Rapture
Rapture
Restriction-site associated DNA capture (Rapture) is a massively parallel targeted DNA sequencing technique that combines RAD-Seq and sequence capture to compare multiple genes of interest between large numbers of samples. The targeted sequencing is based on specifically identifying restriction enzyme sites near the loci of interest.
Genomic DNA samples are pooled into individual well-plates and digested with selected restriction enzymes. Biotinylated RAD adapters with well-specific barcodes are ligated to the sticky ends before pooling all the wells in each plate. Barcoded DNA fragments are then randomly sheared and bound to streptavidin beads. Again, using restriction enzymes, fragments are cleaved from the streptavidin beads and used in standard DNA library preparation kits with plate-specific barcode labels. Now, libraries from both plates are pooled and hybridized with biotinylated bait-oligos specific to each RAD tags before a final streptavidin pull-down. Isolated DNA fragments are sequenced and arranged according to their RAD tags, plate-barcodes, and well-barcodes.
Pros:
- Massively-parallel targeted DNA sequencing for SNP identification
- Improved number of mapped fragments and loci coverage compared to RAD-Seq
Cons:
- RAD tags needs to be designated prior to the experiment
- Bias towards sequences closer to the restriction cut site