Integration of Population-Level Genotype Data with Functional Annotation Reveals Over-Representation of Long Noncoding RNAs at Ovarian Cancer Susceptibility Loci

DOI: 10.1158/1055-9965.EPI-16-0341 Published January 2017

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Figure 1.
Proportion of EOC-associated SNPs in lncRNA genes compared with whole genome. Histograms of the proportion of EOC-associated SNPs (P < 1.0 × 10⁻⁵) from analysis of (A) main histologic subgroups and (B) serous histology by grade for whole genome (WG), all lncRNA, and ovarian-active lncRNA regions. Significant differences compared with (*) whole-genome and (**) all lncRNA are annotated.
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Figure 2.
Ovarian tissue expression and biologic processes of EOC-associated lncRNA genes. A, Expression of 53 EOC-associated lncRNA for 412 ovarian tumor tissues and 35 normal ovarian tissues. B, Heatmap of significant P values (FDR < 15%) for 18 biologic processes associated with 20 of 53 EOC-associated lncRNAs.
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Figure 3.
Selected boxplots for significant eQTL within novel regions associated with EOC risk.

Table 1.

SNPs associated with EOC risk are enriched in lncRNA genes

	Whole genome (15,159,372 SNPs)		13,442 lncRNA genes (1,757,495 SNPs)				5,287 ovarian-active lncRNA genes (457,227 SNPs)
Tumor histology	SNPs P < 10⁻⁵	Independent regions^a	SNPs P < 10⁻⁵	P^b	Independent regions^a	P^c	SNPs P < 10⁻⁵	P^d	Independent regions^a	P^e
All invasive	5,294	130	1,464	0.047	72	0.0005	873	0.009	46	0.043
Serous	5,922	147	1,572	0.044	81	0.009	960	0.002	51	0.16
High grade	5,367	178	1,467	0.045	89	0.002	899	0.004	50	0.25
Low grade	1,916	1,104	219	0.48	385	0.64	50	0.70	169	0.15

↵^aSNPs with r² > 0.2 and within a 250-kb distance were grouped into independent regions.
↵^bProportion of risk SNPs within lncRNA genes compared with whole-genome distribution. Empirical P values based on 10,000 permutations of lncRNA genes across the whole genome.
↵^cProportion of regions overlapping lncRNA genes compared with whole-genome distribution. Empirical P values based on 10,000 permutations of independent regions across the whole genome.
↵^dProportion of risk SNPs in ovarian-active lncRNA genes compared with all lncRNAs. Empirical P values based on 10,000 permutations of active/inactive classification of lncRNAs.
↵^eProportion of regions overlapping ovarian-active lncRNA genes compared with all lncRNAs. Empirical P values based on 10,000 permutations of independent regions that overlapped lncRNAs.

Table 2.

Novel EOC risk regions (P < 1.0 × 10⁻⁵) with allele-specific effects on lncRNA gene expression

Locus	Independent regions (length, kB)	Overlap lncRNA^a (ovarian-active?)	Top SNP	MAF	R²	OR (95% CI)	P	SNP hits/eQTL SNPs	lncRNA eQTL targets (distance, kB)
11p15.5	chr11:2116492-2190591 (74)	IGF2-AS (Y)	rs3741205 (A>C)	0.28	0.99	0.93 (0.91–0.94)	3.94E−06	4/2	FAM99A (429)
		AC132217.4 (N)
11p13	chr11:36325764-36396678 (71)	RP11-514F3.4 (N)	rs10501153 (C>T)	0.34	0.82	0.92 (0.90–0.93)	3.76E−07	12/8	RP11-219O3.2 (50)
16q21	chr16:58944508-59028237 (84)	RP11-410D17.2 (Y)	rs6499994 (A>G)	0.09	0.71	0.91 (0.89–0.93)	8.57E−08	28/4	CTB-134F13.1 (-791)
									RP11-430C1.1 (+861)
16q22.1	chr16:67625872-68029739 (404)	RP11-167P11.2 (Y)	rs12325430 (T>C)	0.44	0.75	0.92 (0.90–0.93)	2.91E−07	2/2	RP11-167P11.2 (0)
		CTC-479C5.10 (Y)
		CTC-479C5.17 (N)
		AC009095.4 (Y)
	chr16:67950613-68429047 (478)	RP11-96D1.5 (Y)	chr16:68187782 (CT>C)	0.40	0.73	0.92 (0.90–0.93)	2.10E−07	11/1	RP11-167P11.2 (177)
		RP11-96D1.9 (N)
		RP11-96D1.6 (Y)
		RP11-96D1.7 (Y)
		RP11-96D1.10 (Y)
		RP11-96D1.11 (Y)
		RP11-96D1.3 (Y)
		RP11-67A1.2 (Y)
		CTC-479C5.6 (N)
		CTC-479C5.17 (Y)
19q13.12-13	chr19:38201712-38474127 (272)	CTD-2554C21.3 (N)	chr19:38451511 (TA>T)	0.14	0.81	1.12 (1.09–1.15)	5.74E−06	9/7	AC012309.5 (459)
		CTD-2554C21.2 (Y)
		CTD-2528L19.6 (N)
		CTC-244M17.1 (N)
		AC016582.2 (N)

Abbreviation: R² = Imputation quality r².
↵^alncRNAs in bold contain SNP hits within their coordinates and non-bolded lncRNAs are in LD with SNP hits.

Supplementary Data

Supplemental Tables and Figures - Supplemental Figure S1. Flowchart for epigenomic annotation of lncRNAs. Supplemental Figure S2. Distribution of ovarian tissue histone marks in lncRNA genes. Supplemental Table S1. Study participants for GWAS meta-analysis of epithelial ovarian cancer. Supplemental Figure S3. Distribution of number of EOC risk SNPs for 10,000 permutations of lncRNA-sized regions. Supplemental Table S2. SNPs associated with risk for less common ovarian cancer subtypes are not enriched in lncRNAs. Supplemental Figure S4. Genomic coverage of GENCODE v19 lncRNA genes (n=13,442 with GWAS SNPs). Supplemental Table S3. Density of EOC-associated SNPs in lncRNA genes versus whole genome (All histologies). Supplemental Table S4. Density of EOC-associated SNPs in lncRNA genes by histologic subtype. Supplemental Table S5. Promoter and transcription factor motifs enriched in EOC-associated lncRNA regions. Supplemental Table S6. Biological processes of putative promoter and transcription factors enriched in 53 EOC-associated lncRNA. Supplemental Figure S5. Regional plots for five novel loci associated with EOC risk and expression of lncRNA genes.
Supplemental Methods - Density Measures of lncRNA Enrichment at Independent EOC-associated Regions