Genome-wide association meta-analysis identifies new endometriosis risk loci
Open accessAbstract
We conducted a genome-wide association meta-analysis of 4,604 endometriosis cases and 9,393 controls of Japanese and European ancestry. We show that rs12700667 on chromosome 7p15.2, previously found to associate with disease in Europeans, replicates in Japanese (P = 3.6 × 10(-3)), and we confirm association of rs7521902 at 1p36.12 near WNT4. In addition, we establish an association of rs13394619 in GREB1 at 2p25.1 with endometriosis and identify a newly associated locus at 12q22 near VEZT (rs10859871). Excluding cases of European ancestry of minimal or unknown severity, we identified additional previously unknown loci at 2p14 (rs4141819), 6p22.3 (rs7739264) and 9p21.3 (rs1537377). All seven SNP effects were replicated in an independent cohort and associated at P <5 × 10(-8) in a combined analysis. Finally, we found a significant overlap in polygenic risk for endometriosis between the genome-wide association cohorts of European and Japanese descent (P = 8.8 × 10(-11)), indicating that many weakly associated SNPs represent true endometriosis risk loci and that risk prediction and future targeted disease therapy may be transferred across these populations.
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The WNT4 variant associated with endometriosis is involved in hormone metabolism and the development and functioning of the woman's genital tract.
“The second variant is located near the WNT4gene, which is involved in hormone metabolism and the development and functioning of the woman’s genital tract.”
From Endometriosis: Epidemiology, Classification, Pathogenesis, Treatment and Genetics (Review of Literature) (2021) · cites this paper as [183]
Two regions of the genome are associated with an increased risk of endometriosis in European women: one on chromosome 7 and one near the WNT4 gene.
“The team identified two regions of the genome associated with an increased risk of endometriosis.”
From Endometriosis: Epidemiology, Classification, Pathogenesis, Treatment and Genetics (Review of Literature) (2021) · cites this paper as [183]
In Japanese population studies, polymorphism rs10965235 in the CDKN2BAS gene at locus 9p21 and rs16826658 in the WNT4 gene area at locus 1p36 are associated with endometriosis.
“Studies of the Japanese population showed the relationship of polymorphism rs10965235, in the CDKN2BAS gene at locus 9p21 and rs16826658, in the area of the WNT4 gene at locus 1p36 [183].”
From Endometriosis: Epidemiology, Classification, Pathogenesis, Treatment and Genetics (Review of Literature) (2021) · cites this paper as [183]
The chromosome 7 region associated with endometriosis may be involved in the regulation of nearby genes involved in the development of the uterus and its lining.
“This region may be involved in the regulation of nearby genes involved in the development of the uterus and its lining.”
From Endometriosis: Epidemiology, Classification, Pathogenesis, Treatment and Genetics (Review of Literature) (2021) · cites this paper as [183]
The current meta-analysis represents an approximate five-fold increase in effective sample size compared with the previously largest multi-ethnic GWA meta-analysis of 4,604 endometriosis cases and 9,393 controls.
“the current meta-analysis represents an approximate five-fold increase in the effective sample size13 in comparison to the previously largest multi-ethnic GWA meta-analysis of 4,604 endometriosis cases and 9,393 controls from Australia, United Kingdom and Japan8.”
From Meta-analysis identifies five novel loci associated with endometriosis highlighting key genes involved in hormone metabolism (2017) · cites this paper as [8]
Previous GWA studies of endometriosis have implicated WNT signalling, oestrogen responsive genes and genes involved in the actin cytoskeleton and cellular adhesion.
“Previous GWA studies of endometriosis have implicated WNT signalling, oestrogen responsive genes and genes involved in the actin cytoskeleton and cellular adhesion1233.”
From Meta-analysis identifies five novel loci associated with endometriosis highlighting key genes involved in hormone metabolism (2017) · cites this paper as [33]
The index SNP associated with endometriosis on chromosome 2p25.1 is a common splice variant in GREB1 and SNPs associated with endometriosis on chromosome 12q22 increase expression of VEZT in RNA from blood and endometrium.
“The index SNP associated with endometriosis on chromosome 2p25.1 is a common splice variant in the oestrogen-responsive growth regulation by oestrogen in breast cancer 1 (GREB1) gene3337 and SNPs associated with endometriosis on chromosome 12q22 increase expression of the transmembrane adherens junctions protein coding gene vezatin (VEZT) in RNA from blood and endometrium38.”
From Meta-analysis identifies five novel loci associated with endometriosis highlighting key genes involved in hormone metabolism (2017) · cites this paper as [33]
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- Authors
- Nyholt, D. R., Low, S.-K., Anderson, C. A., Painter, J. N., Uno, S., Morris, A. P., MacGregor, S., Gordon, S. D., Henders, A. K., Martin, N. G., Attia, J., Holliday, E. G., McEvoy, M., Scott, R. J., Kennedy, S. H., Treloar, S. A., Missmer, S. A., Adachi, S., Tanaka, K., Nakamura, Y., Zondervan, K. T., Zembutsu, H., & Montgomery, G. W.
- Affiliations
- QIMR Berghofer Medical Research Institute (AU)
- Institute of Medical Science, The University of Tokyo (JP)
- Wellcome Sanger Institute (GB)
- Sapporo Medical University (JP)
- Centre for Human Genetics (GB)
- Hunter Medical Research Institute (AU)
- John Radcliffe Hospital (GB)
- The University of Queensland (AU)
- Brigham and Women's Hospital (US)
- Niigata University (JP)
- Corresponding author
- Nyholt, Dale R
- Zondervan, Krina T
- Zembutsu, Hitoshi
- Montgomery, Grant W
- ORCID
- Nyholt, Dale R
- Low, Siew-Kee
- Anderson, Carl A
- Painter, Jodie N
- Morris, Andrew P
- MacGregor, Stuart
- Gordon, Scott D
- Henders, Anjali K
- Martin, Nicholas G
- Attia, John
- Holliday, Elizabeth G
- McEvoy, Mark
- Scott, Rodney J
- Kennedy, Stephen H
- Treloar, Susan A
- Adachi, Sosuke
- Tanaka, Kenichi
- Nakamura, Yusuke
- Zondervan, Krina T
- Zembutsu, Hitoshi
- Montgomery, Grant W
- Venue
- Nature Genetics
- Published
- 2012-10-28
- Volume
- 44
- Issue
- 12
- Pages
- 1355-1359
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- PMC
- PMC3527416
- OpenAlex
- W2159594119
- Cited by
- 315
- References
- 40
- Citations by year
- 2026: 12 · 2025: 12 · 2024: 14 · 2023: 19 · 2022: 18 · 2021: 25 · 2020: 25 · 2019: 23 · 2018: 24 · 2017: 31 · 2016: 32 · 2015: 24 · 2014: 31 · 2013: 25
- FWCI
- 29.81
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Genetics (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- QUT ePrints (Queensland University of Technology) (submittedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- NOVA (University of Newcastle Australia) (submittedVersion)
- Funders
- Wellcome Trust (098017, 085475, 085235, 084766, WT085235/Z/08/Z, 090532, WT084766/Z/08/Z, 098051, 076113)
- National Health and Medical Research Council (496739, 496610, 389891, 552498, 613705, 496674, 631096, 241944, 442915, 389875, 389892)
- Topics
- Health Sciences › Medicine › Reproductive Medicine › Endometriosis Research and Treatment
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Keywords
- endometriosis, genetic susceptibility loci, Wnt4, GREB1, polygenic risk, 9p21.3
- MeSH terms
- Carrier Proteins, Chromosomes, Human, Pair 1, Chromosomes, Human, Pair 2, Chromosomes, Human, Pair 6, Chromosomes, Human, Pair 7, Chromosomes, Human, Pair 9, Endometriosis, Female, Humans, Membrane Proteins, Neoplasm Proteins, Risk, Severity of Illness Index, Cohort Studies, Genetic Predisposition to Disease, Polymorphism, Single Nucleotide, White People, Asian People, Genome-Wide Association Study, Genetic Loci, Wnt4 Protein
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