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Johnstone EB, Gorsi B, Coelho E, Moore B, Farr AM, Cooper AR, Mardis ER, Rajkovic A, Chow CY, Yandell M, Welt CK. DIS3 Variants are Associated With Primary Ovarian Insufficiency: Importance of Transcription/Translation in Oogenesis. J Clin Endocrinol Metab 2023; 108:2330-2335. [PMID: 36869713 PMCID: PMC10686695 DOI: 10.1210/clinem/dgad126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 02/27/2023] [Accepted: 03/01/2023] [Indexed: 03/05/2023]
Abstract
CONTEXT A genetic etiology accounts for the majority of unexplained primary ovarian insufficiency (POI). OBJECTIVE We hypothesized a genetic cause of POI for a sister pair with primary amenorrhea. DESIGN The study was an observational study. Subjects were recruited at an academic institution. SUBJECTS Subjects were sisters with primary amenorrhea caused by POI and their parents. Additional subjects included women with POI analyzed previously (n = 291). Controls were recruited for health in old age or were from the 1000 Genomes Project (total n = 233). INTERVENTION We performed whole exome sequencing, and data were analyzed using the Pedigree Variant Annotation, Analysis and Search Tool, which identifies genes harboring pathogenic variants in families. We performed functional studies in a Drosophila melanogaster model. MAIN OUTCOME Genes with rare pathogenic variants were identified. RESULTS The sisters carried compound heterozygous variants in DIS3. The sisters did not carry additional rare variants that were absent in publicly available datasets. DIS3 knockdown in the ovary of D. melanogaster resulted in lack of oocyte production and severe infertility. CONCLUSIONS Compound heterozygous variants in highly conserved amino acids in DIS3 and failure of oocyte production in a functional model suggest that mutations in DIS3 cause POI. DIS3 is a 3' to 5' exoribonuclease that is the catalytic subunit of the exosome involved in RNA degradation and metabolism in the nucleus. The findings provide further evidence that mutations in genes important for transcription and translation are associated with POI.
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Affiliation(s)
- Erica Boiman Johnstone
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Bushra Gorsi
- Utah Center for Genetic Discovery, Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Emily Coelho
- Utah Center for Genetic Discovery, Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Barry Moore
- Utah Center for Genetic Discovery, Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Ashley M Farr
- Division of Endocrinology, Metabolism and Diabetes, University of Utah, Salt Lake City, UT, USA
| | | | - Elaine R Mardis
- Institute for Genomic Medicine, Nationwide Children's Hospital, Ohio State University College of Medicine, Columbus, OH, USA
| | - Aleksander Rajkovic
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
- Institute of Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Clement Y Chow
- Utah Center for Genetic Discovery, Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Mark Yandell
- Utah Center for Genetic Discovery, Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Corrine K Welt
- Division of Endocrinology, Metabolism and Diabetes, University of Utah, Salt Lake City, UT, USA
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Gorsi B, Hernandez E, Moore MB, Moriwaki M, Chow CY, Coelho E, Taylor E, Lu C, Walker A, Touraine P, Nelson LM, Cooper AR, Mardis ER, Rajkovic A, Yandell M, Welt CK. Causal and Candidate Gene Variants in a Large Cohort of Women With Primary Ovarian Insufficiency. J Clin Endocrinol Metab 2022; 107:685-714. [PMID: 34718612 PMCID: PMC9006976 DOI: 10.1210/clinem/dgab775] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Indexed: 11/19/2022]
Abstract
CONTEXT A genetic etiology likely accounts for the majority of unexplained primary ovarian insufficiency (POI). OBJECTIVE We hypothesized that heterozygous rare variants and variants in enhanced categories are associated with POI. DESIGN The study was an observational study. SETTING Subjects were recruited at academic institutions. PATIENTS Subjects from Boston (n = 98), the National Institutes of Health and Washington University (n = 98), Pittsburgh (n = 20), Italy (n = 43), and France (n = 32) were diagnosed with POI (amenorrhea with an elevated follicle-stimulating hormone level). Controls were recruited for health in old age or were from the 1000 Genomes Project (total n = 233). INTERVENTION We performed whole exome sequencing (WES), and data were analyzed using a rare variant scoring method and a Bayes factor-based framework for identifying genes harboring pathogenic variants. We performed functional studies on identified genes that were not previously implicated in POI in a D. melanogaster model. MAIN OUTCOME Genes with rare pathogenic variants and gene sets with increased burden of deleterious variants were identified. RESULTS Candidate heterozygous variants were identified in known genes and genes with functional evidence. Gene sets with increased burden of deleterious alleles included the categories transcription and translation, DNA damage and repair, meiosis and cell division. Variants were found in novel genes from the enhanced categories. Functional evidence supported 7 new risk genes for POI (USP36, VCP, WDR33, PIWIL3, NPM2, LLGL1, and BOD1L1). CONCLUSIONS Candidate causative variants were identified through WES in women with POI. Aggregating clinical data and genetic risk with a categorical approach may expand the genetic architecture of heterozygous rare gene variants causing risk for POI.
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Affiliation(s)
- Bushra Gorsi
- Utah Center for Genetic Discovery, Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Edgar Hernandez
- Utah Center for Genetic Discovery, Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Marvin Barry Moore
- Utah Center for Genetic Discovery, Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Mika Moriwaki
- Division of Endocrinology, Metabolism and Diabetes, University of Utah, Salt Lake City, UT, USA
| | - Clement Y Chow
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Emily Coelho
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Elaine Taylor
- University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Claire Lu
- University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Amanda Walker
- University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Philippe Touraine
- Sorbonne Universite, Hôpital Universitaire Pitié Salpêtrière-Charles Foix, Service d’Endocrinologie et Médecine de la Reproduction, Centre de Maladies Endocriniennes Rares de la Croissance et du Développement, Centre de Pathologies Gynécologiques Rares, Paris, France
| | | | | | - Elaine R Mardis
- Institute for Genomic Medicine, Nationwide Children’s Hospital, Ohio State University College of Medicine, Columbus, OH, USA
| | - Aleksander Rajkovic
- Department of Pathology, University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Mark Yandell
- Utah Center for Genetic Discovery, Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Corrine K Welt
- Division of Endocrinology, Metabolism and Diabetes, University of Utah, Salt Lake City, UT, USA
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Sasani TA, Pedersen BS, Gao Z, Baird L, Przeworski M, Jorde LB, Quinlan AR. Large, three-generation human families reveal post-zygotic mosaicism and variability in germline mutation accumulation. eLife 2019; 8:e46922. [PMID: 31549960 PMCID: PMC6759356 DOI: 10.7554/elife.46922] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Accepted: 08/13/2019] [Indexed: 12/27/2022] Open
Abstract
The number of de novo mutations (DNMs) found in an offspring's genome increases with both paternal and maternal age. But does the rate of mutation accumulation in human gametes differ across families? Using sequencing data from 33 large, three-generation CEPH families, we observed significant variability in parental age effects on DNM counts across families, ranging from 0.19 to 3.24 DNMs per year. Additionally, we found that ~3% of DNMs originated following primordial germ cell specification in a parent, and differed from non-mosaic germline DNMs in their mutational spectra. We also discovered that nearly 10% of candidate DNMs in the second generation were post-zygotic, and present in both somatic and germ cells; these gonosomal mutations occurred at equivalent frequencies on both parental haplotypes. Our results demonstrate that rates of germline mutation accumulation vary among families with similar ancestry, and confirm that post-zygotic mosaicism is a substantial source of human DNM.
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Affiliation(s)
- Thomas A Sasani
- Department of Human GeneticsUniversity of UtahSalt Lake CityUnited States
| | - Brent S Pedersen
- Department of Human GeneticsUniversity of UtahSalt Lake CityUnited States
| | - Ziyue Gao
- Howard Hughes Medical Institute and Department of GeneticsStanford UniversityStanfordUnited States
| | - Lisa Baird
- Department of Human GeneticsUniversity of UtahSalt Lake CityUnited States
| | - Molly Przeworski
- Department of Biological SciencesColumbia UniversityNew York CityUnited States
- Department of Systems BiologyColumbia UniversityNew York CityUnited States
| | - Lynn B Jorde
- Department of Human GeneticsUniversity of UtahSalt Lake CityUnited States
- USTAR Center for Genetic DiscoveryUniversity of UtahSalt Lake CityUnited States
| | - Aaron R Quinlan
- Department of Human GeneticsUniversity of UtahSalt Lake CityUnited States
- USTAR Center for Genetic DiscoveryUniversity of UtahSalt Lake CityUnited States
- Department of Biomedical InformaticsUniversity of UtahSalt Lake CityUnited States
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Prescott SM, Lalouel JM, Leppert M. From Linkage Maps to Quantitative Trait Loci: The History and Science of the Utah Genetic Reference Project. Annu Rev Genomics Hum Genet 2008; 9:347-58. [DOI: 10.1146/annurev.genom.9.081307.164441] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Jean Marc Lalouel
- Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112;
| | - Mark Leppert
- Department of Human Genetics, University of Utah, Salt Lake City, Utah 84112;
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Rio Frio T, Civic N, Ransijn A, Beckmann JS, Rivolta C. Two trans-acting eQTLs modulate the penetrance of PRPF31 mutations. Hum Mol Genet 2008; 17:3154-65. [PMID: 18640990 DOI: 10.1093/hmg/ddn212] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Dominant mutations in the gene encoding the ubiquitously-expressed splicing factor PRPF31 cause retinitis pigmentosa, a form of hereditary retinal degeneration, with reduced penetrance. We and others have previously shown that penetrance is tightly correlated with PRPF31 expression, as lymphoblastoid cell lines (LCLs) from affected patients produce less abundant PRPF31 transcripts than LCLs from their unaffected relatives carrying the same mutation. We have investigated the genetic elements determining the variable expression of PRPF31, and therefore possibly influencing the penetrance of its mutations, by quantifying PRPF31 mRNA levels in LCLs derived from 15 CEPH families (200 individuals), representative of the general population. We found that PRPF31 transcript abundance was a highly variable and highly heritable character. Moreover, by linkage analysis we showed that PRPF31 expression was significantly associated with at least one expression quantitative trait locus (eQTL), spanning a 8.2-Mb region on chromosome 14q21-23. We also investigated a previously mapped penetrance factor located near PRPF31 itself in LCLs from individuals belonging to selected families segregating PRPF31 mutations that displayed reduced penetrance. Our results indicate that, despite its constant association with the non-mutant allele, this factor was able to modulate the expression of both PRPF31 alleles. Furthermore, we showed that LCLs from affected patients have less PRPF31 RNA than those of asymptomatic patients, even at the pre-splicing stage. Altogether, these data demonstrate that PRPF31 mRNA expression and consequently the penetrance of PRPF31 mutations is managed by diffusible compounds encoded by at least two modifiers, acting in a co-regulatory system on both PRPF31 alleles during transcription.
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Affiliation(s)
- Thomas Rio Frio
- Department of Medical Genetics, University of Lausanne, Rue du Bugnon 27, Lausanne 1005, Switzerland
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Sung YJ, Thompson EA, Wijsman EM. MCMC-based linkage analysis for complex traits on general pedigrees: multipoint analysis with a two-locus model and a polygenic component. Genet Epidemiol 2007; 31:103-14. [PMID: 17123301 DOI: 10.1002/gepi.20194] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We describe a new program lm_twoqtl, part of the MORGAN package, for parametric linkage analysis with a quantitative trait locus (QTL) model having one or two QTLs and a polygenic component, which models additional familial correlation from other unlinked QTLs. The program has no restriction on number of markers or complexity of pedigrees, facilitating use of more complex models with general pedigrees. This is the first available program that can handle a model with both two QTLs and a polygenic component. Competing programs use only simpler models: one QTL, one QTL plus a polygenic component, or variance components (VC). Use of simple models when they are incorrect, as for complex traits that are influenced by multiple genes, can bias estimates of QTL location or reduce power to detect linkage. We compute the likelihood with Markov Chain Monte Carlo (MCMC) realization of segregation indicators at the hypothesized QTL locations conditional on marker data, summation over phased multilocus genotypes of founders, and peeling of the polygenic component. Simulated examples, with various sized pedigrees, show that two-QTL analysis correctly identifies the location of both QTLs, even when they are closely linked, whereas other analyses, including the VC approach, fail to identify the location of QTLs with modest contribution. Our examples illustrate the advantage of parametric linkage analysis with two QTLs, which provides higher power for linkage detection and better localization than use of simpler models.
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Affiliation(s)
- Yun Ju Sung
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195-7720, USA
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Greenwood TA, Rao F, Stridsberg M, Mahapatra NR, Mahata M, Lillie EO, Mahata SK, Taupenot L, Schork NJ, O'Connor DT. Pleiotropic effects of novel trans-acting loci influencing human sympathochromaffin secretion. Physiol Genomics 2006; 25:470-9. [PMID: 16554546 DOI: 10.1152/physiolgenomics.00295.2005] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Family studies have suggested a genetic contribution to variation in blood pressure, but the genes responsible have thus far eluded identification. The use of intermediate phenotypes associated with hypertension, such as chromogranin plasma concentrations, may assist the discovery of hypertension-predisposing loci. We measured the concentrations of four chromogranin A (CHGA) and B (CHGB) peptides in 742 individuals from 235 nuclear families. The CHGA- and CHGB-derived peptides displayed significant heritability and revealed significant genetic correlations, most strikingly observed between CHGA(361-372) (catestatin) and CHGB(439-451). A 5-cM microsatellite genome scan revealed significant and suggestive evidence for linkage on several chromosomes for three of the peptides. Subsequent bivariate linkage analysis for peptides CHGA(361-372) and CHGB(439-451), which showed evidence for convergent linkage peaks on chromosomes 2, 7, and 13, resulted in increased evidence for linkage to these regions, suggesting pleiotropic effects of these three loci on multiple chromogranin traits. Because CHGA itself is on chromosome 14q32, and CHGB itself is on chromosome 20pter-p12, the pleiotropic regions on chromosomes 2, 7, and 13 must represent trans-acting quantitative trait loci coordinately affecting CHGA/CHGB biosynthesis and/or exocytotic secretion, likely by regulating efferent sympathetic outflow, a conclusion consistent with the in vitro studies presented here of the dual control of both exocytosis and transcription of these peptides by secretory stimuli in chromaffin cells. The results suggest a new approach to heritable autonomic control of circulation and the genetic basis of cardiovascular diseases such as systemic hypertension.
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