TY - JOUR T1 - Systematic Design and Comparison of Expanded Carrier Screening Panels JF - bioRxiv DO - 10.1101/080713 SP - 080713 AU - Kyle A. Beauchamp AU - Dale Muzzey AU - Kenny K. Wong AU - Gregory J. Hogan AU - Kambiz Karimi AU - Sophie I. Candille AU - Nikita Mehta AU - Rebecca Mar-Heyming AU - K. Eerik Kaseniit AU - H. Peter Kang AU - Eric A. Evans AU - James D. Goldberg AU - Gabriel A. Lazarin AU - Imran S. Haque Y1 - 2016/01/01 UR - http://biorxiv.org/content/early/2016/11/11/080713.abstract N2 - Purpose The recent growth in pan-ethnic expanded carrier screening (ECS) has raised questions about how such panels might be designed and evaluated in a principled manner. Systematic design principles for ECS panels might improve clinical detection of at-risk couples and facilitate objective discussions of panel choice.Methods Guided by medical-society statements, we propose a method for the design of ECS panels that aims to maximize both the aggregate and per-disease sensitivity and specificity across a range of Mendelian disorders considered “severe” or “profound” by a systematic classification scheme. We evaluated this method retrospectively using results from 474,644 de-identified carrier screens. We then constructed several idealized panels to highlight strengths and limitations of different ECS methodologies.Results Based on modeled fetal risks for “severe” and “profound” diseases, a commercially available ECS panel (Counsyl Family Prep Screen) is expected to detect 183 affected conceptuses per 100,000 in the US population. A screen’s sensitivity is greatly impacted by two factors: (1) the methodology used (e.g., full-exon sequencing finds up to 46 more affected fetuses per 100,000 than targeted genotyping with an optimal 50 variant panel), and (2) the detection rate of the screen for diseases with high prevalence and complex molecular genetics (e.g., fragile X syndrome, spinal muscular atrophy, 21-hydroxylase deficiency, and alpha-thalassemia account for 54 affected fetuses per 100,000).Conclusion The described approaches allow principled, quantitative evaluation of which diseases and methodologies are appropriate for pan-ethnic expanded carrier screening. ER -