Genome-Wide Association Study Link Novel Loci to Endometriosis

Hans Albertsen, Hans M Albertsen, Rakesh Chettier, Pamela Farrington, P. Farrington, Kenneth Ward
PloS one · 2013 · vol. 8(3) , pp. e58257 · doi:10.1371/journal.pone.0058257 · PMID:23472165 · PMC3589333 · W2051994829
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⚙ AI-generated summary by claude@2026-06, 2026-06-07 ⓘ

This genome-wide association study identified novel genetic loci, including LINC00339-WNT4 and RND3-RBM43, associated with endometriosis in a European cohort.

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⚙ AI-generated deep summary by claude@2026-06, 2026-06-07 ⓘ

Albertsen et al. performed a two-stage genome-wide association study in a European cohort with 2,019 surgically confirmed endometriosis cases and 14,471 controls, using Illumina OmniExpress genotyping, stringent filtering for ancestry and relatedness, and PCA-adjusted association to address population stratification (λ reduced from 1.18 to 1.05). In combined analyses, they identified genome-wide significant associations at multiple loci, including two strongest signals in the LINC00339–WNT4 region on 1p36.12 and the RND3–RBM43 region on 2q23.3, plus two additional loci (RNF144B–ID4 and HNRNPA3P1–LOC100130539). Imputation localized the WNT4 signal to a ~150 kb LD block incorporating WNT4, CDC42, and LINC00339, and they report that a univariate analysis of infertility, age at menarche, and family history did not show allelic association with the marker SNPs, with clinical data showing delayed diagnosis and correlation between severity and infertility; the paper also acknowledges measurable population stratification and uses stringent thresholds to mitigate it. This paper is centrally about endometriosis—identifying novel genetic loci and refining the WNT4-region association through a large GWAS and imputation.

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Abstract

Endometriosis is a common gynecological condition with complex etiology defined by the presence of endometrial glands and stroma outside the womb. Endometriosis is a common cause of both cyclic and chronic pelvic pain, reduced fertility, and reduced quality-of-life. Diagnosis and treatment of endometriosis is, on average, delayed by 7-10 years from the onset of symptoms. Absence of a timely and non-invasive diagnostic tool is presently the greatest barrier to the identification and treatment of endometriosis. Twin and family studies have documented an increased relative risk in families. To identify genetic factors that contribute to endometriosis we conducted a two-stage genome-wide association study (GWAS) of a European cohort including 2,019 surgically confirmed endometriosis cases and 14,471 controls. Three of the SNPs we identify associated at P<5×10(-8) in our combined analysis belong to two loci: LINC00339-WNT4 on 1p36.12 (rs2235529; P = 8.65×10(-9), OR = 1.29, CI = 1.18-1.40) and RND3-RBM43 on 2q23.3 (rs1519761; P = 4.70×10(-8), OR = 1.20, Cl = 1.13-1.29, and rs6757804; P = 4.05×10(-8), OR = 1.20, Cl = 1.13-1.29). Using an adjusted Bonferoni significance threshold of 4.51×10(-7) we identify two additional loci in our meta-analysis that associate with endometriosis:, RNF144B-ID4 on 6p22.3 (rs6907340; P = 2.19×10(-7), OR = 1.20, Cl = 1.12-1.28), and HNRNPA3P1-LOC100130539 on 10q11.21 (rs10508881; P = 4.08×10(-7), OR = 1.19, Cl = 1.11-1.27). Consistent with previously suggested associations to WNT4 our study implicate a 150 kb region around WNT4 that also include LINC00339 and CDC42. A univariate analysis of documented infertility, age at menarche, and family history did not show allelic association with these SNP markers. Clinical data from patients in our study reveal an average delay in diagnosis of 8.4 years and confirm a strong correlation between endometriosis severity and infertility (n = 1182, P<0.001, OR = 2.18). This GWAS of endometriosis was conducted with high diagnostic certainty in cases, and with stringent handling of population substructure. Our findings broaden the understanding of the genetic factors that play a role in endometriosis.

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Condition tags

endometriosischronic_pelvic_paininfertility

MeSH descriptors

Endometriosis Endometriosis Genetic Predisposition to Disease Genome-Wide Association Study Adult Algorithms Alleles Case-Control Studies Cohort Studies Endometriosis Female Genotype Humans Polymorphism, Single Nucleotide Principal Component Analysis Reproducibility of Results Software Young Adult

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