title: A Statistical Guide to the Design of Deep Mutational Scanning Experiments.
abstract: The characterization of the distribution of mutational effects is a key goal in evolutionary biology. Recently developed deep-sequencing approaches allow for accurate and simultaneous estimation of the fitness effects of hundreds of engineered mutations by monitoring their relative abundance across time points in a single bulk competition. Naturally, the achievable resolution of the estimated fitness effects depends on the specific experimental setup, the organism and type of mutations studied, and the sequencing technology utilized, among other factors. By means of analytical approximations and simulations, we provide guidelines for optimizing time-sampled deep-sequencing bulk competition experiments, focusing on the number of mutants, the sequencing depth, and the number of sampled time points. Our analytical results show that sampling more time points together with extending the duration of the experiment improves the achievable precision disproportionately compared with increasing the sequencing depth or reducing the number of competing mutants. Even if the duration of the experiment is fixed, sampling more time points and clustering these at the beginning and the end of the experiment increase experimental power and allow for efficient and precise assessment of the entire range of selection coefficients. Finally, we provide a formula for calculating the 95%-confidence interval for the measurement error estimate, which we implement as an interactive web tool. This allows for quantification of the maximum expected a priori precision of the experimental setup, as well as for a statistical threshold for determining deviations from neutrality for specific selection coefficient estimates.
authors.affiliation: School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics, Lausanne, Switzerland sebastian.matuszewski@epfl.ch evoldynamics@gmail.com.
authors.forename: Sebastian
authors.identifier: http://orcid.org/0000-0002-4393-9283
authors.initials: S
authors.lastname: Matuszewski
authors.affiliation: School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland School of Basic Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
authors.forename: Marcel E
authors.initials: ME
authors.lastname: Hildebrandt
authors.affiliation: Instituto Gulbenkian de Ciência, Oeiras, Portugal.
authors.forename: Ana-Hermina
authors.identifier: http://orcid.org/0000-0002-9088-2232
authors.initials: AH
authors.lastname: Ghenu
authors.affiliation: School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics, Lausanne, Switzerland.
authors.forename: Jeffrey D
authors.initials: JD
authors.lastname: Jensen
authors.affiliation: School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland Swiss Institute of Bioinformatics, Lausanne, Switzerland Instituto Gulbenkian de Ciência, Oeiras, Portugal sebastian.matuszewski@epfl.ch evoldynamics@gmail.com.
authors.forename: Claudia
authors.identifier: http://orcid.org/0000-0003-4730-758X
authors.initials: C
authors.lastname: Bank
mesh_terms: D005075:Biological Evolution; D001699:Biometry; D004252:DNA Mutational Analysis / Q000379:methods*; D056084:Genetic Fitness; D005828:Genetics, Population / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D008957:Models, Genetic; D015233:Models, Statistical; D009154:Mutation; D012641:Selection, Genetic
keywords: distribution of fitness effects; experimental design; experimental evolution; mutation; population genetics