Targeting de novo loss-of-function variants in constrained disease genes improves diagnostic rates in the 100,000 Genomes Project
Eleanor G. Seaby, Neil Thomas, Amy Webb, Helen Brittain, Ana Lisa Taylor Tavares, John C. Ambrose, Prabhu Arumugam, R. Bevers, Marta Bleda, F Boardman-Pretty, C. R. Boustred, Helen Brittain, Mark J. Caulfield, G. C. Chan, Tom Fowler, Adam Giess, Angela Hamblin, S. A. Henderson, Tim Hubbard, Robert B. Jackson, Lesley Jones, Dalia Kasperavičiūtė, Melis Kayikci, Athanasios Kousathanas, L. Lahnstein, S. E. A. Leigh, Ivone Leong, F. J. Lopez, F. Maleady-Crowe, Meriel McEntagart, Federico Minneci, Loukas Moutsianas, M. Mueller, Nirupa Murugaesu, Anna C. Need, Peter O’Donovan, Christopher A. Odhams, Christine Patch, D. Perez-Gil, Mariana Buongermino Pereira, J. Pullinger, T. Rahim, Álvaro Rendón, Thomas R. Rogers, K Savage, K. Sawant, Richard H. Scott, Afshan Siddiq, A. Sieghart, Sophie Smith, Alona Sosinsky, Ashley Stuckey, M. Tanguy, Ana Lisa Taylor Tavares, Elizabeth R. Thomas, S. R. Thompson, Arianna Tucci, M. J. Welland, Eleanor Williams, Kate Witkowska, S. M. Wood, Diana Baralle, Heidi L. Rehm, Anne O’Donnell‐Luria, Sarah Ennis
Abstract
BACKGROUND: Genome sequencing was first offered clinically in the UK through the 100,000 Genomes Project (100KGP). Analysis was restricted to predefined gene panels associated with the patient's phenotype. However, panels rely on clearly characterised phenotypes and risk missing diagnoses outside of the panel(s) applied. We propose a complementary method to rapidly identify pathogenic variants, including those missed by 100KGP methods. METHODS: The Loss-of-function Observed/Expected Upper-bound Fraction (LOEUF) score quantifies gene constraint, with low scores correlated with haploinsufficiency. We applied DeNovoLOEUF, a filtering strategy to sequencing data from 13,949 rare disease trios in the 100KGP, by filtering for rare, de novo, loss-of-function variants in disease genes with a LOEUF score < 0.2. We compared our findings with the corresponding patient's diagnostic reports. RESULTS: 324/332 (98%) of the variants identified using DeNovoLOEUF were diagnostic or partially diagnostic (whereby the variant was responsible for some of the phenotype). We identified 39 diagnoses that were "missed" by 100KGP standard analyses, which are now being returned to patients. CONCLUSION: We have demonstrated a highly specific and rapid method with a 98% positive predictive value that has good concordance with standard analysis, low false-positive rate, and can identify additional diagnoses. Globally, as more patients are being offered genome sequencing, we anticipate that DeNovoLOEUF will rapidly identify new diagnoses and facilitate iterative analyses when new disease genes are discovered.