GWAS shows the genetics behind cell-free DNA and highlights the importance of p.Arg206Cys in DNASE1L3 for non-invasive testing

Cell Rep. 2024 Oct 22;43(10):114799. doi: 10.1016/j.celrep.2024.114799. Epub 2024 Sep 25.

Abstract

The 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 the concentration and fragmentation properties of cfDNA using a genome-wide association study (GWAS) based on low-coverage whole-genome sequencing data of 140,000 Dutch non-invasive prenatal tests (NIPTs). Our GWAS detects many genome-wide significant loci, functional enrichments for phagocytes, liver, adipose tissue, and 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.

Keywords: CP: Genomics; DFFB; DNASE1L3; NIPT; PADI4; PANX1; VeriSeq; cell-free DNA; fetal fraction; fragmentomics; rs35677470.

MeSH terms

  • Cell-Free Nucleic Acids* / genetics
  • Endodeoxyribonucleases* / genetics
  • Endodeoxyribonucleases* / metabolism
  • Female
  • Fetus / metabolism
  • Genome-Wide Association Study* / methods
  • Humans
  • Noninvasive Prenatal Testing / methods
  • Pregnancy

Substances

  • Cell-Free Nucleic Acids
  • DNASE1L3 protein, human
  • Endodeoxyribonucleases