Suzanne de Bruijn

226 Chapter 4 SUPPLEMENTARY REFERENCES 1. den Hollander, A.I., van der Velde-Visser, S.D., Pinckers, A.J.L.G., Hoyng, C.B., Brunner, H.G. & Cremers, F.P.M. Refined mapping of the gene for autosomal dominant retinitis pigmentosa (RP17) on chromosome 17q22. Human Genetics 104 , 73-76 (1999). 2. Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25 , 1754-1760 (2009). 3. McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research 20 , 1297-1303 (2010). 4. Boeva, V., Popova, T., Bleakley, K., Chiche, P., Cappo, J., Schleiermacher, G. et al. Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data. Bioinformatics 28 , 423-425 (2012). 5. Robinson, J.T., Thorvaldsdóttir, H., Winckler, W., Guttman, M., Lander, E.S., Getz, G. et al. Integrative genomics viewer. Nature Biotechnology 29 , 24-26 (2011). 6. Karczewski, K.J., Francioli, L.C., Tiao, G., Cummings, B.B., Alföldi, J., Wang, Q. et al. The mutational constraint spectrum quantified from variation in 141,456 humans. Nature 581 , 434-443 (2020). 7. Fiorentino, A., Fujinami, K., Arno, G., Robson, A.G., Pontikos, N., Arasanz Armengol, M. et al. Missense variants in the X-linked gene PRPS1 cause retinal degeneration in females. Human Mutation 39 , 80-91 (2018). 8. Desvignes, J.-P., Bartoli, M., Delague, V., Krahn, M., Miltgen, M., Béroud, C. et al. VarAFT: a variant annotation and filtration system for human next generation sequencing data. Nucleic Acids Research 46 , W545-W553 (2018). 9. Plagnol, V., Curtis, J., Epstein, M., Mok, K.Y., Stebbings, E., Grigoriadou, S. et al. A robust model for read count data in exome sequencing experiments and implications for copy number variant calling. Bioinformatics 28 , 2747-2754 (2012). 10. Roller, E., Ivakhno, S., Lee, S., Royce, T. & Tanner, S. Canvas: versatile and scalable detection of copy number variants. Bioinformatics 32 , 2375-2377 (2016). 11. Chen, X., Schulz-Trieglaff, O., Shaw, R., Barnes, B., Schlesinger, F., Källberg, M. et al. Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications. Bioinformatics 32 , 1220-1222 (2016). 12. Fiorentino, A., Yu, J., Arno, G., Pontikos, N., Halford, S., Broadgate, S. et al. Novel homozygous splicing mutations in ARL2BP cause autosomal recessive retinitis pigmentosa. Molecular Vision 24 , 603-612 (2018). 13. Sievers, F., Wilm, A., Dineen, D., Gibson, T.J., Karplus, K., Li, W. et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Molecular Systems Biology 7 , 539 (2011). 14. Smit, A., Hubley, R. & Green, P. RepeatMasker Open-4.0. Available from: http://www. repeatmasker.org .

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