Copy number variation analysis detects novel candidate genes involved in follicular growth and oocyte maturation in a cohort of premature ovarian failure cases.
Can spontaneous premature ovarian failure (POF) patients derived from population-based biobanks reveal the association between copy number variations (CNVs) and POF?



CNVs can hamper the functional capacity of ovaries by disrupting key genes and pathways essential for proper ovarian function.



POF is defined as the cessation of ovarian function before the age of 40 years. POF is a major reason for female infertility, although its cause remains largely unknown.



The current retrospective CNV study included 301 spontaneous POF patients and 3188 control individuals registered between 2003 and 2014 at Estonian Genome Center at the University of Tartu (EGCUT) biobank.



DNA samples from 301 spontaneous POF patients were genotyped by Illumina HumanCoreExome (258 samples) and HumanOmniExpress (43 samples) BeadChip arrays. Genotype and phenotype information was drawn from the EGCUT for the 3188 control population samples, previously genotyped with HumanCNV370 and HumanOmniExpress BeadChip arrays. All identified CNVs were subjected to functional enrichment studies for highlighting the POF pathogenesis. Real-time quantitative PCR was used to validate a subset of CNVs. Whole-exome sequencing was performed on six patients carrying hemizygous deletions that encompass genes essential for meiosis or folliculogenesis.



Eleven novel microdeletions and microduplications that encompass genes relevant to POF were identified. For example, FMN2 (1q43) and SGOL2 (2q33.1) are essential for meiotic progression, while TBP (6q27), SCARB1 (12q24.31), BNC1 (15q25) and ARFGAP3 (22q13.2) are involved in follicular growth and oocyte maturation. The importance of recently discovered hemizygous microdeletions of meiotic genes SYCE1 (10q26.3) and CPEB1 (15q25.2) in POF patients was also corroborated.



This is a descriptive analysis and no functional studies were performed. Anamnestic data obtained from population-based biobank lacked clinical, biological (hormone levels) or ultrasonographical data, and spontaneous POF was predicted retrospectively by excluding known extraovarian causes for premature menopause.



The present study, with high number of spontaneous POF cases, provides novel data on associations between the genomic aberrations and premature menopause of ovarian cause and demonstrates that population-based biobanks are powerful source of biological samples and clinical data to reveal novel genetic lesions associated with human reproductive health and disease, including POF.



This study was supported by the Estonian Ministry of Education and Research (IUT20-43, IUT20-60, IUT34-16, SF0180027s10 and 9205), Enterprise Estonia (EU30020 and EU48695), Eureka's EUROSTARS programme (NOTED, EU41564), grants from European Union's FP7 Marie Curie Industry-Academia Partnerships and Pathways (IAPP, SARM, |EU324509) and Horizon 2020 innovation programme (WIDENLIFE, 692065), Academy of Finland and the Sigrid Juselius Foundation.
Institute of Bio- and Translational Medicine, University of Tartu, Ravila 19, Tartu 50411, Estonia Competence Centre on Health Technologies, Tiigi 61b, Tartu 50410, Estonia Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Riia 23, Tartu 51010, Estonia.
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Tšuiko
Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Riia 23, Tartu 51010, Estonia Estonian Genome Center, University of Tartu, Riia 23b, Tartu 51010, Estonia.
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Nõukas
Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Riia 23, Tartu 51010, Estonia Department of Genetics, United Laboratory, Tartu University Hospital, L. Puusepa 2, Tartu 51014, Estonia.
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Žilina
Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Riia 23, Tartu 51010, Estonia.
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Hensen
Department of Obstetrics and Gynecology, Helsinki University Hospital, Haartmaninkatu 2, Helsinki 00290, Finland Department of Obstetrics and Gynecology, Oulu University and Oulu University Hospital, Kajaanintie 50, Oulu 90220, Finland.
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Tapanainen
Estonian Genome Center, University of Tartu, Riia 23b, Tartu 51010, Estonia Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Riia 23, Tartu 51010, Estonia.
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Mägi
Estonian Genome Center, University of Tartu, Riia 23b, Tartu 51010, Estonia.
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Kals
Estonian Genome Center, University of Tartu, Riia 23b, Tartu 51010, Estonia.
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Kivistik
Institute of Bio- and Translational Medicine, University of Tartu, Ravila 19, Tartu 50411, Estonia Competence Centre on Health Technologies, Tiigi 61b, Tartu 50410, Estonia Department of Obstetrics and Gynecology, University of Tartu, L. Puusepa 8, Tartu 51014, Estonia.
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Haller-Kikkatalo
Institute of Bio- and Translational Medicine, University of Tartu, Ravila 19, Tartu 50411, Estonia Competence Centre on Health Technologies, Tiigi 61b, Tartu 50410, Estonia Department of Obstetrics and Gynecology, University of Tartu, L. Puusepa 8, Tartu 51014, Estonia.
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Salumets
Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, Riia 23, Tartu 51010, Estonia akurg@ebc.ee.
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Kurg
D000328:Adult; D000368:Aged; D056915:DNA Copy Number Variations; D030541:Databases, Genetic; D005260:Female; D005838:Genotype; D006801:Humans; D008875:Middle Aged; D009865:Oocytes / Q000254:growth & development* / Q000378:metabolism; D006080:Ovarian Follicle / Q000254:growth & development* / Q000378:metabolism; D010641:Phenotype; D016649:Primary Ovarian Insufficiency / Q000235:genetics* / Q000378:metabolism; D012189:Retrospective Studies
CNV; POF; SNP genotyping; copy number variation; menopause; population-based biobank; premature ovarian failure