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Disclaimer: Supplementary materials have been peer-reviewed but not copyedited.

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Appendix A A model for genotypic counts with discordant relative pairs.

Appendix B Simulations to investigate sampling properties of the penetrance odds ratio estimates.

Appendix C Simulations to assess departures from assumptions.

Table S1 Explicit maximum likelihood estimates and log likelihood values when there are three or fewer zero counts.

Table S2 Simulated power of the tests with extra binomial variation, inline image, inline image, inline image

Table S3 Simulated power of the tests when there is a single covariate: inline image, inline image, inline image and inline image and inline image

Table S4 Simulated power of the tests when there is a single covariate: inline image, inline image, inline image and inline image and inline image

Table S5 Simulated power of the tests with extra binomial variation, inline image, inline image, inline image

Table S6 Simulated power of the tests when there is a single covariate: inline image, inline image, inline image and inline image and inline image

Table S7 Simulated power of the tests when there is a single covariate inline image, inline image, inline image and inline image and inline image

Table S8 Simulated significance level for the LR and Score tests.

Figure S1 Bias and precision of penetrance odds estimates, inline image, inline image

Figure S2 Bias and precision of penetrance odds estimates, inline image, inline image.

Figure S3 Bias and precision of penetrance odds estimates, inline image, inline image

Figure S4 Bias and precision of penetrance odds estimates, inline image, inline image

Figure S5 Bias and precision of penetrance odds estimates, inline image, inline image

Figure S6 Bias and precision of penetrance odds estimates, inline image, inline image

Figure S7 Bias and precision of penetrance odds estimates, inline image, inline image

Figure S8 Bias and precision of penetrance odds estimates, inline image, inline image

Figure S9 Bias and precision of penetrance odds estimates, inline image, inline image

Figure S10 Contours of asymptotic power for inline image, inline image and inline image

Figure S11 Contours of approximate power for inline image, inline image and inline image

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