Cell-Free DNA GWAS Reveals Importance of p.Arg206Cys in DNASE1L3 for Non-Invasive Testing

SUMMARY Properties of cell-free DNA (cfDNA) are intensely studied for their potential as non-invasive biomarkers. We explored the effect of common genetic variants on concentration and fragmentation properties of cfDNA using a GWAS based on low-coverage whole genome sequencing data of 140.000 Dutch Non-Invasive Prenatal Tests (NIPT). Our GWAS detects many genome-wide significant loci, functional enrichments for Phagocytes, Liver, Adipose tissue, Macrophages and genetic correlations with autoimmune and cardiovascular disease. A common (7%) missense variant in DNASE1L3 (p.Arg206Cys), strongly affects all cfDNA properties. It increases the size of fragments, lowers cfDNA concentrations, affects the distribution of cleave-site motifs and increases the fraction of circulating fetal DNA during pregnancy. For the application of NIPT, and potentially other cfDNA-based tests, this variant has direct clinical consequences as it increases the odds of inconclusive results and impairs the sensitivity of NIPT by causing predictors to overestimate the fetal fraction. HIGHLIGHTS Common variants affect properties of plasma cell-free DNA p.Arg206Cys in DNASE1L3 strongly affects the size of cell-free DNA fragments Fragmentomics-based fetal fraction predictors are affected by p.Arg206Cys Genetics behind cfDNA overlaps with autoimmune and cardiovascular diseases Competing Interest Statement The authors have declared no competing interest. Funding Statement This study was funded by a grant from the Netherlands Organization for Health Research and Development (ZonMw, No. 543002001). Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The Medical Ethics Review Committee of VU University Medical Center gave ethical approval for this work I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. 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, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes Data Availability All data produced in the present study are available upon reasonable request to the authors