Clinical sequencing is looming and recently I've heard more, and better, arguments for using whole genomes. These have mainly focused on the quality of PCR-free genomes, which have uniform coverage and few regions of missing or very low coverage. Compared to the PCR and hybridisation-capture artefact's in exomes, or the focus on a biased set of genes a genome can sound very convincing (especially if you ignore the analysis/storage issues). Until recently the cost has still been too high, but Illumina recently released PCR-free on X Ten reducing the cost substantially. However there are so many different arguments that it is difficult to determine if we can perform a one-size-fits-all sequencing experiment.
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Comparison of Illumina PCR-free to PCR+ kits |
Recently I started talking to people who use terms like analytic validity, clinical validity and clinical utility - these meant something to me, but what they meant for genome sequencing assays, exomes and amplicomes I was not so sure so I thought I'd find out.