An exploration of heterogeneity in genetic analysis of complex pedigrees: linkage and association using whole genome sequencing data in the MAP4 region

Table 1 Replicate 1 linkage LOD scores, association p values, and regression coefficients for pedigree-specific and combined all pedigree analysis of locus 10 in MAP4

Pedigree	MAF	MAP4 maxLOD	Locus 10 LOD	QTDT pvalue	MG pvalue	QTDT β_w	QTDT β_b	MG β	MG se(β)
2	0.01	0.36	0.06	0.42	0.012	−9.2	−29.6	−21.3	8.5
4	0.02	1.39	0.01	1	1	NA	NA	NA
5	0.11	1.64	1.60	0.002	6.70E-04	−17.4	−14.5	−14.6	3.4
9	0.12	0.08	0	0.64	0.18	9.0	−13.2	−10.1	7.2
10	0.07	0.27	0.26	0.002	2.40E-05	−21.1	−19.5	−19.5	4.2
11	0.03	0.13	0	1	0.04	NA	NA	−22.5	10.6
14	0.01	0	0	1	1	NA	NA	NA
16	0.04	0.14	0	1	0.005	NA	NA	−27.6	9.3
20	0.04	0.06	0	1	0.004	NA	NA	−25.8	8.8
21	0.04	0	0	0.98	0.99	0.01	−0.006	NA	10.4
25	0.05	0	0	0.62	0.73	−0.1	0.001	−0.9	7.8
27	0.06	0.35	0.32	0.04	5.40E-04	−17.9	−36.7	−28.2	6.0
Combined	0.03		2.26	1.5 × 10 ⁻⁵	1.3 × 10 ⁻¹⁴	−15.9	−18.4	−17.4	2.1

Location is 48040283 bp with effect size beta = −9.91. SBP %variation explained = 0.028. The variant is segregating in 12/20 pedigrees.

ISSN: 1753-6561