Harnessing the 100,000 Genomes Project whole genome sequencing data - an unbiased systematic tool to filter by biologically validated regions of functionality

Whole genome sequencing (WGS ) is championed by the UK National Health Service (NHS) to identify genetic variants that cause particular diseases. The full potential of WGS has yet to be realised as early data analytic steps prioritise protein-coding genes, and effectively ignore the less well annotated non-coding genome which is rich in transcribed and critical regulatory regions. To address, we developed a filter, which we call GROFFFY, and validated in WGS data from hereditary haemorrhagic telangiectasia patients within the 100,000 Genomes Project. Before filter application, the mean number of DNA variants compared to human reference sequence GRCh38 was 4,867,167 (range 4,786,039-5,070,340), and one-third lay within intergenic areas. GROFFFY removed a mean of 2,812,015 variants per DNA. In combination with allele frequency and other filters, GROFFFY enabled a 99.56% reduction in variant number. The proportion of intergenic variants was maintained, and no pathogenic variants in disease genes were lost. We conclude that the filter applied to NHS diagnostic samples in the 100,000 Genomes pipeline offers an efficient method to prioritise intergenic, intronic and coding gDNA variants. Reducing the overwhelming number of variants while retaining functional genome variation of importance to patients, enhances the near-term value of WGS in clinical diagnostics. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This research was made possible through access to the data and findings generated by the 100,000 Genomes Project. The 100,000 Genomes Project is managed by Genomics England Limited (a wholly owned company of the Department of Health and Social Care). The 100,000 Genomes Project is funded by the National Institute for Health Research (NIHR) and NHS England. The Wellcome Trust, Cancer Research UK and the Medical Research Council have also funded research infrastructure. The 100,000 Genomes Project uses data provided by patients and collected by the National Health Service as part of their care and support. We thank the National Health Service staff of the UK Genomic Medicine Centres and the participants for their willing participation. This research was co-funded by the NIHR Imperial Biomedical Research Centre. The views expressed are those of the authors and not necessarily those of funders, the NHS, the NIHR, or the Department of Health and Social Care. ### Author Declarations All relevant ethical guidelines have been followed; any necessary IRB and/or ethics committee approvals have been obtained and details of the IRB/oversight body are included in the manuscript. Yes All necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes Primary data in an anonymised format are available to Researchers within the Genomics England Research Environment.