Suzanne de Bruijn

144 Chapter 3.1 SUPPLEMENTARY REFERENCES 1. Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25 , 1754-1760 (2009). 2. 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). 3. Krumm, N., Sudmant, P.H., Ko, A., O'Roak, B.J., Malig, M., Coe, B.P. et al. Copy number variation detection and genotyping from exome sequence data. Genome Research 22 , 1525-1532 (2012). 4. 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). 5. 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). 6. Robinson, J.T., Thorvaldsdóttir, H., Winckler, W., Guttman, M., Lander, E.S., Getz, G. et al. Integrative genomics viewer. Nature Biotechnology 29 , 24 (2011). 7. Hardenbol, P., Banér, J., Jain, M., Nilsson, M., Namsaraev, E.A., Karlin-Neumann, G.A. et al. Multiplexed genotyping with sequence-tagged molecular inversion probes. Nature Biotechnology 21 , 673 (2003). 8. Khandelwal, K.D., Ishorst, N., Zhou, H., Ludwig, K.U., Venselaar, H., Gilissen, C. et al. Novel IRF6 mutations detected in orofacial cleft patients by targeted massively parallel sequencing. Journal of Dental Research 96 , 179-185 (2016). 9. Tarpey, T. Linear transformations and the k-means clustering algorithm: Applications to clustering curves. Journal of the American Statistical Association 61 , 34-40 (2007). 10. Ketchen, D.J. & Shook, C.L. The application of cluster analysis in strategic management research: an analysis and critique. Strategic Management Journal 17 , 441-458 (1996). 11. Oonk, A.M., Beynon, A.J., Peters, T.A., Kunst, H.P., Admiraal, R.J., Kremer, H. et al. Vestibular function and temporal bone imaging in DFNB1. Hearing Research 327 , 227-34 (2015). 12. Vanspauwen, R., Wuyts, F.L., Krijger, S. & Maes, L.K. Comparison of different electrode configurations for the oVEMP with bone-conducted vibration. Ear and Hearing 38 , 205-211 (2017). 13. Papathanasiou, E.S., Murofushi, T., Akin, F.W. & Colebatch, J.G. International guidelines for the clinical application of cervical vestibular evoked myogenic potentials: an expert consensus report. Clin Neurophysiol 125 , 658-666 (2014). 14. Pfaffl, M.W. A newmathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Research 29 , e45-e45 (2001). 15. Diaz-Horta, O., Abad, C., Cengiz, F.B., Bademci, G., Blackwelder, P., Walz, K. et al. Ripor2 is involved in auditory hair cell stereociliary bundle structure and orientation. Journal of Molecular Medicine 96 , 1227-1238 (2018).

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