SNP Fine Mapping

CD genomics provides SNP fine mapping service for large SNP number and high volume of samples to help you validate and confirm the SNP loci of interest based on a subset of the detected SNPs.

SNP fine mapping often follows large-scale whole genome SNP genotyping studies to zoom into potential genes associated with the phenotypes of interest. Fine mapping studies generally involve fewer SNPs and a large sample size. Once a genome wide SNP screening has been done and the potential targets have been identified, fine mapping should be performed. A good genotyping platform for fine mapping should achieve a high call rate for all selected SNPs, at a relatively high multiplex level without time-consuming assay optimization processes. Primer extension and allele-specific ligation-based platforms are suitable for fine mapping applications.

We offer several assay types for verifying SNP markers discovered by RADseq, GBS, SNP chips or similar technologies. They include:

MassARRAY SNP Genotyping. A non-fluorescent detection platform utilizing mass spectrometry to accurately and sensitively measure PCR-derived amplicons

SNaPshot. A primer extension-based method for genotyping known SNP positions through the automated DNA analyzer.

TaqMan SNP Genotyping. A commonly used SNP genotyping method developed by Life Technologies.

These platforms can achieve uniplex (TaqMan SNP Genotyping and SNaPshot) or multiplex (MassARRAY SNP Genotyping) genotyping. These platforms are also highly flexible. The throughput of SNP number and sample size can be balanced at the users’ discretion, and failed SNP assays can be redesigned and reordered quickly.

Our experts offer consultation for you with genotyping strategy determination and experiment planning to meet your specific research needs in the best and most economical way as soon as possible.