Strategies for selection of subjects for sequencing after detection of a linkage peak

BMC Proceedings

Table 2 Association analysis for C17S4578 comparing case subjects to opposite extreme control subjects in eight linked pedigrees

Strategy	Case subject genotype counts^a	Control subject genotype counts^a	Dominant model		Recessive model
			Effect size	Benefit-cost ratio	Effect size	Benefit-cost ratio
Strategies focused on age
A. Youngest haplotype-carrier case subject in each pedigree vs. oldest non-haplotype-carrier control subject	5/1/2	1/5/2	1	0.06	11.67	0.73
B. Youngest case subject vs. oldest control subject in each pedigree	4/4/0	1/3/4	16.0^b	1.0	7	0.44
Strategies focused on low-covariate status
C. All low-covariate haplotype-carrier case subjects vs. all high-covariate non-haplotype-carrier control subjects	7/5/1	0/4/6	18^c	0.78	23.3^b,d	1.01
D. Families with 2+ low-covariate haplotype-carrier case subjects vs. all high-covariate non-haplotype-carrier control subjects	4/4/1	0/4/6	12^c	0.63	16.0^b,d	0.84
E. All low-covariate case subjects vs. all high-covariate control subjects	7/6/3	0/4/7	7.58	0.28	17.1^b,d	0.63
F. Lowest covariate case subject vs. highest covariate control subject per pedigree	3/4/1	0/4/4	7	0.44	5.3	0.33
Other strategies
G. All haplotype-carrier case subjects vs. all non-haplotype-carrier control subjects per pedigree	10/21/9	7/66/104	4.91^c	0.02	8.1^c	0.04
H. All case subjects vs. all control subjects	10/40/31	10/86/110	1.85^c	0.01	2.76^c	0.01
I. Random case subject vs. random control subject per pedigree	0/5/3	1/2/5	2.78	0.17	0	0.00

^a The three values are the counts for homozygote rare, heterozygote, and wild-type variants.
^b For cells with zero count, we added 0.5 to the cell to compute the odds ratio.
^cp < 0.05.
^d Unable to compute significance because of a zero cell, and either case or control subjects or both are related.

ISSN: 1753-6561