What is low-pass whole genome sequencing with target capture?
Low-pass whole genome sequencing with target capture and imputation combines a number of different, highly effective sequencing approaches in a single assay. With lp-WGS, the genome is shotgun sequenced at a low coverage (typically <1x), delivering genome-wide data which is then imputed to a haplotype reference panel to provide genome-wide genotype calls. In addition, target capture techniques are employed to capture specific regions of interest by the design and use of custom probes to target desired genomic regions. These probes selectively bind to and capture the regions of interest from the whole-genome sequencing library, allowing for a higher-fidelity analysis at key high-value loci.
The combination of low-pass whole-genome sequencing and target capture allows us to efficiently analyze and study specific genomic regions while still obtaining a broad overview of the entire genome. This approach is particularly useful when investigating specific genomic regions associated with particular traits, as it provides a cost-effective and targeted solution for genomic analysis while still supporting breeding objectives.
Alongside providing soybean DNA samples, Gencove identified 11 soybean gene targets of interest. These genes have previously been the subject of gene editing experiments. Therefore projects involving discovery of standing natural variation, as well as ongoing management of gene editing events could be of interest to a breeding program. The team at Twist sequenced the samples to 1x coverage with lp-WGS, and at 30x at the 11 target sites. Gencove then performed variant calling, low-pass imputation and QC on output data, and returned results on the success of capture at the 11 target sites.