Table 1 Variant frequencies in breast cancer patients from the Helsinki and Tampere regions.

From: NTHL1 is a recessive cancer susceptibility gene

Variant	Group	Total	Carriers	%	OR	95% CI	P value
MAD1L1	Controls	3974	2	0.05
c.1947C>G	All BC	4083	12	0.3	5.94	1.62–38.2	0.020
p.(Tyr649Ter)	Familial BC	1524	6	0.4	8.13	1.86–55.7	0.011
rs121908981	Unselected BC	3327	8	0.2	4.81	1.20–31.9	0.047
	ER-positive BC	3172	10	0.3	6.46	1.70–42.1	0.016
	ER-negative BC	720	2	0.3	5.61	0.67–46.9	0.085
SERPINA3	Controls	3978	10	0.3
c.918-1G>C	All BC	4095	11	0.3	1.03	0.43–2.47	0.95
rs199710314	Familial BC	1527	3	0.2	0.75	0.17–2.46	0.66
	Unselected BC	3339	9	0.3	1.07	0.42–2.65	0.89
	ER-positive BC	3184	9	0.3	1.08	0.43–2.69	0.86
	ER-negative BC	720	1	0.1	0.54	0.03–2.83	0.56
ERCC6L2	Controls	2083	12	0.6
c.1424del	All BC	3142	12	0.4	0.76	0.33–1.75	0.51
p.(Ile475ThrfsTer36)	Familial BC	1369	6	0.4	1.00	0.34–2.68	1.00
rs768081343	Unselected BC	2386	8	0.3	0.64	0.25–1.57	0.34
	ER-positive BC	2386	10	0.4	0.86	0.35–2.03	0.72
	ER-negative BC	573	1	0.2	0.42	0.02–2.20	0.41
FANCG	Controls	2086	1	0.05
c.1182_1192delinsC	All BC	3147	6	0.2	3.08	0.53–58.2	0.30
p.(Glu395TrpfsTer5)	Familial BC	1368	4	0.3	4.49	0.66–87.9	0.18
rs397507559	Unselected BC	2391	3	0.1	2.21	0.28–44.8	0.49
	ER-positive BC	2389	5	0.2	3.39	0.55–65.0	0.27
	ER-negative BC	576	1	0.2	2.82	0.11–71.4	0.46
NTHL1	Controls	2081	17	0.8
c.244C>T	All BC	3117	30	1.0	1.35	0.74–2.54	0.33
p.(Gln82Ter)	Familial BC	1357	16	1.2	1.77	0.86–3.64	0.12
rs150766139	Unselected BC	2370	22	0.9	1.25	0.66–2.41	0.49
	ER-positive BC	2366	17	0.7	0.99	0.49–1.99	0.98
	ER-negative BC	573	9	1.6	2.32	0.97–5.21	0.048
USP45	Controls	2088	3	0.1
c.2190C>A	All BC	3148	21	0.7	4.16	1.42–17.7	0.022
p.(Tyr730Ter)	Familial BC	1368	12	0.9	5.49	1.70–24.6	0.0097
rs118066385	Unselected BC	2392	17	0.7	4.59	1.53–19.7	0.015
	ER-positive BC	2389	17	0.7	4.31	1.43–18.6	0.021
	ER-negative BC	576	2	0.3	2.59	0.33–16.2	0.31
USP45	Controls	2086	6	0.3
c.1008del	All BC	3148	13	0.4	1.29	0.50–3.73	0.61
p.(Val337SerfsTer9)	Familial BC	1369	8	0.6	1.92	0.65–6.01	0.24
rs554927779	Unselected BC	2392	9	0.4	1.23	0.44–3.69	0.70
	ER-positive BC	2390	11	0.5	1.46	0.55–4.30	0.46
	ER-negative BC	575	2	0.3	1.24	0.18–5.53	0.80

The familial and the unselected patient groups overlap: 775 patients were included in both groups in the analyses of the MAD1L1 and SERPINA3 variants and 614 in the analyses of the other variants. Two of the NTHL1 c.244C>T carriers included in the analysis were homozygous.

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Table 1 Variant frequencies in breast cancer patients from the Helsinki and Tampere regions.

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