In-solution hybridisation for the targeted enrichment of the whole mitochondrial genome

A detailed protocol is presented for the targeted enrichment of whole mitochondrial genomes based on an in-solution hybridisation strategy. Bait is produced in-house by sonication of two-long range PCR amplicons and ligation of biotinylated double-stranded adapters. Indexed target DNA is hybridised with the bait in a multiplex enrichment reaction and pulled down using magnetic streptavidin beads followed by subsequent post-enrichment PCR and sequencing on an Illumina MiSeq. This strategy removes the need for expensive commercial bait probes while allowing enrichment of multiple samples in a single hybridisation reaction. The method is particularly suitable for degraded DNA as it is able to enrich short DNA fragments and is not susceptible to polymerase artefacts introduced during PCR-based assays.edition: 2status: publishe