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      A systematic review and standardized clinical validity assessment of genes involved in female reproductive failure

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          Abstract

          Genetic testing is becoming increasingly required at almost every stage of failed female reproduction/infertility. Nonetheless, clinical evidence for the majority of identified gene–disease relationships is ill-defined, thus leading to difficult gene variant interpretation and poor translation of existing knowledge into clinics. We aimed to identify the genes that have ever been implicated in monogenic female reproductive failure in humans and to classify the identified gene–disease relationship pairs using a standardized clinical validity assessment. A PubMed search following PRISMA guidelines was conducted on 20 September 2021 aiming to identify studies pertaining to genetic causes of phenotypes of female reproductive failure. The clinical validity of identified gene–disease pairs was assessed using standardized criteria, counting whether sufficient genetic and experimental evidence has been accumulated to consider a single gene ‘characterized’ for a single Mendelian disease. In total, 1256 articles were selected for the data extraction; 183 unique gene–disease pairs were classified spanning the following phenotypes: hypogonadotropic hypogonadism, ovarian dysgenesis, premature ovarian failure/insufficiency, ovarian hyperstimulation syndrome, empty follicle syndrome, oocyte maturation defect, fertilization failure, early embryonic arrest, recurrent hydatidiform mole, adrenal disfunction and Mullerian aplasia. Twenty-four gene–disease pairs showed definitive evidence, 36 – strong, 19 – moderate, 81 – limited and 23 – showed no evidence. Here, we provide comprehensive, systematic and timely information on the genetic causes of female infertility. Our classification of genetic causes of female reproductive failure will facilitate the composition of up-to-date guidelines on genetic testing in female reproduction, the development of diagnostic gene panels and the advancement of reproductive decision-making.

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          Most cited references68

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          Standards and Guidelines for the Interpretation of Sequence Variants: A Joint Consensus Recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology

          The American College of Medical Genetics and Genomics (ACMG) previously developed guidance for the interpretation of sequence variants. 1 In the past decade, sequencing technology has evolved rapidly with the advent of high-throughput next generation sequencing. By adopting and leveraging next generation sequencing, clinical laboratories are now performing an ever increasing catalogue of genetic testing spanning genotyping, single genes, gene panels, exomes, genomes, transcriptomes and epigenetic assays for genetic disorders. By virtue of increased complexity, this paradigm shift in genetic testing has been accompanied by new challenges in sequence interpretation. In this context, the ACMG convened a workgroup in 2013 comprised of representatives from the ACMG, the Association for Molecular Pathology (AMP) and the College of American Pathologists (CAP) to revisit and revise the standards and guidelines for the interpretation of sequence variants. The group consisted of clinical laboratory directors and clinicians. This report represents expert opinion of the workgroup with input from ACMG, AMP and CAP stakeholders. These recommendations primarily apply to the breadth of genetic tests used in clinical laboratories including genotyping, single genes, panels, exomes and genomes. This report recommends the use of specific standard terminology: ‘pathogenic’, ‘likely pathogenic’, ‘uncertain significance’, ‘likely benign’, and ‘benign’ to describe variants identified in Mendelian disorders. Moreover, this recommendation describes a process for classification of variants into these five categories based on criteria using typical types of variant evidence (e.g. population data, computational data, functional data, segregation data, etc.). Because of the increased complexity of analysis and interpretation of clinical genetic testing described in this report, the ACMG strongly recommends that clinical molecular genetic testing should be performed in a CLIA-approved laboratory with results interpreted by a board-certified clinical molecular geneticist or molecular genetic pathologist or equivalent.
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            Preferred reporting items for systematic reviews and meta-analyses: the PRISMA statement.

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              Analysis of protein-coding genetic variation in 60,706 humans

              Summary Large-scale reference data sets of human genetic variation are critical for the medical and functional interpretation of DNA sequence changes. We describe the aggregation and analysis of high-quality exome (protein-coding region) sequence data for 60,706 individuals of diverse ethnicities generated as part of the Exome Aggregation Consortium (ExAC). This catalogue of human genetic diversity contains an average of one variant every eight bases of the exome, and provides direct evidence for the presence of widespread mutational recurrence. We have used this catalogue to calculate objective metrics of pathogenicity for sequence variants, and to identify genes subject to strong selection against various classes of mutation; identifying 3,230 genes with near-complete depletion of truncating variants with 72% having no currently established human disease phenotype. Finally, we demonstrate that these data can be used for the efficient filtering of candidate disease-causing variants, and for the discovery of human “knockout” variants in protein-coding genes.
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                Author and article information

                Journal
                Reproduction
                Reproduction
                REP
                Reproduction (Cambridge, England)
                Bioscientifica Ltd (Bristol )
                1470-1626
                1741-7899
                29 March 2022
                01 June 2022
                : 163
                : 6
                : 351-363
                Affiliations
                [1 ]Scientific Laboratory of Molecular Genetics , Riga Stradins University, Riga, Latvia
                [2 ]E. Gulbja Laboratory , Riga, LV-1006, Latvia
                [3 ]Department of Obstetrics and Gynaecology , Riga Stradins University, Riga, Latvia
                [4 ]Riga Maternity Hospital , Riga, LV-1013, Latvia
                Author notes
                Correspondence should be addressed to L Volozonoka; Email: ludmilavolozonoka@ 123456gmail.com
                Author information
                http://orcid.org/0000-0003-0413-1481
                Article
                REP-21-0486
                10.1530/REP-21-0486
                9066658
                35451369
                78ae1c37-dfb3-4f14-8fac-54b4bc73e24e
                © The authors

                This work is licensed under a Creative Commons Attribution 4.0 International License.

                History
                : 08 December 2021
                : 29 March 2022
                Categories
                Research

                Obstetrics & Gynecology
                Obstetrics & Gynecology

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