Celemics SNP Genotyping and Targeted Sequencing
SNP genotyping is a technology used to identify and analyze single nucleotide polymorphisms (SNPs) within the genome. SNPs are the most common form of genetic variation and play an important role in understanding disease susceptibility, drug response, and other genetic traits. SNP analysis is also widely applied in plant and animal breeding, helping to identify desirable genotypes linked to beneficial traits for improving breeds. SNP genotyping encompasses various methods, which can be selected based on the number of SNPs to analyze and sample size.
PCR-based genotyping is ideal for quickly analyzing a small number of SNP sites; efficient genotyping can be performed by designing PCR primers that target variant sites or by using fluorescent labels to monitor amplification. This method is straightforward and fast, making it advantageous for processing large sample numbers. However, it has limitations in scaling up the number of SNPs analyzed.
Microarray technology uses chips with predefined probes for multiple SNP sites, which bind to sample DNA to detect genotypes through fluorescence signals. Depending on the chip’s capacity, large numbers of SNPs can be analyzed simultaneously, and it offers rapid analysis for validated SNP lists, making it effective for large population studies. However, microarrays are limited to predetermined SNP targets, making it challenging to add or remove SNPs. Additionally, only designated sites on the chip can be analyzed, restricting the acquisition of information on adjacent regions.
Moreover, Genotyping-by-Sequencing (GBS) uses restriction enzymes to fragment DNA samples, allowing targeted regions to be sequenced. GBS enables high-resolution SNP analysis and allows examination of the surrounding sequence of SNPs. However, it requires restriction sites near the target SNPs, which can limit the regions that can be analyzed, and typically results in lower coverage.
Targeted sequencing involves enrichment of regions of interest and using NGS to sequence and analyze the SNPs. Depending on the number of SNPs, either multiplex PCR or hybridization-based targeted enrichment methods can be applied. Multiplex PCR is simpler and suited for fewer SNPs, while hybridization methods are more complex but can analyze a larger number of SNPs. Unlike GBS, targeted sequencing has no restriction site limitations and can detect not only SNPs but also indels and structural variations, offering high flexibility. Additionally, it is capable of gathering adjacent sequence information, facilitating novel marker discovery.
In summary, each genotyping method has unique strengths and limitations depending on the number of SNPs, sample throughput, and type of information desired. Choosing the appropriate technique based on the analysis goals and environment is essential for your successful research and/or diagnostic journey.
