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© 2020 Morgan et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Background Research funders use a wide variety of application assessment processes yet there is little evidence on their relative advantages and disadvantages. A broad distinction can be made between processes with a single stage assessment of full proposals and those that first invite an outline, with full proposals invited at a second stage only for those which are shortlisted. This paper examines the effects of changing from a one-stage to a two-stage process within the UK’s National Institute for Health Research’s (NIHR) Research for Patient Benefit (RfPB) Programme which made this change in 2015. Methods A retrospective comparative design was used to compare eight one-stage funding competitions (912 applications) with eight two-stage funding competitions (1090 applications). Comparisons were made between the number of applications submitted, number of peer and lay reviews required, the duration of the funding round, average external peer review scores, and the total costs involved. Results There was a mean number of 114 applications per funding round for the one-stage process and 136 for the two-stage process. The one-stage process took a mean of 274 days and the two-stage process 348 days to complete, although those who were not funded (i.e. the majority) were informed at a mean of 195 days (mean 79 days earlier) under the two-stage process. The mean peer review score for full applications using the one-stage process was 6.46 and for the two-stage process 6.82 (5.6% difference using a 1–10 scale (with 10 being the highest), but there was no significant difference between the lay reviewer scores. The one-stage process required a mean of 423 peer reviews and 102 lay reviewers and the two-stage process required a mean of 208 peer reviews and 50 lay reviews (mean difference of 215 peer reviews and 52 lay reviews) per funding round. Overall cost per funding round changed from £148,908 for the one-stage process to £105,342 for the two-stage process saving approximately £43,566 per round. Conclusion We conclude that a two-stage application process increases the number of applications submitted to a funding round, is less burdensome and more efficient for all those involved with the process, is cost effective and has a small increase in peer reviewer scores. For the addition of fewer than 11 weeks to the process substantial efficiencies are gained which benefit funders, applicants and science. Funding agencies should consider adopting a two-stage application assessment process.

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