Genetic variants in long noncoding RNA H19 contribute to the risk of breast cancer in a southeast China Han population

Figures & data

Table 1 Distributions of selected characteristics in breast cancer cases and cancer-free controls

Characteristics	Cases (n=1,005), n (%)	Controls (n=1,020), n (%)	P-value
Age at diagnosis, years (mean ± SD)	46.5±10.2	46.7±11.1	0.646
Body mass index, kg/m^2 (mean ± SD)	23±3.2	22.5±2.6	<0.001
Age at menarche, years (mean ± SD)	15.5±1.7	15.2±1.6	0.001
Age at menopause, years (mean ± SD)	49.8±3.6	49.9±3.5	0.598
Age at first live birth, years (mean ± SD)	25±3.5	24.2±3.4	<0.001
Menopausal status			0.059
Premenopausal	656 (65.3)	668 (65.5)
Postmenopausal	342 (34)	333 (32.6)
Unnatural menopausea	7 (0.7)	19 (1.9)
Pregnancies, n			<0.001
≤2	570 (56.7)	404 (39.6)
>2	435 (43.3)	616 (60.4)
Hormone therapy			0.013
Yes	45 (4.5)	25 (2.5)
No	960 (95.5)	995 (97.5)
Previous benign breast disease			0.054
Yes	41 (4.1)	26 (2.5)
No	964 (95.9)	994 (97.5)
Family history of breast cancer			<0.001
Yes	75 (7.5)	12 (1.2)
No	930 (92.5)	1,008 (98.8)
ER status
Positive	678 (67.5)
Negative	327 (32.5)
PR status
Positive	618 (61.5)
Negative	387 (38.5)
HER2 status
Positive	275 (27.4)
Negative	730 (72.6)

Note:

a Included hysterectomy operation and other status.

Abbreviations: ER, estrogen receptor; HER2, human epidermal growth factor receptor 2; PR, progesterone receptor.

Figure 1 Relative position of rs217727 and rs2839698 in H19.

Table 2 Hardy–Weinberg equilibrium (HWE) tests for H19 long noncoding RNA polymorphisms

SNP	Reference allele/risk allele	HWE	P-valuea
rs217727	C/T	0.063	0.968
rs2839698	C/T	0.275	0.871

Note:

a For HWE test.

Table 3 Genotype frequencies of H19 long noncoding RNA polymorphisms in breast cancer cases and controls

SNP	Genotype	Cases (n=1,005), n (%)	Controls (n=1,020), n (%)	P-valuea	Adjusted OR (95% CI)b	P-value (trend)c
rs217727
C/T	CC	403 (40.1)	465 (45.6)		1
	CT	471 (46.9)	450 (44.1)	0.023*	1.25 (1.03–1.51)
	TT	131 (13)	105 (10.3)	0.004*	1.56 (1.15–2.09)	0.006
	CT + TT	602 (59.9)	555 (54.4)	0.004d,*	1.31 (1.09–1.57)
rs2839698
C/T	CC	452 (45)	484 (47.5)		1
	CT	440 (43.8)	432 (42.3)	0.554	1.06 (0.88–1.28)
	TT	113 (11.2)	104 (10.2)	0.5	1.11 (0.82–1.51)	0.234
	CT + TT	553 (55.0)	536 (52.5)	0.466d	1.07 (0.89–1.28)

Notes:

a P<0.025,

* significant after Bonferroni correction;

b adjusted by age, body mass index, age at menarche and menopause, menopausal status, number of pregnancies, and family history of breast cancer where appropriate;

c for genotypes between cases and cancer-free controls;

d two-sided χ² test for differences in frequency distribution of combined genotypes (dominant model) between cases and controls.

Abbreviation: SNP, single-nucleotide polymorphism.

Table 4 Stratified analyses of H19 long noncoding RNA polymorphisms and breast cancer susceptibility

	rs217727					rs2839698
	Cases (CC/CT + TT)	Controls (CC/CT + TT)	P-valuea	OR (95% CI)b	P-valuec	Cases (CC/CT + TT)	Controls (CC/CT + TT)	P-valuea	OR (95% CI)b	P-valuec
Age, years
<40	108/176	140/148	0.011	1.57 (1.11–2.22)	0.251	130/154	137/151	0.972	0.99 (0.71–1.4)	0.606
≥40	295/426	325/407	0.08	1.21 (0.98–1.51)		322/399	347/385	0.394	1.1 (0.89–1.36)
Body mass index, kg/m^2
<23	264/286	201/269	0.059	1.31 (0.99–1.74)	0.987	263/287	262/329	0.912	1.02 (0.77–1.34)	0.586
≥23	244/347	159/255	0.03	1.31 (1.2–1.87)		221/249	190/224	0.313	1.13 (0.89–1.44)
Age at menarche, years
<16	217/297	247/284	0.115	1.23 (0.95–1.58)	0.655	236/278	238/293	0.604	0.94 (0.73–1.2)	0.138
≥16	186/305	218/271	0.036	1.34 (1.02–1.75)		216/275	246/243	0.903	1.25 (0.96–1.63)
Menopausal status
Premenopausal	267/389	133/209	0.016	1.32 (1.05–1.65)	0.97	292/364	311/357	0.601	1.06 (0.85–1.32)	0.963
Postmenopausal	309/359	148/185	0.108	1.31 (0.94–1.81)		159/183	164/169	0.699	1.07 (0.77–1.47)
Age at menopause, years
≤50	94/137	71/95	0.684	1.09 (0.71–1.69)	0.226	115/116	85/81	0.671	1.1 (0.71–1.69)	0.642
>50	54/100	76/91	0.03	1.71 (1.05–2.8)		70/84	77/90	0.813	0.94 (0.59–1.52)
Age at first live birth, years
<25	164/268	248/306	0.016	1.39 (1.06–1.82)	0.533	201/231	269/285	0.498	1.1 (0.84–1.43)	0.963
≥25	216/315	192/227	0.13	1.23 (0.94–1.6)		235/296	197/222	0.437	1.11 (0.85–1.44)
Pregnancies, n
≤2	240/330	199/205	0.047	1.31 (1–1.7)	0.968	245/325	185/219	0.482	1.1 (0.85–1.43)	0.765
>2	163/272	266/350	0.045	1.3 (1–1.68)		207/228	299/317	0.768	1.04 (0.81–1.34)

Notes:

a P<0.0035;

b adjusted by age, body mass index, age at menarche and menopause, menopausal status, number of pregnancies, and family history of breast cancer where appropriate;

c heterogeneity test.

Table 5 Associations of H19 long noncoding RNA polymorphisms and specific molecular subtypes for breast cancer patients

	rs217727				rs2839698
	Cases (CC/CT + TT)	P-valuea	OR (95% CI)b	P-valuec	Cases (CC/CT + TT)	P-valuea	OR (95% CI)b	P-valuec
ER status
Positive	268/410	0.004*	1.34 (1.09–1.64)	0.577	291/387	0.134	1.17 (0.95–1.43)	0.111
Negative	135/192	0.135	1.22 (0.94–1.58)		161/166	0.418	0.9 (0.7–1.16)
PR status
Positive	247/371	0.006	1.34 (1.08–1.66)	0.675	259/359	0.075	1.21 (0.98–1.49)	0.088
Negative	156/231	0.072	1.25 (0.98–1.59)		193/194	0.313	0.88 (0.7–1.12)
HER2 status
Positive	118/157	0.651	1.07 (0.81–1.41)	0.71	138/137	0.364	0.88 (0.67–1.16)	0.126
Negative	285/445	0.001*	1.40 (1.14–1.71)		313/416	0.186	1.14 (0.94–1.39)
HR^+ HER2^−	208/336	0.001*	1.45 (1.16–1.81)		231/313	0.169	1.16 (0.94–1.45)
TNBC	68/100	0.198	1.25 (0.89–1.75)		77/91	0.759	1.05 (0.75–1.47)

Notes:

a P<0.005,

* significant after Bonferroni correction;

b adjusted by age, body-mass index, age at menarche and menopause, menopausal status, number of pregnancies, and family history of breast cancer;

c for heterogeneity test.

Abbreviations: CI, confidence interval; ER, estrogen receptor; HER2, human epidermal growth factor receptor 2; HR, hormone receptor; OR, odds ratio; PR, progesterone receptor; TNBC, triple-negative breast cancer.

Table 6 False-positive report probability values for associations between breast cancer risk and genotypes in stratified factors

Genotype	Stratified factors	Positive OR (95% CI)a	P-valueb	Prior probability
				0.25	0.1	0.01	0.001
rs217727
CT/CC	All subjects	1.25 (1.03–1.51)	0.023	0.06	0.161	0.678	0.955
TT/CC	All subjects	1.56 (1.15–2.09)	0.004	0.021	0.061	0.419	0.879
CT + TT/CC	All subjects	1.31 (1.09–1.57)	0.004	0.007	0.022	0.197	0.712
	ER^+	1.34 (1.09–1.64)	0.004	0.015	0.045	0.341	0.84
	HER2^−	1.4 (1.14–1.71)	0.001	0.004	0.012	0.114	0.565
	HR^+ HER2^−	1.45 (1.16–1.81)	0.001	0.005	0.015	0.141	0.623

Notes:

a Crude OR;

b logistic regression analysis for genotype-frequency distributions.

Abbreviations: CI, confidence interval; ER, estrogen receptor; HER2, human epidermal growth factor receptor 2; HR, hormone receptor; OR, odds ratio.

Figure 2 Functional assay of rs217727 on H19.

Notes: (A) Relative expression levels of H19 mRNA in cancerous and corresponding normal tissue; (B) relative H19 mRNA expression levels in ER-positive subtype; (C) relative H19 mRNA expression levels in HER2-negative subtype; (D) relative H19 mRNA expression levels in HR-positive–HER2-negative subtype.
Abbreviations: ER, estrogen receptor; HER2, human epidermal growth factor receptor 2; HR, hormone receptor.