Systematic reanalysis of genomic data improves quality of variant interpretation

• Published in: Clinical genetics Vol. 94; no. 1; pp. 174 - 178
• Main Authors: Hiatt, S.M., Amaral, M.D., Bowling, K.M., Finnila, C.R., Thompson, M.L., Gray, D.E., Lawlor, J.M.J., Cochran, J.N., Bebin, E.M., Brothers, K.B., East, K.M., Kelley, W.V., Lamb, N.E., Levy, S.E., Lose, E.J., Neu, M.B., Rich, C.A., Simmons, S., Myers, R.M., Barsh, G.S., Cooper, G.M.
• Format: Journal Article
• Language: English
• Published: Oxford, UK Blackwell Publishing Ltd 01-07-2018
• Subjects: clinical sequencing; CSER; data sharing; developmental delay; Developmental disabilities; Genetic diversity; intellectual disability; reanalysis; VUS; clinical sequencing; CSER; VUS; developmental delay; reanalysis; data sharing; intellectual disability
• ISSN: 0009-9163; 1399-0004
• DOI: 10.1111/cge.13259

As genomic sequencing expands, so does our knowledge of the link between genetic variation and disease. Deeper catalogs of variant frequencies improve identification of benign variants, while sequencing affected individuals reveals disease‐associated variation. Accumulation of human genetic data thus makes reanalysis a means to maximize the benefits of clinical sequencing. We implemented pipelines to systematically reassess sequencing data from 494 individuals with developmental disability. Reanalysis yielded pathogenic or likely pathogenic (P/LP) variants that were not initially reported in 23 individuals, 6 described here, comprising a 16% increase in P/LP yield. We also downgraded 3 LP and 6 variants of uncertain significance (VUS) due to updated population frequency data. The likelihood of identifying a new P/LP variant increased over time, as ~22% of individuals who did not receive a P/LP variant at their original analysis subsequently did after 3 years. We show here that reanalysis and data sharing increase the diagnostic yield and accuracy of clinical sequencing.