. Author manuscript; available in PMC: 2013 Sep 1.

Published in final edited form as: Hum Genet. 2012 Jun 12;131(9):1507–1517. doi: 10.1007/s00439-012-1187-x

Table 3.

Haplotype frequency between glioma cases with and without family history of PBT in the discovery study

Chromosome	Haplotype^*	Family history of PBT, Haplotype frequency		OR (95% CI)^#	P-value	Global score test ^&
Chromosome	Haplotype^*	Yes (n=88)	No (n=1100)	OR (95% CI)^#	P-value	Global score test ^&
6p22.3	AG	0.76	0.87	1 (reference)		0.0010
	GG	0.13	0.08	1.96 (1.22 – 3.16)	0.005
	Rare	0.11	0.05	2.24 (1.35 – 3.71)	0.002
12p13	GTAT	0.20	0.25	1 (reference)		<0.0001

	GCAT	0.23	0.17	1.63 (0.91 – 2.90)	0.09
	ATAT	0.11	0.12	0.99 (0.47 – 2.08)	0.98
	ACAT	0.21	0.11	2.68 (1.55 – 4.37)	0.0003
	Rare	0.25	0.35	1.61 (0.96 – 2.68)	0.07

17q12-21.32	GGA	0.22	0.19	1 (reference)	---	0.00088
	TGA	0.19	0.17	1.11 (0.71 – 1.99)	0.88
	GGG	0.19	0.15	0.83 (0.48 – 1.73)	0.49
	TGG	0.17	0.14	1.17 (0.67 – 2.03)	0.73
	TAG	0.08	0.16	2.71 (1.42 – 4.57)	0.003
	rare	0.16	0.19	1.62 (0.87 – 3.09)	0.15

17q22-23.2	CT	0.55	0.44	1 (reference)		0.027
	TT	0.30	0.35	1.53 (1.04 – 2.23)	0.03
	CG	0.10	0.14	1.93 (1.08 – 3.43)	0.02
	TG	0.05	0.07	1.68 (0.80 – 3.49)	0.17

NOTE: PBT, primary brain tumor; OR, odds ratio; CI, confidence interval. Two loci chosen for 6p22: rs2064193 rs16886628; Four loci chosen for 12p13: rs17780102, rs2418087, rs7961199, rs7305773; Three loci chosen for 17q12-21: rs9303521, rs1530364, rs6504618; Two loci chosen for 17q22-23.2: rs1879145, rs868728.

Haplotypes with a frequency <0.03 were pooled into a combined group.

Adjusted for age, sex, and histology.

From 10,000 simulations.