and Analysis

SNP Genotyping and Analysis: Unlocking Genetic Secrets

Single nucleotide polymorphisms, commonly known as SNPs, are variations in DNA sequences between individuals. By genotyping and analyzing SNPs, researchers can gain valuable insights into human health, disease susceptibility and more.

What are SNPs?
SNPs occur when a single nucleotide in the genome sequence is altered. For example, the nucleotide could be changed from cytosine to thymine. Most SNPs have no effect, but some can influence traits and disease risk. SNPs act as genetic markers that allow researchers to track DNA variations across populations. With over 10 million known SNPs in the human genome, they provide an abundance of data for analysis.

Methods of SNP Genotyping

Several laboratory techniques can be used to genotype SNPs, but the main methods are microarrays and sequencing. Microarrays entail placing DNA samples onto chips containing probes for known SNPs. Laser detection identifies which alleles are present based on hybridization patterns. Next-generation sequencing directly reads the DNA sequences and identifies SNP positions. Both approaches have workflow automation for high-throughput genotyping of thousands to millions of SNPs simultaneously.

Linkage and Association Studies
One key use of SNP Genotyping and Analysis is linkage analysis, which maps chromosome regions statistically associated with disease. By comparing the SNP patterns of affected individuals and their relatives, researchers can locate genes likely involved in causing certain illnesses. Genome-wide association studies (GWAS) also examine patterns of SNPs across large populations but investigate associations independently, rather than through family pedigree analysis. Both methods have pinpointed genetic factors contributing to cancers, heart disease, diabetes and more.

Ancestry and Admixture Mapping
Genotyping SNP data from diverse human populations enables inference of ancestry proportions through admixture mapping. By analyzing ancestry informative markers that vary significantly between ethnic groups, researchers can determine an individual’s ancestral origins with high resolution. Admixture mapping additionally detects disease-related SNPs that display different frequencies between ancestral populations. This has led to discoveries in prostate cancer, asthma and other conditions exhibiting ancestry disparities.

Pharmacogenomics and Toxicogenomics
The cytochrome P450 enzymes metabolize many drugs and environmental chemicals in our bodies. Genetic variations in these enzymes, including SNPs, influence inter-individual variability in drug response and toxicity risk. Pharmacogenomic studies aim to personalize medication by correlating SNP profiles with treatment outcomes. Similarly, toxicogenomics examines how genetic factors impact toxicity susceptibility. Both fields have implications for precision medicine approaches tailored to a patient’s genome.

Personal Genomics and Direct-to-Consumer Testing
The declining costs of DNA sequencing and genotyping enable personal genomic services available directly to consumers. Companies offer to analyze hundreds of thousands or even millions of SNPs from saliva samples to report on ancestry,traits and health risks. However, the health implications from personal genomics require careful consideration of limitations like incomplete genomic contributions and environmental factors not addressed. Overall, as techniques advance, SNP analysis continues revealing more secrets encoded in our DNA.

1. Source: Coherent Market Insights, Public sources, Desk research
2. We have leveraged AI tools to mine information and compile it