Table 3.

FBAT analysis for chromosome 17q11.2-q23.3 SNPs that showed positive allelic associations with VL at CCL1 and CCL16 under an additive model.

			Additive Model
Gene/SNP	Allele	Frequency	Z score	P value	Pc
CCL1/rs159271	C	0.87	+2.18	0.02	0.03
	T	0.13	−2.18	0.02	0.03
CCL1/rs159273	G	0.88	+1.95	0.02	0.05
	T	0.12	−1.95	0.02	0.05
CCL16/rs2063979	A	0.58	+2.21	0.03	0.03
	G	0.42	−2.21	0.03	0.03
CCL16/rs854680	G	0.62	+2.06	0.02	0.04
	T	0.38	−2.06	0.02	0.04

A total of 80 SNPs (see Supplementary Information Table 1) within or adjacent to candidate genes across the chromosome 17q11.2-q23.3 region were genotyped for all DNAs from the Belém Family Study (Table 1). SNP allele frequencies were determined from unrelated individuals in the families using SPLINK.³¹ Tests for deviation from Hardy-Weinberg equilibrium (HWE) were performed within STATA v8.0 (_{Electronic Database Information 4}) using the GenAssoc package (_{Electronic Database Information 5}). One marker that showed significant deviation from HWE was eliminated from the analysis. Nine markers with minor allele frequencies <0.1 (see Supplementary Information Table 1) were not informative for allelic association testing. Association tests were performed using the family-based transmission disequilibrium test (TDT)³² generalized to allow additive, dominant and genotype analyses within FBAT.¹⁵ An empirical estimator of the variance (fbat –e) was used to detect allelic association in the presence of linkage (P corrected = Pc). FBAT is available online (_{Electronic Database Information 6}). TDT power approximations for trios were carried out using the method of Knapp.³³ A sample of 200 child-parent trios, equivalent to the Belém Family Study families, has 99% power to detect an effect (OR = 2; p=0.05) for SNPs with variant allele frequency of 0.4; 72% power for SNP with variant allele frequency of 0.1.