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Figure S1. The MAF distribution of rare variants in the selected gene, estimated in the 1000 Genomes Project CEU data, Release August 2010.

Figure S2. LD plot for LowLD pattern. Top: D’ values of LD. Bottom: r2 values of LD.

Figure S3. LD plot for MedLD pattern. Top: D’ values of LD. Bottom: r2 values of LD.

Figure S4. LD plot for HighLD pattern. Top: D’ values of LD. Bottom: r2 values of LD.

Figure S5. LD plot in the real data of the 1000 Genomes Project CEU haplotypes. Top: D’ values of LD. Bottom: r2 values of LD. The linked image cannot be displayed. The file may have been moved, renamed, or deleted. Verify that the link points to the correct file and location.

Figure S6. Power of famSKAT and famWS in the MedLD pattern. c is the number of causal variants. A) c= 6; B) c= 18. M0, M30 and M50 represent the proportion of protective variants (0%, 30% and 50% respectively).

Figure S7. Power of famSKAT and famWS in the HighLD pattern. c is the number of causal variants. A) c= 6; B) c= 18. M0, M30 and M50 represent the proportion of protective variants (0%, 30% and 50% respectively).

Figure S8. Power of famSKAT in the scenario of 18 causal variants for LowLD, MedLD, and HighLD. M0, M30 and M50 represent the proportion of protective variants (0%, 30% and 50% respectively).

Figure S9. Power of famSKAT in the scenario of six causal variants and the HighLD pattern. M0, M30 and M50 represent the proportion of protective variants (0%, 30% and 50% respectively). Dense100 is the analysis using all individuals sequenced. Dense20 is the analysis using 20% of individuals sequenced, from each pedigree. Imputation20 is the analysis in imputation data based on the previous sequenced individuals (20%). The association test is based on allelic dosages.

Figure S10. Power of famSKAT in the scenario of 12 causal variants and the HighLD pattern. M0, M30 and M50 represent the proportion of protective variants (0%, 30% and 50% respectively). Dense100 is the analysis using all individuals sequenced. Dense20 is the analysis using 20% of individuals sequenced, from each pedigree. Imputation20 is the analysis in imputation data based on the previous sequenced individuals (20%). The association test is based on allelic dosages.

Table S1. Type I error of famSKAT and famWS: in the sequence data (for three proportions of dense markers individuals, d = 30%, d = 40% and d = 80%).

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