P0073Efficient High-Throughput SNP Discovery and Genotyping Using LGC’s Normalised Genotyping-By-Sequencing (nGBS) Method
Large-scale genotyping programs require efficient tools for high-density SNP discovery. Whole genome shotgun (WGS) sequencing of parental genotypes is a commonly utilised technique yet this is often prohibitively expensive and resource intensive. Instead, traditional Genotyping-by-Sequencing (GBS) is used whereby genome sequence complexity is reduced to certain regions or features that can then be efficiently sequenced for a large number of samples.
LGC present an optimised, self-tuning GBS method called normalised GBS (nGBS) that is applicable to any kind of genome, regardless of size, methylation pattern, and type and abundance of repetitive elements. This method efficiently reduces the genome complexity of any species to a few hundred thousand loci across the complete genome, with no prior knowledge of the genome. The selected loci are reliably sequenced across large sample batches using next generation sequencing. As a result, simultaneous SNP discovery and genotyping is carried out for between 48 and several thousand samples at low cost per sample and without prior assay design effort and bias. Typically, a set of 5000 – 50000 polymorphic loci with high-quality genotype calls in ≥75% of samples is generated. The entire data analysis process can be performed using publically available analysis packages or an LGC-developed pipeline optimised for nGBS data.