**Appendices: Newbury, Simpson, Thompson & Bishop** Variation in neurodevelopmental outcomes in children with sex chromosome trisomies: protocol for a test of the double hit hypothesis **Appendix 1**: R scripts used in protocol **Appendix 2**: Extrapolation of norms for NEPSY subtests **Appendix 3**: Confirmatory factor analysis for general language measure **Appendix 4**: Creating a global measure of impairment **Appendix 5**: Prioritisation of genes for analysis **Appendix 6** - Genotyped SNPs in CNTNAP2 analysis region **Appendix 7** - Genotyped SNPs in NRXN1 analysis region **Appendix 8** is the xlsx file called **SCT_SNPlist_final forWOR** which contains details of the SNPs used in the analysis and their correlation structure Please see APPENDICES FOR RESULTS for **Appendix 9** Association of individual SNPs/phenotypes N.B. These Appendices have been reordered to match order of mention in the text but are otherwise unchanged from the original protocol.