Table 3.

Gene-by-gene correction for multiple testing of SNPs that are in linkage disequilibrium (LD), based on the spectral decomposition (SpD) of pairwise LD matrices for SNP pairs.¹

Gene Symbol	Number of SNPs	M 2	Meff3	Adjusted threshold 4	Smallest P value for individual SNP
XPF	17	17	11.83	0.004	0.005
XRCC3	15	15	11.48	0.004	0.006
CHEK2	20	20	16.99	0.003	0.01
RPA3	39	39	33.62	0.001	0.013
POLK	13	13	9.89	0.005	0.018
RPA1	31	31	26.83	0.002	0.019
PARP1	13	13	9.26	0.005	0.02
XPC	17	17	12.89	0.004	0.021
MSH3	42	42	36.17	0.001	0.022
NEIL2	37	37	30.71	0.002	0.025
FANCG	12	12	9.15	0.005	0.03
CHEK1	12	12	10.16	0.005	0.03
APE1	17	17	13.59	0.004	0.037
FANCC	14	14	10.58	0.005	0.038
ATR	14	14	12.11	0.004	0.039
POLD	13	13	11.61	0.004	0.044
Ku70	7	7	5.40	0.009	0.044
XRCC4	42	42	35.63	0.001	0.047
PMS1	20	20	16.44	0.003	0.064
Artemis	19	19	15.08	0.003	0.068
XPA	14	14	11.87	0.004	0.069
LIG1	25	25	19.39	0.003	0.073
LIG4	17	17	13.84	0.004	0.076
MGMT	69	69	63.12	0.001	0.081
XRCC2	19	19	16.42	0.003	0.091
DNA-PK	17	17	14.20	0.004	0.096
XRCC1	14	14	11.95	0.004	0.10
FANCE	16	16	13.10	0.004	0.101
RAD52	21	21	18.51	0.003	0.101
BLM	37	37	31.51	0.002	0.101
MSH6	17	17	13.66	0.004	0.11
OGG1	19	19	15.23	0.003	0.116
PMS2	19	19	16.83	0.003	0.118
TP53	10	10	8.82	0.006	0.123
PCNA	14	14	12.03	0.004	0.123
FANCD2	7	7	4.42	0.011	0.127
NBS1	14	14	10.14	0.005	0.138
POLB	10	10	7.76	0.006	0.145
XPD	12	12	9.51	0.005	0.15
NEIL1	5	5	3.44	0.015	0.16
MLH1	8	8	5.18	0.010	0.179
LIG3	11	11	8.63	0.006	0.181
XPG	16	16	13.39	0.004	0.199
CSB	23	23	18.43	0.003	0.202
FANCF	8	8	6.95	0.007	0.225
ERCC1	11	11	7.77	0.006	0.236
RAD51	7	7	5.55	0.009	0.239
POLE	15	15	11.34	0.004	0.244
MRE11	13	13	8.63	0.006	0.251
Ku80	26	26	21.91	0.002	0.263
FEN1	8	8	5.83	0.009	0.267
MSH2	24	24	17.37	0.003	0.286
CSA	11	11	8.22	0.006	0.288
RPA2	6	6	4.01	0.012	0.305
XPB	12	12	9.55	0.005	0.313
RAD50	8	8	5.24	0.010	0.316
FANCA	19	19	13.10	0.004	0.35
ATM	15	15	11.60	0.004	0.357
POLI	10	10	8.20	0.006	0.413
MLH3	9	9	4.86	0.010	0.518

¹Calculated using the SNPSpD method available at: http://genepi.qimr.edu.au/general/daleN/SNPSpD/

²M: Original (total) number of marker loci after removing redundant (collinear) SNPs

³M_eff: Effective number of independent marker loci (caclulated using the formula: M_eff = 1+(M−1) (1−Var(λ_obs)/M). The genome-wide significance threshold after Bonferoni correction would be α_nominal/M_eff = 0.05/850.92 = 5.88 × 10⁻⁵.

⁴Adjusted threshold for significance for each gene, which is 0.05/M_eff.