51
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Miyahara K, Tatehana M, Kikkawa T, Osumi N. Investigating the impact of paternal aging on murine sperm miRNA profiles and their potential link to autism spectrum disorder. Sci Rep 2023; 13:20608. [PMID: 38062235 PMCID: PMC10703820 DOI: 10.1038/s41598-023-47878-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 11/17/2023] [Indexed: 12/18/2023] Open
Abstract
Paternal aging has consistently been linked to an increased risk of neurodevelopmental disorders, including autism spectrum disorder (ASD), in offspring. Recent evidence has highlighted the involvement of epigenetic factors. In this study, we aimed to investigate age-related alterations in microRNA (miRNA) profiles of mouse sperm and analyze target genes regulated by differentially expressed miRNAs (DEmiRNAs). Microarray analyses were conducted on sperm samples from mice at different ages: 3 months (3 M), over 12 M, and beyond 20 M. We identified 26 miRNAs with differential expression between the 3 and 20 M mice, 34 miRNAs between the 12 and 20 M mice, and 2 miRNAs between the 3 and 12 M mice. The target genes regulated by these miRNAs were significantly associated with apoptosis/ferroptosis pathways and the nervous system. We revealed alterations in sperm miRNA profiles due to aging and suggest that the target genes regulated by these DEmiRNAs are associated with apoptosis and the nervous system, implying a potential link between paternal aging and an increased risk of neurodevelopmental disorders such as ASD. The observed age-related changes in sperm miRNA profiles have the potential to impact sperm quality and subsequently affect offspring development.
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Affiliation(s)
- Kazusa Miyahara
- Department of Developmental Neuroscience, Center for Advanced Research and Translational Medicine (ART), Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Misako Tatehana
- Department of Developmental Neuroscience, Center for Advanced Research and Translational Medicine (ART), Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Takako Kikkawa
- Department of Developmental Neuroscience, Center for Advanced Research and Translational Medicine (ART), Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Noriko Osumi
- Department of Developmental Neuroscience, Center for Advanced Research and Translational Medicine (ART), Tohoku University Graduate School of Medicine, Sendai, Japan.
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52
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Hinch R, Donnelly P, Hinch AG. Meiotic DNA breaks drive multifaceted mutagenesis in the human germ line. Science 2023; 382:eadh2531. [PMID: 38033082 PMCID: PMC7615360 DOI: 10.1126/science.adh2531] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 09/29/2023] [Indexed: 12/02/2023]
Abstract
Meiotic recombination commences with hundreds of programmed DNA breaks; however, the degree to which they are accurately repaired remains poorly understood. We report that meiotic break repair is eightfold more mutagenic for single-base substitutions than was previously understood, leading to de novo mutation in one in four sperm and one in 12 eggs. Its impact on indels and structural variants is even higher, with 100- to 1300-fold increases in rates per break. We uncovered new mutational signatures and footprints relative to break sites, which implicate unexpected biochemical processes and error-prone DNA repair mechanisms, including translesion synthesis and end joining in meiotic break repair. We provide evidence that these mechanisms drive mutagenesis in human germ lines and lead to disruption of hundreds of genes genome wide.
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Affiliation(s)
- Robert Hinch
- Big Data Institute, University of Oxford; Oxford, UK
| | - Peter Donnelly
- Wellcome Centre for Human Genetics, University of Oxford; Oxford, UK
- Genomics plc; Oxford, UK
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53
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Klutstein M, Gonen N. Epigenetic aging of mammalian gametes. Mol Reprod Dev 2023; 90:785-803. [PMID: 37997675 DOI: 10.1002/mrd.23717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 11/09/2023] [Accepted: 11/12/2023] [Indexed: 11/25/2023]
Abstract
The process of aging refers to physiological changes that occur to an organism as time progresses and involves changes to DNA, proteins, metabolism, cells, and organs. Like the rest of the cells in the body, gametes age, and it is well established that there is a decline in reproductive capabilities in females and males with aging. One of the major pathways known to be involved in aging is epigenetic changes. The epigenome is the multitude of chemical modifications performed on DNA and chromatin that affect the ability of chromatin to be transcribed. In this review, we explore the effects of aging on female and male gametes with a focus on the epigenetic changes that occur in gametes throughout aging. Quality decline in oocytes occurs at a relatively early age. Epigenetic changes constitute an important part of oocyte aging. DNA methylation is reduced with age, along with reduced expression of DNA methyltransferases (DNMTs). Histone deacetylases (HDAC) expression is also reduced, and a loss of heterochromatin marks occurs with age. As a consequence of heterochromatin loss, retrotransposon expression is elevated, and aged oocytes suffer from DNA damage. In sperm, aging affects sperm number, motility and fecundity, and epigenetic changes may constitute a part of this process. 5 methyl-cytosine (5mC) methylation is elevated in sperm from aged men, but methylation on Long interspersed nuclear elements (LINE) elements is reduced. Di and trimethylation of histone 3 lysine 9 (H3K9me2/3) is reduced in sperm from aged men and trimethylation of histone 3 lysine 27 (H3K27me3) is elevated. The protamine makeup of sperm from aged men is also changed, with reduced protamine expression and a misbalanced ratio between protamine proteins protamine P1 and protamine P2. The study of epigenetic reproductive aging is recently gaining interest. The current status of the field suggests that many aspects of gamete epigenetic aging are still open for investigation. The clinical applications of these investigations have far-reaching consequences for fertility and sociological human behavior.
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Affiliation(s)
- Michael Klutstein
- Institute of Biomedical and Oral Research, Faculty of Dental Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Nitzan Gonen
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, Israel
- Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
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54
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Maslov AY, Vijg J. Somatic mutation burden in relation to aging and functional life span: implications for cellular reprogramming and rejuvenation. Curr Opin Genet Dev 2023; 83:102132. [PMID: 37931583 PMCID: PMC10841402 DOI: 10.1016/j.gde.2023.102132] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 09/02/2023] [Accepted: 10/07/2023] [Indexed: 11/08/2023]
Abstract
The accrual of somatic mutations has been implicated as causal factors in aging since the 1950s. However, the quantitative analysis of somatic mutations has posed a major challenge due to the random nature of de novo mutations in normal tissues, which has limited analysis to tumors and other clonal lineages. Advances in single-cell and single-molecule next-generation sequencing now allow to obtain, for the first time, detailed insights into the landscape of somatic mutations in different human tissues and cell types as a function of age under various conditions. Here, we will briefly recapitulate progress in somatic mutation analysis and discuss the possible relationship between somatic mutation burden with functional life span, with a focus on differences between germ cells, stem cells, and differentiated cells.
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Affiliation(s)
- Alexander Y Maslov
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Laboratory of Applied Genomic Technologies, Voronezh State University of Engineering Technologies, Voronezh, Russia.
| | - Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
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55
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Behdarvandian P, Nasr-Esfahani A, Tavalaee M, Pashaei K, Naderi N, Darmishonnejad Z, Hallak J, Aitken RJ, Gharagozloo P, Drevet JR, Nasr-Esfahani MH. Sperm chromatin structure assay (SCSA ®) and flow cytometry-assisted TUNEL assay provide a concordant assessment of sperm DNA fragmentation as a function of age in a large cohort of approximately 10,000 patients. Basic Clin Androl 2023; 33:33. [PMID: 38030992 PMCID: PMC10688019 DOI: 10.1186/s12610-023-00208-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 09/19/2023] [Indexed: 12/01/2023] Open
Abstract
BACKGROUND Sperm DNA integrity is increasingly seen as a critical characteristic determining reproductive success, both in natural reproduction and in assisted reproductive technologies (ART). Despite this awareness, sperm DNA and nuclear integrity tests are still not part of routine examinations for either infertile men or fertile men wishing to assess their reproductive capacity. This is not due to the unavailability of DNA and sperm nuclear integrity tests. On the contrary, several relevant but distinct tests are available and have been used in many clinical trials, which has led to conflicting results and confusion. The reasons for this are mainly the lack of standardization between different clinics and between the tests themselves. In addition, the small number of samples analyzed in these trials has often weakened the value of the analyses performed. In the present work, we used a large cohort of semen samples, covering a wide age range, which were simultaneously evaluated for sperm DNA fragmentation (SDF) using two of the most frequently used SDF assays, namely the TUNEL assay and the sperm chromatin structure assay (SCSA®). At the same time, as standard seminal parameters (sperm motility, sperm morphology, sperm count) were available for these samples, correlations between age, SDF and conventional seminal parameters were analyzed. RESULTS We show that the SCSA® and TUNEL assessments of SDF produce concordant data. However, the SDF assessed by TUNEL is systematically lower than that assessed by SCSA®. Regardless of the test used, the SDF increases steadily during aging, while the HDS parameter (High DNA stainability assessed via SCSA®) remains unchanged. In the cohort analyzed, conventional sperm parameters do not seem to discriminate with aging. Only sperm volume and motility were significantly lower in the oldest age group analyzed [50-59 years of age]. CONCLUSIONS In the large cohort analyzed, SDF is an age-dependent parameter, increasing linearly with aging. The SCSA® assessment of SDF and the flow cytometry-assisted TUNEL assessment are well correlated, although TUNEL is less sensitive than SCSA®. This difference in sensitivity should be taken into account in the final assessment of the true level of fragmentation of the sperm nucleus of a given sample. The classical sperm parameters (motility, morphology, sperm count) do not change dramatically with age, making them inadequate to assess the fertility potential of an individual.
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Affiliation(s)
- Paria Behdarvandian
- Department of Animal Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, 8165131378, Iran
| | - Ali Nasr-Esfahani
- Department of Animal Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, 8165131378, Iran.
- Isfahan Fertility and Infertility Center, Isfahan, Iran.
| | - Marziyeh Tavalaee
- Department of Animal Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, 8165131378, Iran
| | - Kosar Pashaei
- Isfahan Fertility and Infertility Center, Isfahan, Iran
| | - Nushin Naderi
- Department of Animal Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, 8165131378, Iran
| | - Zahra Darmishonnejad
- Department of Animal Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, 8165131378, Iran
| | - Jorge Hallak
- Androscience, Science and Innovation Center in Andrology and High-Complex Clinical and Research Andrology Laboratory, Sao Paulo, 04534-011, Brazil
| | - Robert J Aitken
- Priority Research Centre for Reproductive Science, Discipline of Biological Sciences, School of Environmental and Life Sciences, College of Engineering Science and Environment, University of Newcastle, Callaghan, NSW, 2308, Australia
| | | | - Joël R Drevet
- Faculty of Medicine, Université Clermont Auvergne, GReD Institute, CRBC, 63000, Clermont-Ferrand, France.
| | - Mohammad Hossein Nasr-Esfahani
- Department of Animal Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, 8165131378, Iran.
- Isfahan Fertility and Infertility Center, Isfahan, Iran.
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56
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Potabattula R, Prell A, Dittrich M, Nava C, Depienne C, Bejaoui Y, El Hajj N, Hahn T, Schorsch M, Haaf T. Effects of paternal and chronological age on BEGAIN methylation and its possible role in autism. Aging (Albany NY) 2023; 15:12763-12779. [PMID: 38019471 DOI: 10.18632/aging.205275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 10/23/2023] [Indexed: 11/30/2023]
Abstract
Children from old fathers carry an increased risk for autism spectrum (ASD) and other neurodevelopmental disorders, which may at least partially be mediated by paternal age effects on the sperm epigenome. The brain enriched guanylate kinase associated (BEGAIN) protein is involved in protein-protein interactions at and transmission across synapses. Since several epigenome-wide methylation screens reported a paternal age effect on sperm BEGAIN methylation, here we confirmed a significant negative correlation between BEGAIN promoter methylation and paternal age, using more sensitive bisulfite pyrosequencing and a larger number of sperm samples. Paternal age-associated BEGAIN hypomethylation was also observed in fetal cord blood (FCB) of male but not of female offspring. There was no comparable maternal age effect on FCB methylation. In addition, we found a significant negative correlation between BEGAIN methylation and chronological age (ranging from 1 to 70 years) in peripheral blood samples of male but not of female donors. BEGAIN hypomethylation was more pronounced in male children, adolescents and adults suffering from ASD compared to controls. Both genetic variation (CC genotype of SNP rs7141087) and epigenetic factors may contribute to BEGAIN promoter hypomethylation. The age- and sex-specific BEGAIN methylation trajectories in the male germ line and somatic tissues, in particular the brain, support a role of this gene in ASD development.
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Affiliation(s)
- Ramya Potabattula
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | - Andreas Prell
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | - Marcus Dittrich
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
- Department of Bioinformatics, Julius Maximilians University, Würzburg, Germany
| | - Caroline Nava
- U.F. de Neurogénétique Moléculaire et Cellulaire, Dpt. de Génétique et Cytogénétique, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - Christel Depienne
- Institute of Human Genetics, University Hospital Essen, Essen, Germany
| | - Yosra Bejaoui
- College of Health and Life Sciences and College of Science and Engineering, Hamad Bin Khalifa University, Doha, Qatar
| | - Nady El Hajj
- College of Health and Life Sciences and College of Science and Engineering, Hamad Bin Khalifa University, Doha, Qatar
| | | | | | - Thomas Haaf
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
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57
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Hahn MW, Peña-Garcia Y, Wang RJ. The 'faulty male' hypothesis for sex-biased mutation and disease. Curr Biol 2023; 33:R1166-R1172. [PMID: 37989088 DOI: 10.1016/j.cub.2023.09.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
Biological differences between males and females lead to many differences in physiology, disease, and overall health. One of the most prominent disparities is in the number of germline mutations passed to offspring: human males transmit three times as many mutations as do females. While the classic explanation for this pattern invokes differences in post-puberty germline replication between the sexes, recent whole-genome evidence in humans and other mammals has cast doubt on this mechanism. Here, we review recent work that is inconsistent with a replication-driven model of male-biased mutation, and propose an alternative, 'faulty male' hypothesis. This model proposes that males are less able to repair and/or protect DNA from damage compared to females. Importantly, we suggest that this new model for male-biased mutation may also help to explain several pronounced differences between the sexes in cancer, aging, and DNA repair. Although the detailed contributions of genetic, epigenetic, and hormonal influences of biological sex on mutation remain to be fully understood, a reconsideration of the mechanisms underlying these differences will lead to a deeper understanding of evolution and disease.
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Affiliation(s)
- Matthew W Hahn
- Department of Biology, Indiana University, 1001 E. 3(rd) Street, Bloomington, IN 47405, USA; Department of Computer Science, 700 N. Woodlawn Avenue, Bloomington, IN 47405, USA.
| | - Yadira Peña-Garcia
- Department of Biology, Indiana University, 1001 E. 3(rd) Street, Bloomington, IN 47405, USA
| | - Richard J Wang
- Department of Biology, Indiana University, 1001 E. 3(rd) Street, Bloomington, IN 47405, USA; Department of Computer Science, 700 N. Woodlawn Avenue, Bloomington, IN 47405, USA
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58
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Derks LLM, van Boxtel R. Stem cell mutations, associated cancer risk, and consequences for regenerative medicine. Cell Stem Cell 2023; 30:1421-1433. [PMID: 37832550 PMCID: PMC10624213 DOI: 10.1016/j.stem.2023.09.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/05/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023]
Abstract
Mutation accumulation in stem cells has been associated with cancer risk. However, the presence of numerous mutant clones in healthy tissues has raised the question of what limits cancer initiation. Here, we review recent developments in characterizing mutation accumulation in healthy tissues and compare mutation rates in stem cells during development and adult life with corresponding cancer risk. A certain level of mutagenesis within the stem cell pool might be beneficial to limit the size of malignant clones through competition. This knowledge impacts our understanding of carcinogenesis with potential consequences for the use of stem cells in regenerative medicine.
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Affiliation(s)
- Lucca L M Derks
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands; Oncode Institute, Jaarbeursplein 6, 3521 AL Utrecht, the Netherlands
| | - Ruben van Boxtel
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, 3584 CS Utrecht, the Netherlands; Oncode Institute, Jaarbeursplein 6, 3521 AL Utrecht, the Netherlands.
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59
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Peel A, Saini A, Deluao JC, McPherson NO. Sperm DNA damage: The possible link between obesity and male infertility, an update of the current literature. Andrology 2023; 11:1635-1652. [PMID: 36789664 DOI: 10.1111/andr.13409] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/13/2023] [Accepted: 02/08/2023] [Indexed: 02/16/2023]
Abstract
Obesity prevalence worldwide is increasing significantly. Whilst maternal obesity has clear detrimental impacts on fertility, pregnancy and foetal outcomes, more recently there has been an increasing focus on the role of paternal obesity in human fertility. Recent meta-analyses have indicated that obesity in men negatively affects basic sperm parameters such as sperm count, concentration and motility, increases the incidence of infertility and reduces the chances of conception. Sperm DNA damage, typically characterised by DNA strand breaks and oxidation of DNA nucleotides, is a specialised marker of sperm quality that has been independently associated with recurrent miscarriage, reduced assisted reproduction success and increased mutational loads in subsequent offspring. Whilst, there are still conflicting data in humans as to the association of obesity in men with sperm DNA damage, evidence from rodent models is clear, indicating that male obesity increases sperm DNA damage. Human data are often conflicting because of the large heterogeneity amongst studies, the use of body mass index as the indicator of obesity and the methods used for detection of sperm DNA damage. Furthermore, comorbidities of obesity (i.e., heat stress, adipokines, insulin resistance, changes in lipids, hypogonadism and obstructive sleep apnoea) are also independently associated with increased sperm DNA damage that is not always modified in men with obesity, and as such may provide a causative link to the discrepancies amongst human studies. In this review, we provide an update on the literature regarding the associations between obesity in men and fertility, basic sperm parameters and sperm DNA damage. We further discuss potential reasons for the discrepancies in the literature and outline possible direct and indirect mechanisms of increased sperm DNA damage resulting from obesity. Finally, we summarise intergenerational obesity through the paternal linage and how sperm DNA damage may contribute to the transmission.
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Affiliation(s)
- Andrew Peel
- Robinson Research Institute, The University of Adelaide, Adelaide, South Australia, Australia
- Freemasons Centre for Male Health and Wellbeing, The University of Adelaide, Adelaide, South Australia, Australia
- Adelaide Health and Medical School, School of Biomedicine, Discipline of Reproduction and Development, The University of Adelaide, Adelaide, South Australia, Australia
| | - Anmol Saini
- Robinson Research Institute, The University of Adelaide, Adelaide, South Australia, Australia
- Adelaide Health and Medical School, School of Biomedicine, Discipline of Reproduction and Development, The University of Adelaide, Adelaide, South Australia, Australia
| | - Joshua C Deluao
- Robinson Research Institute, The University of Adelaide, Adelaide, South Australia, Australia
- Freemasons Centre for Male Health and Wellbeing, The University of Adelaide, Adelaide, South Australia, Australia
- Adelaide Health and Medical School, School of Biomedicine, Discipline of Reproduction and Development, The University of Adelaide, Adelaide, South Australia, Australia
| | - Nicole O McPherson
- Robinson Research Institute, The University of Adelaide, Adelaide, South Australia, Australia
- Freemasons Centre for Male Health and Wellbeing, The University of Adelaide, Adelaide, South Australia, Australia
- Adelaide Health and Medical School, School of Biomedicine, Discipline of Reproduction and Development, The University of Adelaide, Adelaide, South Australia, Australia
- Repromed IVF Adelaide, Dulwich, South Australia, Australia
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60
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Zhang H, Lundberg M, Tarka M, Hasselquist D, Hansson B. Evidence of Site-Specific and Male-Biased Germline Mutation Rate in a Wild Songbird. Genome Biol Evol 2023; 15:evad180. [PMID: 37793164 PMCID: PMC10627410 DOI: 10.1093/gbe/evad180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 09/07/2023] [Accepted: 09/26/2023] [Indexed: 10/06/2023] Open
Abstract
Germline mutations are the ultimate source of genetic variation and the raw material for organismal evolution. Despite their significance, the frequency and genomic locations of mutations, as well as potential sex bias, are yet to be widely investigated in most species. To address these gaps, we conducted whole-genome sequencing of 12 great reed warblers (Acrocephalus arundinaceus) in a pedigree spanning 3 generations to identify single-nucleotide de novo mutations (DNMs) and estimate the germline mutation rate. We detected 82 DNMs within the pedigree, primarily enriched at CpG sites but otherwise randomly located along the chromosomes. Furthermore, we observed a pronounced sex bias in DNM occurrence, with male warblers exhibiting three times more mutations than females. After correction for false negatives and adjusting for callable sites, we obtained a mutation rate of 7.16 × 10-9 mutations per site per generation (m/s/g) for the autosomes and 5.10 × 10-9 m/s/g for the Z chromosome. To demonstrate the utility of species-specific mutation rates, we applied our autosomal mutation rate in models reconstructing the demographic history of the great reed warbler. We uncovered signs of drastic population size reductions predating the last glacial period (LGP) and reduced gene flow between western and eastern populations during the LGP. In conclusion, our results provide one of the few direct estimates of the mutation rate in wild songbirds and evidence for male-driven mutations in accordance with theoretical expectations.
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Affiliation(s)
- Hongkai Zhang
- Department of Biology, Lund University, Lund, Sweden
| | - Max Lundberg
- Department of Biology, Lund University, Lund, Sweden
| | - Maja Tarka
- Department of Biology, Lund University, Lund, Sweden
| | | | - Bengt Hansson
- Department of Biology, Lund University, Lund, Sweden
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61
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Tran NT, Vo ST, Nguyen DA, Nguyen CC, Dinh LT, Tran MTT, Tran DC, Luong LAT, Doan KP, Huy Nguyen VQ, Thi Ha TM, Truong LGT, Cao PTM, Tran VTN, Nhut Trinh TH, Le QT, Nguyen VT, Hoang DTT, Nguyen MNB, Bui CT, Tran STT, Lam DT, Le HT, Nguyen MNB, Ho VT, Nguyen MT, Dao TT, Nguyen PM, Nguyen THL, Ha NP, Lu YT, Do TTT, Truong DK, Phan MD, Nguyen HN, Giang H, Tang HS. De novo variants of dominant monogenic disorders in Vietnam detected by a noninvasive prenatal test: a case series. Per Med 2023; 20:467-475. [PMID: 37937420 DOI: 10.2217/pme-2023-0105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
Background: Noninvasive prenatal tests for monogenic diseases (NIPT-SGG) have recently been reported as helpful in early-stage antenatal screening. Our study describes the clinical and genetic features of cases identified by NIPT-SGG. Materials & methods: In a cohort pregnancy with abnormal sonograms, affected cases were confirmed by invasive diagnostic tests concurrently, with NIPT-SGG targeting 25 common dominant single-gene diseases. Results: A total of 13 single-gene fetuses were confirmed, including Noonan and Costello syndromes, thanatophoric dysplasia, achondroplasia, osteogenesis imperfecta and Apert syndrome. Two novel variants seen were tuberous sclerosis complex (TSC2 c.4154G>A) and Alagille syndrome (JAG1 c.3452del). Conclusion: NIPT-SGG and standard tests agree on the results for 13 fetuses with monogenic disorders. This panel method of screening can benefit high-risk Vietnamese pregnancies, but further research is encouraged to expand on the causative gene panel.
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Affiliation(s)
- Nhat-Thang Tran
- University of Medicine & Pharmacy at Ho Chi Minh City, Ho Chi Minh City, 70000, Vietnam
- University Medical Center, Ho Chi Minh City, 70000, Vietnam
| | - Son Ta Vo
- Vinmec Health Care System, Hanoi City, 10000, Vietnam
| | - Duy-Anh Nguyen
- Hanoi Obstetrics & Gynecology Hospital, Hanoi City, 10000, Vietnam
- Hanoi Medical University, Hanoi City, 10000, Vietnam
| | - Canh-Chuong Nguyen
- Hanoi Obstetrics & Gynecology Hospital, Hanoi City, 10000, Vietnam
- Hanoi Medical University, Hanoi City, 10000, Vietnam
| | - Linh Thuy Dinh
- Hanoi Obstetrics & Gynecology Hospital, Hanoi City, 10000, Vietnam
| | | | - Danh-Cuong Tran
- National Hospital of Obstetrics & Gynecology, Hanoi City, 10000, Vietnam
| | | | - Kim-Phuong Doan
- Hanoi Medical University Hospital, Hanoi City, 10000, Vietnam
| | | | - Thi Minh Thi Ha
- University of Medicine & Pharmacy, Hue University, 49100, Vietnam
| | | | - Phuong Thi-Mai Cao
- University of Medicine & Pharmacy at Ho Chi Minh City, Ho Chi Minh City, 70000, Vietnam
- University Medical Center, Ho Chi Minh City, 70000, Vietnam
| | | | | | | | | | | | | | - Chi-Thuong Bui
- Gia Dinh People's Hospital, Ho Chi Minh City, 70000, Vietnam
| | - Son-Tra Thi Tran
- Vietnam-Cuba Friendship Dong Hoi Hospital, Dong Hoi City, 47100, Vietnam
| | - Duc-Tam Lam
- Can Tho University of Medicine & Pharmacy, Can Tho, 94000, Vietnam
| | - Hong-Thinh Le
- Can Tho Obstetrics & Gynecology Hospital, Can Tho, 94000, Vietnam
| | | | - Viet-Thang Ho
- University of Medicine & Pharmacy at Ho Chi Minh City, Ho Chi Minh City, 70000, Vietnam
| | | | - Trang Thi Dao
- Hanoi Medical University, Hanoi City, 10000, Vietnam
| | - Phuong Minh Nguyen
- Medical Genetics Institute, Ho Chi Minh City, 70000, Vietnam
- Gene Solutions, Ho Chi Minh City, 70000, Vietnam
| | - Thu-Hang Le Nguyen
- Medical Genetics Institute, Ho Chi Minh City, 70000, Vietnam
- Gene Solutions, Ho Chi Minh City, 70000, Vietnam
| | - Nhung Phuong Ha
- Medical Genetics Institute, Ho Chi Minh City, 70000, Vietnam
- Gene Solutions, Ho Chi Minh City, 70000, Vietnam
| | - Y-Thanh Lu
- Medical Genetics Institute, Ho Chi Minh City, 70000, Vietnam
- Gene Solutions, Ho Chi Minh City, 70000, Vietnam
| | | | | | - Minh-Duy Phan
- Medical Genetics Institute, Ho Chi Minh City, 70000, Vietnam
- Gene Solutions, Ho Chi Minh City, 70000, Vietnam
| | - Hoai-Nghia Nguyen
- Medical Genetics Institute, Ho Chi Minh City, 70000, Vietnam
- Gene Solutions, Ho Chi Minh City, 70000, Vietnam
| | - Hoa Giang
- Medical Genetics Institute, Ho Chi Minh City, 70000, Vietnam
- Gene Solutions, Ho Chi Minh City, 70000, Vietnam
| | - Hung-Sang Tang
- Medical Genetics Institute, Ho Chi Minh City, 70000, Vietnam
- Gene Solutions, Ho Chi Minh City, 70000, Vietnam
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Burda K, Konczal M. Validation of machine learning approach for direct mutation rate estimation. Mol Ecol Resour 2023; 23:1757-1771. [PMID: 37486035 DOI: 10.1111/1755-0998.13841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 06/16/2023] [Accepted: 07/05/2023] [Indexed: 07/25/2023]
Abstract
Mutations are the primary source of all genetic variation. Knowledge about their rates is critical for any evolutionary genetic analyses, but for a long time, that knowledge has remained elusive and indirectly inferred. In recent years, parent-offspring comparisons have yielded the first direct mutation rate estimates. The analyses are, however, challenging due to high rate of false positives and no consensus regarding standardized filtering of candidate de novo mutations. Here, we validate the application of a machine learning approach for such a task and estimate the mutation rate for the guppy (Poecilia reticulata), a model species in eco-evolutionary studies. We sequenced 4 parents and 20 offspring, followed by screening their genomes for de novo mutations. The initial large number of candidate de novo mutations was hard-filtered to remove false-positive results. These results were compared with mutation rate estimated with a supervised machine learning approach. Both approaches were followed by molecular validation of all candidate de novo mutations and yielded similar results. The ML method uniquely identified three mutations, but overall required more hands-on curation and had higher rates of false positives and false negatives. Both methods concordantly showed no difference in mutation rates between families. Estimated here the guppy mutation rate is among the lowest directly estimated mutation rates in vertebrates; however, previous research has also found low estimated rates in other teleost fishes. We discuss potential explanations for such a pattern, as well as future utility and limitations of machine learning approaches.
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Affiliation(s)
- Katarzyna Burda
- Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Mateusz Konczal
- Evolutionary Biology Group, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
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63
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Durkin J, Poe AR, Belfer SJ, Rodriguez A, Tang SH, Walker JA, Kayser MS. Neurofibromin 1 regulates early developmental sleep in Drosophila. Neurobiol Sleep Circadian Rhythms 2023; 15:100101. [PMID: 37593040 PMCID: PMC10428071 DOI: 10.1016/j.nbscr.2023.100101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 06/30/2023] [Accepted: 08/06/2023] [Indexed: 08/19/2023] Open
Abstract
Sleep disturbances are common in neurodevelopmental disorders, but knowledge of molecular factors that govern sleep in young animals is lacking. Evidence across species, including Drosophila, suggests that juvenile sleep has distinct functions and regulatory mechanisms in comparison to sleep in maturity. In flies, manipulation of most known adult sleep regulatory genes is not associated with sleep phenotypes during early developmental (larval) stages. Here, we examine the role of the neurodevelopmental disorder-associated gene Neurofibromin 1 (Nf1) in sleep during numerous developmental periods. Mutations in Neurofibromin 1 (Nf1) are associated with sleep and circadian disorders in humans and adult flies. We find in flies that Nf1 acts to regulate sleep across the lifespan, beginning during larval stages. Nf1 is required in neurons for this function, as is signaling via the Alk pathway. These findings identify Nf1 as one of a small number of genes positioned to regulate sleep across developmental periods.
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Affiliation(s)
- Jaclyn Durkin
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Amy R. Poe
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Samuel J. Belfer
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Anyara Rodriguez
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Si Hao Tang
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - James A. Walker
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA
| | - Matthew S. Kayser
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Chronobiology and Sleep Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
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64
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Rabaya S, Nairat S, Bader K, Herzallah MM, Darwish HM. Iron metabolism in autism spectrum disorder; inference through single nucleotide polymorphisms in key iron metabolism genes. J Neurol Sci 2023; 453:120817. [PMID: 37813049 DOI: 10.1016/j.jns.2023.120817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 09/21/2023] [Accepted: 09/24/2023] [Indexed: 10/11/2023]
Abstract
Autism spectrum disorder (ASD) is a heterogeneous group of neurodevelopmental problems with various genetic and environmental components. The ASD diagnosis is based on symptom expression without reliance on any biomarkers. The genetic contributions in ASD remain elusive. Various studies have linked ASD with iron. Since iron plays a crucial role in brain development, neurotransmitter synthesis, neuronal myelination and mitochondrial function, we hypothesized that iron dysregulation in the brain could play a role and contribute to the pathogenesis of ASD. In this study, we investigated single nucleotide polymorphisms in ASD in various iron metabolism genes, including the Transferrin Receptor (TFRC) gene (rs11915082), the Solute Carrier Family 11 Member 2 (SLC11A2) gene (rs1048230 and rs224589), the Solute Carrier Family 40 Member 1 (SLC40A1) gene (rs1439816), and hepcidin antimicrobial peptide (HAMP) gene (rs10421768). We recruited 48 patients with ASD and 88 matched non-ASD controls. Our results revealed a significant difference between ASD and controls in the G allele of the TFRC gene rs11915082, and in the C allele of the SLC40A1 gene rs1439816. In silico analysis demonstrated potential positive role of the indicated genetic variations in ASD development and pathogenesis. These results suggest that specific genetic variations in iron metabolism genes may represent part of early genetic markers for early diagnosis of ASD. A significant effect of SNPs, groups (ASD/control) as well as interaction between SNPs and groups was revealed. Follow-up post hoc tests showed a significant difference between the ASD and control groups in rs11915082 (TFRC gene) and rs1439816 (SLC40A1 gene). Backward conditional logistic regression using both the genotype and allele data showed similar ability in detecting ASD using allel model (Nagelkerke R2 = 0.350 p = 0.967; Variables: rs1439816, rs11915082) compared to genotype model (Nagelkerke R2 = 0.347, p = 0.430; Variables: rs1439816 G, rs1439816 C, rs10421768 A). ROC curve showed 54% sensitivity in detecting ASD compared to 47% for the genotype model. Both models differentiated controls with high accuracy; the allele model had a specificity of 91% compared to 92% for the genotype model. In conclusion, our findings suggest that specific genetic variations in iron metabolism may represent early biomarkers for a diagnosis of ASD. Further research is needed to correlate these markers with specific blood iron indicators and their contribution to brain development and behavior.
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Affiliation(s)
- Sabha Rabaya
- Department of Health Sciences, Molecular Genetics and Genetic Toxicology Program, Arab American University, Ramallah,Palestine
| | - Sameera Nairat
- Palestinian Neuroscience Initiative, Al-Quds University, Abu Dis, Jerusalem, Palestine
| | - Khaldoun Bader
- Faculty of Public Health, Al-Quds University, Abu Dis, Jerusalem, Palestine
| | - Mohammad M Herzallah
- Palestinian Neuroscience Initiative, Al-Quds University, Abu Dis, Jerusalem, Palestine; Center for Molecular and Behavioral Neuroscience, Rutgers University, Newark, NJ, USA.
| | - Hisham M Darwish
- Department of Health Sciences, Molecular Genetics and Genetic Toxicology Program, Arab American University, Ramallah,Palestine; Department of Medical Laboratory Sciences, Faculty ofAllied Medical Sciences, Arab American University, Jenin, Palestine.
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65
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Baker Z, Przeworski M, Sella G. Down the Penrose stairs, or how selection for fewer recombination hotspots maintains their existence. eLife 2023; 12:e83769. [PMID: 37830496 DOI: 10.7554/elife.83769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 10/12/2023] [Indexed: 10/14/2023] Open
Abstract
In many species, meiotic recombination events tend to occur in narrow intervals of the genome, known as hotspots. In humans and mice, double strand break (DSB) hotspot locations are determined by the DNA-binding specificity of the zinc finger array of the PRDM9 protein, which is rapidly evolving at residues in contact with DNA. Previous models explained this rapid evolution in terms of the need to restore PRDM9 binding sites lost to gene conversion over time, under the assumption that more PRDM9 binding always leads to more DSBs. This assumption, however, does not align with current evidence. Recent experimental work indicates that PRDM9 binding on both homologs facilitates DSB repair, and that the absence of sufficient symmetric binding disrupts meiosis. We therefore consider an alternative hypothesis: that rapid PRDM9 evolution is driven by the need to restore symmetric binding because of its role in coupling DSB formation and efficient repair. To this end, we model the evolution of PRDM9 from first principles: from its binding dynamics to the population genetic processes that govern the evolution of the zinc finger array and its binding sites. We show that the loss of a small number of strong binding sites leads to the use of a greater number of weaker ones, resulting in a sharp reduction in symmetric binding and favoring new PRDM9 alleles that restore the use of a smaller set of strong binding sites. This decrease, in turn, drives rapid PRDM9 evolutionary turnover. Our results therefore suggest that the advantage of new PRDM9 alleles is in limiting the number of binding sites used effectively, rather than in increasing net PRDM9 binding. By extension, our model suggests that the evolutionary advantage of hotspots may have been to increase the efficiency of DSB repair and/or homolog pairing.
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Affiliation(s)
- Zachary Baker
- Department of Systems Biology, Columbia University, New York, United States
- Department of Biological Sciences, Columbia University, New York, United States
| | - Molly Przeworski
- Department of Systems Biology, Columbia University, New York, United States
- Department of Biological Sciences, Columbia University, New York, United States
- Program for Mathematical Genomics, Columbia University, New York, United States
| | - Guy Sella
- Department of Biological Sciences, Columbia University, New York, United States
- Program for Mathematical Genomics, Columbia University, New York, United States
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66
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Lee M, Lui ACY, Chan JCK, Doong PHL, Kwong AKY, Mak CCY, Li RHW, Kan ASY, Chung BHY. Revealing parental mosaicism: the hidden answer to the recurrence of apparent de novo variants. Hum Genomics 2023; 17:91. [PMID: 37798624 PMCID: PMC10557286 DOI: 10.1186/s40246-023-00535-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 09/18/2023] [Indexed: 10/07/2023] Open
Abstract
Mosaicism refers to the presence of two or more populations of genetically distinct cells within an individual, all of which originate from a single zygote. Previous literature estimated the percentage of parental mosaicism ranged from 0.33 to 25.9%. In this study, parents whose children had previously been diagnosed with developmental disorders with an apparent de novo variant were recruited. Peripheral blood, buccal and semen samples were collected from these parents if available for the detection of potential parental mosaicism using droplet digital PCR, complemented with the method of blocker displacement amplification. Among the 20 families being analyzed, we report four families with parental mosaicism (4/20, 20%). Two families have maternal gonosomal mosaicism (EYA1 and EBF3) and one family has paternal gonadal mosaicism (CHD7) with a pathogenic/ likely pathogenic variant. One family has a paternal gonosomal mosaicism with a variant of uncertain significance (FLNC) with high clinical relevance. The detectable variant allele frequency in our cohort ranged from 8.7-35.9%, limit of detection 0.08-0.16% based on our in-house EBF3 assay. Detecting parental mosaicism not only informs family with a more accurate recurrence risk, but also facilitates medical teams to create appropriate plans for pregnancy and delivery, offering the most suitable care.
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Affiliation(s)
- Mianne Lee
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Room 115, 1/F, New Clinical Building, Pok Fu Lam, Hong Kong SAR, China
| | - Adrian C Y Lui
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Room 115, 1/F, New Clinical Building, Pok Fu Lam, Hong Kong SAR, China
| | - Joshua C K Chan
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Room 115, 1/F, New Clinical Building, Pok Fu Lam, Hong Kong SAR, China
| | - Phoenix H L Doong
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Room 115, 1/F, New Clinical Building, Pok Fu Lam, Hong Kong SAR, China
| | - Anna K Y Kwong
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Room 115, 1/F, New Clinical Building, Pok Fu Lam, Hong Kong SAR, China
| | - Christopher C Y Mak
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Room 115, 1/F, New Clinical Building, Pok Fu Lam, Hong Kong SAR, China
| | - Raymond H W Li
- Department of Obstetrics and Gynaecology, Queen Mary Hospital, Pok Fu Lam, Hong Kong SAR, China
- Department of Obstetrics and Gynaecology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
| | - Anita S Y Kan
- Department of Obstetrics and Gynaecology, Queen Mary Hospital, Pok Fu Lam, Hong Kong SAR, China
- Department of Obstetrics and Gynaecology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong SAR, China
- Prenatal Diagnostic Laboratory, Department of Obstetrics and Gynaecology, Tsan Yuk Hospital, Sai Wan Ho, Hong Kong SAR, China
| | - Brian H Y Chung
- Department of Paediatrics and Adolescent Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, Queen Mary Hospital, The University of Hong Kong, Room 115, 1/F, New Clinical Building, Pok Fu Lam, Hong Kong SAR, China.
- Department of Paediatrics and Adolescent Medicine, Hong Kong Children's Hospital, Ngau Tau Kok, Hong Kong SAR, China.
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67
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Aitken RJ. Male reproductive ageing: a radical road to ruin. Hum Reprod 2023; 38:1861-1871. [PMID: 37568254 PMCID: PMC10546083 DOI: 10.1093/humrep/dead157] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/21/2023] [Indexed: 08/13/2023] Open
Abstract
In modern post-transition societies, we are reproducing later and living longer. While the impact of age on female reproductive function has been well studied, much less is known about the intersection of age and male reproduction. Our current understanding is that advancing age brings forth a progressive decline in male fertility accompanied by a reduction in circulating testosterone levels and the appearance of age-dependent reproductive pathologies including benign prostatic hypertrophy and erectile dysfunction. Paternal ageing is also associated with a profound increase in sperm DNA damage, the appearance of multiple epigenetic changes in the germ line and an elevated mutational load in the offspring. The net result of such changes is an increase in the disease burden carried by the progeny of ageing males, including dominant genetic diseases such as Apert syndrome and achondroplasia, as well as neuropsychiatric conditions including autism and spontaneous schizophrenia. The genetic basis of these age-related effects appears to involve two fundamental mechanisms. The first is a positive selection mechanism whereby stem cells containing mutations in a mitogen-activated protein kinase pathway gain a selective advantage over their non-mutant counterparts and exhibit significant clonal expansion with the passage of time. The second is dependent on an age-dependent increase in oxidative stress which impairs the steroidogenic capacity of the Leydig cells, disrupts the ability of Sertoli cells to support the normal differentiation of germ cells, and disrupts the functional and genetic integrity of spermatozoa. Given the central importance of oxidative stress in defining the impact of chronological age on male reproduction, there may be a role for antioxidants in the clinical management of this process. While animal studies are supportive of this strategy, carefully designed clinical trials are now needed if we are to realize the therapeutic potential of this approach in a clinical context.
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Affiliation(s)
- R John Aitken
- Priority Research Centre for Reproductive Science, Discipline of Biological Sciences, School of Environmental and Life Sciences, College of Engineering Science and Environment, University of Newcastle, Callaghan, NSW, Australia
- Hunter Medical Research Institute, New Lambton Heights, NSW, Australia
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68
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Tinker RJ, Bastarache L, Ezell K, Kobren SN, Esteves C, Rosenfeld JA, Macnamara EF, Hamid R, Cogan JD, Rinker D, Mukharjee S, Glass I, Dipple K, Phillips JA. The contribution of mosaicism to genetic diseases and de novo pathogenic variants. Am J Med Genet A 2023; 191:2482-2492. [PMID: 37246601 PMCID: PMC11167532 DOI: 10.1002/ajmg.a.63309] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/29/2023] [Accepted: 05/03/2023] [Indexed: 05/30/2023]
Abstract
The contribution of mosaicism to diagnosed genetic disease and presumed de novo variants (DNV) is under investigated. We determined the contribution of mosaic genetic disease (MGD) and diagnosed parental mosaicism (PM) in parents of offspring with reported DNV (in the same variant) in the (1) Undiagnosed Diseases Network (UDN) (N = 1946) and (2) in 12,472 individuals electronic health records (EHR) who underwent genetic testing at an academic medical center. In the UDN, we found 4.51% of diagnosed probands had MGD, and 2.86% of parents of those with DNV exhibited PM. In the EHR, we found 6.03% and 2.99% and (of diagnosed probands) had MGD detected on chromosomal microarray and exome/genome sequencing, respectively. We found 2.34% (of those with a presumed pathogenic DNV) had a parent with PM for the variant. We detected mosaicism (regardless of pathogenicity) in 4.49% of genetic tests performed. We found a broad phenotypic spectrum of MGD with previously unknown phenotypic phenomena. MGD is highly heterogeneous and provides a significant contribution to genetic diseases. Further work is required to improve the diagnosis of MGD and investigate how PM contributes to DNV risk.
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Affiliation(s)
- Rory J. Tinker
- Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Lisa Bastarache
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Kimberly Ezell
- Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | | | - Cecilia Esteves
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - Jill A. Rosenfeld
- Department of Molecular & Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Ellen F. Macnamara
- Undiagnosed Diseases Program, Common Fund, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Rizwan Hamid
- Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Joy D. Cogan
- Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - David Rinker
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Souhrid Mukharjee
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
| | - Ian Glass
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - Katrina Dipple
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - John A. Phillips
- Division of Medical Genetics and Genomic Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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Smith C, Burugula BB, Dunn I, Aradhya S, Kitzman JO, Yee JL. High-Throughput Splicing Assays Identify Known and Novel WT1 Exon 9 Variants in Nephrotic Syndrome. Kidney Int Rep 2023; 8:2117-2125. [PMID: 37850022 PMCID: PMC10577367 DOI: 10.1016/j.ekir.2023.07.033] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 07/31/2023] [Indexed: 10/19/2023] Open
Abstract
Introduction Frasier syndrome (FS) is a rare Mendelian form of nephrotic syndrome (NS) caused by variants which disrupt the proper splicing of WT1. This key transcription factor gene is alternatively spliced at exon 9 to produce 2 isoforms ("KTS+" and "KTS-"), which are normally expressed in the kidney at a ∼2:1 (KTS+:KTS-) ratio. FS results from variants that reduce this ratio by disrupting the splice donor of the KTS+ isoform. FS is extremely rare, and it is unclear whether any variants beyond the 8 already known could cause FS. Methods To prospectively identify other splicing-disruptive variants, we leveraged a massively parallel splicing assay. We tested every possible single nucleotide variant (n = 519) in and around WT1 exon 9 for effects upon exon inclusion and KTS+/- ratio. Results Splice disruptive variants (SDVs) made up 11% of the tested point variants overall and were tightly concentrated near the canonical acceptor and the KTS+/- alternate donors. Our map successfully identified all 8 known FS or focal segmental glomerulosclerosis (FSGS) variants and 16 additional novel variants which were comparably disruptive to these known pathogenic variants. We also identified 19 variants that, conversely, increased the KTS+/KTS- ratio, of which 2 are observed in unrelated individuals with 46,XX ovotesticular disorder of sex development (46,XX OTDSD). Conclusion This splicing effect map can serve as functional evidence to guide the clinical interpretation of newly observed variants in and around WT1 exon 9.
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Affiliation(s)
- Cathy Smith
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Bala Bharathi Burugula
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Ian Dunn
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | | | - Jacob O. Kitzman
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Jennifer Lai Yee
- Department of Pediatrics, Division of Nephrology, University of Michigan, Ann Arbor, Michigan, USA
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Eisenberg ML, Esteves SC, Lamb DJ, Hotaling JM, Giwercman A, Hwang K, Cheng YS. Male infertility. Nat Rev Dis Primers 2023; 9:49. [PMID: 37709866 DOI: 10.1038/s41572-023-00459-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/09/2023] [Indexed: 09/16/2023]
Abstract
Clinical infertility is the inability of a couple to conceive after 12 months of trying. Male factors are estimated to contribute to 30-50% of cases of infertility. Infertility or reduced fertility can result from testicular dysfunction, endocrinopathies, lifestyle factors (such as tobacco and obesity), congenital anatomical factors, gonadotoxic exposures and ageing, among others. The evaluation of male infertility includes detailed history taking, focused physical examination and selective laboratory testing, including semen analysis. Treatments include lifestyle optimization, empirical or targeted medical therapy as well as surgical therapies that lead to measurable improvement in fertility. Although male infertility is recognized as a disease with effects on quality of life for both members of the infertile couple, fewer data exist on specific quantification and impact compared with other health-related conditions.
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Affiliation(s)
- Michael L Eisenberg
- Department of Urology, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Obstetrics & Gynecology, Stanford University School of Medicine, Stanford, CA, USA.
| | - Sandro C Esteves
- ANDROFERT Andrology and Human Reproduction Clinic, Campinas, Brazil
- Division of Urology, Department of Surgery, Faculty of Medical Sciences, State University of Campinas (UNICAMP), Campinas, Brazil
| | - Dolores J Lamb
- Center for Reproductive Genomics, Weill Cornell Medical College, New York, NY, USA
- Englander Institute for Precision Medicine, Weill Cornell Medical College, New York, NY, USA
- Department of Urology, Weill Cornell Medical College, New York, NY, USA
| | - James M Hotaling
- Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA
| | | | - Kathleen Hwang
- University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Yu-Sheng Cheng
- Department of Urology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
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71
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Matheson J, Bertram J, Masel J. Human deleterious mutation rate implies high fitness variance, with declining mean fitness compensated by rarer beneficial mutations of larger effect. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.01.555871. [PMID: 37732183 PMCID: PMC10508744 DOI: 10.1101/2023.09.01.555871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
Each new human has an expected Ud = 2 - 10 new deleterious mutations. This deluge of deleterious mutations cannot all be purged, and therefore accumulate in a declining fitness ratchet. Using a novel simulation framework designed to efficiently handle genome-wide linkage disequilibria across many segregating sites, we find that rarer, beneficial mutations of larger effect are sufficient to compensate fitness declines due to the fixation of many slightly deleterious mutations. Drift barrier theory posits a similar asymmetric pattern of fixations to explain ratcheting genome size and complexity, but in our theory, the cause is Ud > 1 rather than small population size. In our simulations, Ud ~2 - 10 generates high within-population variance in relative fitness; two individuals will typically differ in fitness by 15-40%. Ud ~2 - 10 also slows net adaptation by ~13%-39%. Surprisingly, fixation rates are more sensitive to changes in the beneficial than the deleterious mutation rate, e.g. a 10% increase in overall mutation rate leads to faster adaptation; this puts to rest dysgenic fears about increasing mutation rates due to rising paternal age.
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Affiliation(s)
- Joseph Matheson
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
- Department of Ecology, Behavior, and Evolution, University of California San Diego, San Diego, CA, 92093, USA
| | - Jason Bertram
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
- Department of Mathematics, University of Western Ontario, London ON, Canada
| | - Joanna Masel
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
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72
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Turner TN. Acorn: an R package for de novo variant analysis. BMC Bioinformatics 2023; 24:330. [PMID: 37660114 PMCID: PMC10475174 DOI: 10.1186/s12859-023-05457-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 08/29/2023] [Indexed: 09/04/2023] Open
Abstract
BACKGROUND The study of de novo variation is important for assessing biological characteristics of new variation and for studies related to human phenotypes. Software programs exist to call de novo variants and programs also exist to test the burden of these variants in genomic regions; however, I am unaware of a program that fits in between these two aspects of de novo variant assessment. This intermediate space is important for assessing the quality of de novo variants and to understand the characteristics of the callsets. For this reason, I developed an R package called acorn. RESULTS Acorn is an R package that examines various features of de novo variants including subsetting the data by individual(s), variant type, or genomic region; calculating features including variant change counts, variant lengths, and presence/absence at CpG sites; and characteristics of parental age in relation to de novo variant counts. CONCLUSIONS Acorn is an R package that fills a critical gap in assessing de novo variants and will be of benefit to many investigators studying de novo variation.
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Affiliation(s)
- Tychele N Turner
- Department of Genetics, Washington University School of Medicine, 4523 Clayton Avenue, Campus Box 8232, St. Louis, MO, 63110, USA.
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73
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Xu N, Shi W, Cao X, Zhou X, Jin L, Huang HF, Chen S, Xu C. Parental mosaicism detection and preimplantation genetic testing in families with multiple transmissions of de novo mutations. J Med Genet 2023; 60:910-917. [PMID: 36707240 PMCID: PMC10447385 DOI: 10.1136/jmg-2022-108920] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 01/14/2023] [Indexed: 01/28/2023]
Abstract
BACKGROUND De novo mutations (DNMs) are linked with many severe early-onset disorders ranging from rare congenital malformation to intellectual disability. Conventionally, DNMs are considered to have an estimated recurrence rate of 1%. Recently, studies have revealed a higher prevalence of parental mosaicism, leading to a greater recurrence risk, resulting in a second child harbouring the same DNM as a previous child. METHODS In this study, we included 10 families with DNMs leading to adverse pregnancy outcomes. DNA was extracted from tissue samples, including parental peripheral blood, parental saliva and paternal sperm. High-throughput sequencing was used to screen for parental mosaicism with a depth of more than 5000× on average and a variant allele fraction (VAF) detection limit of 0.5%. RESULTS The presence of mosaicism was detected in sperms in two families, with VAFs of 2.8% and 2.5%, respectively. Both families have a history of multiple adverse pregnancies and DNMs shared by siblings. Preimplantation genetic testing (PGT) and prenatal diagnosis were performed in one family, thereby preventing the reoccurrence of DNMs. CONCLUSION This study is the first to report the successful implementation of PGT for monogenic/single gene defects in the parental mosaicism family. Our study suggests that mosaic detection of paternal sperm is warranted in families with recurrent DNMs leading to adverse pregnancy outcomes, and PGT can effectively block the transmission of the pathogenic mutation.
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Affiliation(s)
- Naixin Xu
- International Peace Maternity and Child Health Hospital, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China
| | - Weihui Shi
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Xianling Cao
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Xuanyou Zhou
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Li Jin
- International Peace Maternity and Child Health Hospital, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - He-Feng Huang
- International Peace Maternity and Child Health Hospital, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
- Research Units of Embryo Original Diseases, Chinese Academy of Medical Sciences (No. 2019RU056), Shanghai, China
| | - Songchang Chen
- International Peace Maternity and Child Health Hospital, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
| | - Chenming Xu
- International Peace Maternity and Child Health Hospital, Shanghai, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China
- Obstetrics and Gynecology Hospital of Fudan University, Shanghai, China
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74
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Hao S, Zhao X, Fan Y, Liu Z, Zhang X, Li W, Yuan H, Zhang J, Zhang Y, Ma T, Tao H. Prevalence and spectrum of cancer predisposition germline mutations in young patients with the common late-onset cancers. Cancer Med 2023; 12:18394-18404. [PMID: 37610374 PMCID: PMC10524041 DOI: 10.1002/cam4.6445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Revised: 06/30/2023] [Accepted: 08/03/2023] [Indexed: 08/24/2023] Open
Abstract
BACKGROUND Pathogenic germline variants (PGVs) can play a vital role in the oncogenesis process in carriers. Previous studies have recognized that PGVs contribute to early onset of tumorigenesis in certain cancer types, for example, colorectal cancer and breast cancer. However, the reported prevalence data of cancer-associated PGVs were highly inconsistent due to nonuniform patient cohorts, sequencing methods, and prominent difficulties in pathogenicity interpretation of variants. In addition to the above difficulties, due to the rarity of cases, the prevalence of cancer PGV carriers in young cancer patients affected by late-onset cancer types has not been comprehensively evaluated to date. METHODS A total of 131 young cancer patients (1-29 years old at diagnosis) were enrolled in this study. The patients were affected by six common late-onset cancer types, namely, lung cancer, liver cancer, colorectal cancer, gastric cancer, renal cancer, and head-neck cancer. Cancer PGVs were identified and analyzed. based on NGS-based targeted sequencing followed by bioinformatic screening and strict further evaluations of variant pathogenicity. RESULTS Twenty-three cancer PGVs in 21 patients were identified, resulting in an overall PGV prevalence of 16.0% across the six included cancer types, which was approximately double the prevalence reported in a previous pancancer study. Nine of the 23 PGVs are novel, thus expanding the cancer PGV spectrum. Seven of the 23 (30.4%) PGVs are potential therapeutic targets of olaparib, with potential implications for clinical manipulation. Additionally, a small prevalence of somatic mutations of some classic cancer hallmark genes in young patients, in contrast to all-age patients, was revealed. CONCLUSION This study demonstrates the high prevalence of PGVs in young cancer patients with the common late-onset cancers and the potentially significant clinical implications of cancer PGVs, the findings highlight the value of PGV screening in young patients across lung cancer, liver cancer, colorectal cancer, gastric cancer, renal cancer, or head-neck cancer.
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Affiliation(s)
- Shaoyu Hao
- Thoracic Surgery, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical SciencesJinanChina
| | - Ximeng Zhao
- Jichenjunchuang Clinical LaboratoryHangzhouChina
| | - Yue Fan
- Department of Integrated Traditional Chinese Medicine and Western MedicineZhong Shan Hospital, Fudan UniversityShanghaiChina
| | - Zhengchuang Liu
- Key Laboratory of Gastroenterology of Zhejiang ProvinceZhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical CollegeHangzhouChina
| | - Xiang Zhang
- Jichenjunchuang Clinical LaboratoryHangzhouChina
| | - Wei Li
- Jichenjunchuang Clinical LaboratoryHangzhouChina
| | | | - Jie Zhang
- Jichenjunchuang Clinical LaboratoryHangzhouChina
| | | | - Tonghui Ma
- Jichenjunchuang Clinical LaboratoryHangzhouChina
| | - Houquan Tao
- Key Laboratory of Gastroenterology of Zhejiang ProvinceZhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical CollegeHangzhouChina
- Department of GastroenterologyZhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical CollegeHangzhouChina
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Costa CIS, da Silva Campos G, da Silva Montenegro EM, Wang JYT, Scliar M, Monfardini F, Zachi EC, Lourenço NCV, Chan AJS, Pereira SL, Engchuan W, Thiruvahindrapuram B, Zarrei M, Scherer SW, Passos-Bueno MR. Three generation families: Analysis of de novo variants in autism. Eur J Hum Genet 2023; 31:1017-1022. [PMID: 37280359 PMCID: PMC10474020 DOI: 10.1038/s41431-023-01398-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 05/10/2023] [Accepted: 05/17/2023] [Indexed: 06/08/2023] Open
Abstract
De novo variants (DNVs) analysis has proven to be a powerful approach to gene discovery in Autism Spectrum Disorder (ASD), which has not yet been shown in a Brazilian ASD cohort. The relevance of inherited rare variants has also been suggested, particularly in oligogenic models. We hypothesized that three-generation analyses of DNVs could provide new insights into the relevance of de novo and inherited variants across generations. To accomplish this goal, we performed whole-exome sequencing of 33 septet families composed of probands, parents, and grandparents (n = 231 individuals) and compared DNV rates (DNVr) between generations and those from two control cohorts. The DNVr in the probands (DNVr = 1.16) was marginally higher than in parents (DNVr = 0.60; p = 0.054), and in controls (DNVr = 0.68; p = 0.035, congenital heart disorder and DNVr = 0.70; p = 0.047, unaffected ASD siblings from Simons Simplex Collection). Moreover, most of the DNVs were found to have paternal origin in both generations (84.6%). Finally, we observed that 40% (6/15) of the DNVs in parents transmitted for probands are in ASD or ASD candidate genes, representing recently emerged risk variants to ASD in their families and suggest ZNF536, MSL2 and HDAC9 as ASD candidate genes. We did not observe an enrichment of risk variants nor sex bias of transmitted variants in the three generations, that can be due to sample size. These results further reinforce the relevance of de novo variants in ASD.
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Affiliation(s)
- Claudia I Samogy Costa
- Departamento de Genética e Biologia Evolutiva, Centro de Estudos do Genoma Humano e Células-tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brasil
| | - Gabriele da Silva Campos
- Departamento de Genética e Biologia Evolutiva, Centro de Estudos do Genoma Humano e Células-tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brasil
| | - Eduarda Morgana da Silva Montenegro
- Departamento de Genética e Biologia Evolutiva, Centro de Estudos do Genoma Humano e Células-tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brasil
| | - Jaqueline Yu Ting Wang
- Departamento de Genética e Biologia Evolutiva, Centro de Estudos do Genoma Humano e Células-tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brasil
| | - Marília Scliar
- Departamento de Genética e Biologia Evolutiva, Centro de Estudos do Genoma Humano e Células-tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brasil
| | - Frederico Monfardini
- Departamento de Genética e Biologia Evolutiva, Centro de Estudos do Genoma Humano e Células-tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brasil
| | - Elaine Cristina Zachi
- Departamento de Genética e Biologia Evolutiva, Centro de Estudos do Genoma Humano e Células-tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brasil
| | - Naila C V Lourenço
- Departamento de Genética e Biologia Evolutiva, Centro de Estudos do Genoma Humano e Células-tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brasil
| | - Ada J S Chan
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Sergio L Pereira
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Worrawat Engchuan
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Bhooma Thiruvahindrapuram
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Mehdi Zarrei
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Stephen W Scherer
- The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular Genetics and McLaughlin Centre, University of Toronto, Toronto, ON, Canada
| | - Maria Rita Passos-Bueno
- Departamento de Genética e Biologia Evolutiva, Centro de Estudos do Genoma Humano e Células-tronco, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brasil.
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76
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Zhang C, Reid K, Sands AF, Fraimout A, Schierup MH, Merilä J. De Novo Mutation Rates in Sticklebacks. Mol Biol Evol 2023; 40:msad192. [PMID: 37648662 PMCID: PMC10503787 DOI: 10.1093/molbev/msad192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 08/21/2023] [Accepted: 08/24/2023] [Indexed: 09/01/2023] Open
Abstract
Mutation rate is a fundamental parameter in population genetics. Apart from being an important scaling parameter for demographic and phylogenetic inference, it allows one to understand at what rate new genetic diversity is generated and what the expected level of genetic diversity is in a population at equilibrium. However, except for well-established model organisms, accurate estimates of de novo mutation rates are available for a very limited number of organisms from the wild. We estimated mutation rates (µ) in two marine populations of the nine-spined stickleback (Pungitius pungitius) with the aid of several 2- and 3-generational family pedigrees, deep (>50×) whole-genome resequences and a high-quality reference genome. After stringent filtering, we discovered 308 germline mutations in 106 offspring translating to µ = 4.83 × 10-9 and µ = 4.29 × 10-9 per base per generation in the two populations, respectively. Up to 20% of the mutations were shared by full-sibs showing that the level of parental mosaicism was relatively high. Since the estimated µ was 3.1 times smaller than the commonly used substitution rate, recalibration with µ led to substantial increase in estimated divergence times between different stickleback species. Our estimates of the de novo mutation rate should provide a useful resource for research focused on fish population genetics and that of sticklebacks in particular.
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Affiliation(s)
- Chaowei Zhang
- Area of Ecology & Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong SAR
| | - Kerry Reid
- Area of Ecology & Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong SAR
| | - Arthur F Sands
- Area of Ecology & Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong SAR
| | - Antoine Fraimout
- Area of Ecology & Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong SAR
- Research Program in Organismal & Evolutionary Biology, Faculty Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | | | - Juha Merilä
- Area of Ecology & Biodiversity, School of Biological Sciences, The University of Hong Kong, Hong Kong, Hong Kong SAR
- Research Program in Organismal & Evolutionary Biology, Faculty Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
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Hu W, Hao Z, Du P, Di Vincenzo F, Manzi G, Cui J, Fu YX, Pan YH, Li H. Genomic inference of a severe human bottleneck during the Early to Middle Pleistocene transition. Science 2023; 381:979-984. [PMID: 37651513 DOI: 10.1126/science.abq7487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 07/11/2023] [Indexed: 09/02/2023]
Abstract
Population size history is essential for studying human evolution. However, ancient population size history during the Pleistocene is notoriously difficult to unravel. In this study, we developed a fast infinitesimal time coalescent process (FitCoal) to circumvent this difficulty and calculated the composite likelihood for present-day human genomic sequences of 3154 individuals. Results showed that human ancestors went through a severe population bottleneck with about 1280 breeding individuals between around 930,000 and 813,000 years ago. The bottleneck lasted for about 117,000 years and brought human ancestors close to extinction. This bottleneck is congruent with a substantial chronological gap in the available African and Eurasian fossil record. Our results provide new insights into our ancestry and suggest a coincident speciation event.
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Affiliation(s)
- Wangjie Hu
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- Key Laboratory of Brain Functional Genomics of Ministry of Education, School of Life Science, East China Normal University, Shanghai, China
| | - Ziqian Hao
- College of Artificial Intelligence and Big Data for Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Pengyuan Du
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- College of Artificial Intelligence and Big Data for Medical Sciences, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | | | - Giorgio Manzi
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
| | - Jialong Cui
- Key Laboratory of Brain Functional Genomics of Ministry of Education, School of Life Science, East China Normal University, Shanghai, China
| | - Yun-Xin Fu
- Department of Biostatistics and Data Science, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX, USA
- Key Laboratory for Conservation and Utilization of Bioresources, Yunnan University, Kunming, China
| | - Yi-Hsuan Pan
- Key Laboratory of Brain Functional Genomics of Ministry of Education, School of Life Science, East China Normal University, Shanghai, China
| | - Haipeng Li
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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Gourinat A, Mazeaud C, Hubert J, Eschwege P, Koscinski I. Impact of paternal age on assisted reproductive technology outcomes and offspring health: a systematic review. Andrology 2023; 11:973-986. [PMID: 36640151 DOI: 10.1111/andr.13385] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 12/18/2022] [Accepted: 01/09/2023] [Indexed: 01/15/2023]
Abstract
BACKGROUND The increase in paternal age and the percentage of births after assisted reproductive technologies (ART) may have consequences on offspring and society's position regarding access to ART must be questioned. Most countries recommend limiting ART to men under 60 years. What is the rationale for this threshold? OBJECTIVE This systematic review assesses scientific arguments to establish links between paternal age, male fertility, and offspring health. MATERIAL AND METHODS Using the PRISMA guidelines, this systematic review of the literature analyzed 111 articles selected after screening PubMed, ScienceDirect, and Web of Science for articles published between January 1, 1995 and December 31, 2021. RESULTS A strong correlation was highlighted between advanced paternal age and a decrease of some sperm parameters (semen volume and sperm motility) and infant morbidity (exponentially increased incidence of achondroplasia and Apert syndrome, and more moderately increased incidence of autism and schizophrenia). The impact of paternal age on pregnancy and fetal aneuploidy rates is more controversial. No association was found with spontaneous abortion rates. DISCUSSION AND CONCLUSION The scientific parameters should be explained to older parents undergoing ART. And for countries that discuss a limit on paternal age for access to ART, the debate requires consideration of social and ethical arguments.
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Affiliation(s)
| | | | - Jacques Hubert
- Department of Urology, University Hospital, Nancy, France
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79
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Ping P, Liu Y, Zheng Z, Ma Y, Dong F, Chen X. Association of embryo aneuploidy and sperm DNA damage in unexplained recurrent implantation failure patients under NGS-based PGT-A cycles. Arch Gynecol Obstet 2023; 308:997-1005. [PMID: 37341853 DOI: 10.1007/s00404-023-07098-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 06/05/2023] [Indexed: 06/22/2023]
Abstract
PURPOSE Recurrent implantation failure (RIF) is one of the most common conditions affecting In Vitro Fertilization (IVF)/Intracytoplasmic sperm injection (ICSI) outcomes. Aneuploidy embryos, one of the main types of embryos-related factors, was reported to be a major contributor to RIF. The present study aimed to examine the association between sperm DNA fragmentation index (DFI) and outcomes of next-generation sequencing (NGS)-based preimplantation genetic testing for aneuploidy (PGT-A) in unexplained RIF patients. METHODS This study analyzed 119 couples with unexplained RIF who underwent 119 PGT-A cycles between January, 2017 and March, 2022. The 119 males were divided into 3 groups according to their sperm DFI levels: Group1 (low, DFI ≤ 15%, n = 50), Group2 (medium, 15% < DFI < 30%, n = 41) and Group3 (high, DFI ≥ 30%, n = 28). Sperm DFI was measured by sperm chromatin structure analysis (SCSA) technique. Trophectoderm biopsy on day 5 or 6 were performed with NGS technique. The following outcomes of PGT-A were analyzed and compared: fertilization, good-quality embryos, aneuploidy rate, miscarriage, live birth and newborn defects. RESULTS The component of aneuploidy embryos was significantly higher in high DFI group (42.71%) than that of medium group (28.39%) and low group (27.80%). The miscarriage rate of high DFI group (27.27%) and medium group (14.29%) is significantly higher than that of low group (0.00%). No significant differences were found regarding fertility, good-quality embryo rate, pregnancy rate, live birth rate or newborn defects among three groups. CONCLUSION The sperm DNA damage is associated with blastocyst aneuploidy and miscarriage rate in unexplained RIF cases. Embryo selection by PGT-A and efforts to decrease sperm DFI before IVF/ICSI treatments should be considered for those male patients with high DFI.
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Affiliation(s)
- Ping Ping
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200135, China
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, 200135, China
| | - Yulin Liu
- Shanghai Ji Ai Genetic and IVF Institute, Shanghai, 200011, China
| | - Zhong Zheng
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200135, China
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, 200135, China
| | - Yi Ma
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200135, China
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, 200135, China
| | - Fan Dong
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200135, China
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, 200135, China
| | - Xiangfeng Chen
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200135, China.
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, 200135, China.
- Shanghai Human Sperm Bank, Shanghai, 200135, China.
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80
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Kemp S, Orsini JJ, Ebberink MS, Engelen M, Lund TC. VUS: Variant of uncertain significance or very unclear situation? Mol Genet Metab 2023; 140:107678. [PMID: 37574344 DOI: 10.1016/j.ymgme.2023.107678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/01/2023] [Accepted: 08/02/2023] [Indexed: 08/15/2023]
Abstract
The advancements in population screening, including newborn screening, enables the identification of disease-causing variants and timely initiation of treatment. However, screening may also identify mild variants, non-disease variants, and variants of uncertain significance (VUS). The identification of a VUS poses a challenge in terms of diagnostic uncertainty and confusion. X-linked adrenoleukodystrophy (ALD) serves as an illustrative example of this complex issue. ALD is a monogenic neurometabolic disease with a complex clinical presentation and a lack of predictive tests for clinical severity. Despite the success of ALD newborn screening, a significant proportion (62%) of missense variants identified through newborn screening exhibit uncertainty regarding their pathogenicity. Resolving this issue requires ongoing efforts to accurately classify variants and refine screening protocols. While it is undisputable that ALD newborn screening greatly benefits boys with the disease, the identification of VUS underscores the need for continuous research and collaboration in improving screening practices.
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Affiliation(s)
- Stephan Kemp
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam UMC location University of Amsterdam, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, the Netherlands.
| | - Joseph J Orsini
- Newborn Screening Program, Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Merel S Ebberink
- Laboratory Genetic Metabolic Diseases, Department of Clinical Chemistry, Amsterdam UMC location University of Amsterdam, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam, the Netherlands
| | - Marc Engelen
- Department of Pediatric Neurology, Amsterdam UMC location University of Amsterdam, Amsterdam Leukodystrophy Center, Emma Children's Hospital, Amsterdam Neuroscience, Amsterdam, the Netherlands
| | - Troy C Lund
- Department of Pediatrics, Blood and Marrow Transplant Program, University of Minnesota Medical School, Minneapolis, MN, USA
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Faruk MO, Rahman MS, Rana MS, Mahmud S, Al-Neyma M, Karim MS, Alam N. Socioeconomic and demographic risk factors of autism spectrum disorder among children and adolescents in Bangladesh: Evidence from a cross-sectional study in 2022. PLoS One 2023; 18:e0289220. [PMID: 37540667 PMCID: PMC10403138 DOI: 10.1371/journal.pone.0289220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 07/13/2023] [Indexed: 08/06/2023] Open
Abstract
Autism spectrum disorder (ASD) is the assorted uneven conditions of the human brain that lead to developmental disabilities. This cross-sectional study aimed to identify the substantial risk factors of ASD among children in Bangladesh. The data were collected using convenience sampling through a questionnaire filled up by the trained interviewers. Mann-Whitney U and Kruskal-Wallis H tests were applied as bivariate analysis, and generalized beta regression was performed to determine the significant risk factors of autism spectrum disorder. The odds ratio (OR) along with 95% confidence interval (CI) were the measuring parameters of the risk factors of ASD. The result revealed that later birth order children have more risk of ASD (OR = 1.13, CI: 1.014-1.264, p = 0.027) compared to the children whose birth order is first. Premature birth of the child (OR: 0.87, CI: 0.76-1.00, p = 0.05) and father's age (OR: 0.86, CI: 0.76-0.97, p = 0.020) substantially affects ASD. The maternal history of specific illness (diabetes, thyroiditis, and hypertension) during pregnancy also significantly affect ASD (OR: 1.34, CI: 1.14-1.61, p = 0.002). The results of this study would assist policymakers in taking necessary steps to reduce the incidence of this disorder by targeting the potential risk factors.
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Affiliation(s)
- Mohammad Omar Faruk
- Department of Statistics, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Md Sahidur Rahman
- One Health Center for Research and Action, Chattogram, Bangladesh
- FETPV Technical Officer, Eastern Mediterranean Public Health Network (GHD|EMPHNET), Bangladesh Country Office, Dhaka, Bangladesh
| | - Md Shohel Rana
- Department of Statistics, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Shohel Mahmud
- Department of Statistics, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Mahmuda Al-Neyma
- Department of Statistics, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Md Sazzadul Karim
- Department of Statistics, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Nazia Alam
- Department of Statistics, Noakhali Science and Technology University, Noakhali, Bangladesh
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Lin Y, Darolti I, van der Bijl W, Morris J, Mank JE. Extensive variation in germline de novo mutations in Poecilia reticulata. Genome Res 2023; 33:1317-1324. [PMID: 37442578 PMCID: PMC10547258 DOI: 10.1101/gr.277936.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 07/07/2023] [Indexed: 07/15/2023]
Abstract
The rate of germline mutation is fundamental to evolutionary processes, as it generates the variation upon which selection acts. The guppy, Poecilia reticulata, is a model of rapid adaptation, however the relative contribution of standing genetic variation versus de novo mutation (DNM) to evolution in this species remains unclear. Here, we use pedigree-based approaches to quantify and characterize germline DNMs in three large guppy families. Our results suggest germline mutation rate in the guppy varies substantially across individuals and families. Most DNMs are shared across multiple siblings, suggesting they arose during early embryonic development. DNMs are randomly distributed throughout the genome, and male-biased mutation rate is low, as would be expected from the short guppy generation time. Overall, our study shows remarkable variation in germline mutation rate and provides insights into rapid evolution of guppies.
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Affiliation(s)
- Yuying Lin
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada;
| | - Iulia Darolti
- Department of Ecology and Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Wouter van der Bijl
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Jake Morris
- School of Biological Science, University of Bristol, Bristol BS8 1TQ, United Kingdom
| | - Judith E Mank
- Department of Zoology and Biodiversity Research Centre, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
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83
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Berteli TS, Wang F, McKerrow W, Navarro PA, Fenyo D, Boeke JD, Kohlrausch FB, Keefe DL. Transposon insertion profiling by sequencing (TIPseq) identifies novel LINE-1 insertions in human sperm. J Assist Reprod Genet 2023; 40:1835-1843. [PMID: 37310664 PMCID: PMC10371950 DOI: 10.1007/s10815-023-02852-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/01/2023] [Indexed: 06/14/2023] Open
Abstract
PURPOSE Long interspersed nuclear element-1 (LINE-1 or L1) comprises 17% of the human genome. Retrotransposons may perturb gene integrity or alter gene expression by altering regulatory regions in the genome. The germline employs a number of mechanisms, including cytosine methylation, to repress retrotransposon transcription throughout most of life. Demethylation during germ cell and early embryo development de-represses retrotransposons. Intriguingly, de novo genetic variation appearing in sperm has been implicated in a number of disorders in offspring, including autism spectrum disorder, schizophrenia, and bipolar disorder. We hypothesize that human sperm exhibit de novo retrotransposition and employ a new sequencing method, single cell transposon insertion profiling by sequencing (scTIPseq) to map them in small amounts of human sperm. METHODS Cross-sectional case-control study of sperm samples (n=10 men; ages 32-55 years old) from consenting men undergoing IVF at NYU Langone Fertility Center. scTIPseq identified novel LINE-1 insertions in individual sperm and TIPseqHunter, a custom bioinformatics pipeline, compared the architecture of sperm LINE-1 to known LINE-1 insertions from the European database of Human specific LINE-1 (L1Hs) retrotransposon insertions (euL1db). RESULTS scTIPseq identified 17 novel insertions in sperm. New insertions were mainly intergenic or intronic. Only one sample did not exhibit new insertions. The location or number of novel insertions did not differ by paternal age. CONCLUSION This study for the first time reports novel LINE-1 insertions in human sperm, demonstrating the feasibility of scTIPseq, and identifies new contributors to genetic diversity in the human germ line.
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Affiliation(s)
- Thalita S Berteli
- Department of Obstetrics and Gynecology, NYU Grossman School of Medicine, New York, NY, USA.
- Human Reproduction Division, Department of Gynecology and Obstetrics, Faculty of Medicine of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, SP, Brazil.
| | - Fang Wang
- Department of Obstetrics and Gynecology, NYU Grossman School of Medicine, New York, NY, USA
| | - Wilson McKerrow
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY, USA
| | - Paula A Navarro
- Human Reproduction Division, Department of Gynecology and Obstetrics, Faculty of Medicine of Ribeirao Preto, University of Sao Paulo, Ribeirao Preto, SP, Brazil
| | - David Fenyo
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY, USA
| | - Jef D Boeke
- Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY, USA
| | - Fabiana B Kohlrausch
- Department of Obstetrics and Gynecology, NYU Grossman School of Medicine, New York, NY, USA
- Biology Institute, Department of General Biology, Fluminense Federal University (UFF), Niteroi, RJ, Brazil
| | - David L Keefe
- Department of Obstetrics and Gynecology, NYU Grossman School of Medicine, New York, NY, USA
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84
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Cirnigliaro M, Chang TS, Arteaga SA, Pérez-Cano L, Ruzzo EK, Gordon A, Bicks LK, Jung JY, Lowe JK, Wall DP, Geschwind DH. The contributions of rare inherited and polygenic risk to ASD in multiplex families. Proc Natl Acad Sci U S A 2023; 120:e2215632120. [PMID: 37506195 PMCID: PMC10400943 DOI: 10.1073/pnas.2215632120] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 06/13/2023] [Indexed: 07/30/2023] Open
Abstract
Autism spectrum disorder (ASD) has a complex genetic architecture involving contributions from both de novo and inherited variation. Few studies have been designed to address the role of rare inherited variation or its interaction with common polygenic risk in ASD. Here, we performed whole-genome sequencing of the largest cohort of multiplex families to date, consisting of 4,551 individuals in 1,004 families having two or more autistic children. Using this study design, we identify seven previously unrecognized ASD risk genes supported by a majority of rare inherited variants, finding support for a total of 74 genes in our cohort and a total of 152 genes after combined analysis with other studies. Autistic children from multiplex families demonstrate an increased burden of rare inherited protein-truncating variants in known ASD risk genes. We also find that ASD polygenic score (PGS) is overtransmitted from nonautistic parents to autistic children who also harbor rare inherited variants, consistent with combinatorial effects in the offspring, which may explain the reduced penetrance of these rare variants in parents. We also observe that in addition to social dysfunction, language delay is associated with ASD PGS overtransmission. These results are consistent with an additive complex genetic risk architecture of ASD involving rare and common variation and further suggest that language delay is a core biological feature of ASD.
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Affiliation(s)
- Matilde Cirnigliaro
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA90095
| | - Timothy S. Chang
- Movement Disorders Program, Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA90095
| | - Stephanie A. Arteaga
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA90095
| | - Laura Pérez-Cano
- STALICLA Discovery and Data Science Unit, World Trade Center, Barcelona08039, Spain
| | - Elizabeth K. Ruzzo
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA90095
- Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA90095
| | - Aaron Gordon
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA90095
| | - Lucy K. Bicks
- Program in Neurogenetics, Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA90095
| | - Jae-Yoon Jung
- Department of Pediatrics, Division of Systems Medicine, Stanford University, Stanford, CA94304
- Department of Biomedical Data Science, Stanford University, Stanford, CA94305
| | - Jennifer K. Lowe
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA90095
- Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA90095
| | - Dennis P. Wall
- Department of Pediatrics, Division of Systems Medicine, Stanford University, Stanford, CA94304
- Department of Biomedical Data Science, Stanford University, Stanford, CA94305
| | - Daniel H. Geschwind
- Department of Psychiatry and Biobehavioral Sciences, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA90095
- Movement Disorders Program, Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA90095
- Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA90095
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA90095
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85
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Wang Y, Obbard DJ. Experimental estimates of germline mutation rate in eukaryotes: a phylogenetic meta-analysis. Evol Lett 2023; 7:216-226. [PMID: 37475753 PMCID: PMC10355183 DOI: 10.1093/evlett/qrad027] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 05/08/2023] [Accepted: 06/08/2023] [Indexed: 07/22/2023] Open
Abstract
Mutation is the ultimate source of all genetic variation, and over the last 10 years the ready availability of whole-genome sequencing has permitted direct estimation of mutation rate for many non-model species across the tree of life. In this meta-analysis, we make a comprehensive search of the literature for mutation rate estimates in eukaryotes, identifying 140 mutation accumulation (MA) and parent-offspring (PO) sequencing studies covering 134 species. Based on these data, we revisit differences in the single-nucleotide mutation (SNM) rate between different phylogenetic lineages and update the known relationships between mutation rate and generation time, genome size, and nucleotide diversity-while accounting for phylogenetic nonindependence. We do not find a significant difference between MA and PO in estimated mutation rates, but we confirm that mammal and plant lineages have higher mutation rates than arthropods and that unicellular eukaryotes have the lowest mutation rates. We find that mutation rates are higher in species with longer generation times and larger genome sizes, even when accounting for phylogenetic relationships. Moreover, although nucleotide diversity is positively correlated with mutation rate, the gradient of the relationship is significantly less than one (on a logarithmic scale), consistent with higher mutation rates in populations with smaller effective size. For the 29 species for which data are available, we find that indel mutation rates are positively correlated with nucleotide mutation rates and that short deletions are generally more common than short insertions. Nevertheless, despite recent progress, no estimates of either SNM or indel mutation rates are available for the majority of deeply branching eukaryotic lineages-or even for most animal phyla. Even among charismatic megafauna, experimental mutation rate estimates remain unknown for amphibia and scarce for reptiles and fish.
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Affiliation(s)
- Yiguan Wang
- Corresponding author: Institute of Ecology and Evolution, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, United Kingdom.
| | - Darren J Obbard
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, United Kingdom
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86
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Du H, Pan B, Alund AW, Yan J, Chen Y, Robison TW, Chen T. Evaluation of mutagenic susceptibility of different stages in germ cell development of Caenorhabditis elegans using whole genome sequencing. Arch Toxicol 2023; 97:2261-2272. [PMID: 37209179 DOI: 10.1007/s00204-023-03526-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 05/11/2023] [Indexed: 05/22/2023]
Abstract
In contrast to somatic mutations, mutations in germ cells affect every cell of any organism derived from the germ cell and therefore are related to numerous genetic diseases. However, there is no suitable assay to evaluate the mutagenic sensitivities of both male and female germ cells. The main type of Caenorhabditis elegans (C. elegans) is hermaphroditic, where spermatogenesis and oogenesis occur chronologically at specific stages, allowing induction of mutations in either sperm or eggs exclusively. In this study, we used the alkylating agent ethyl methanesulfonate and N-ethyl-N-nitrosourea to induce germline mutations in C. elegans at different developmental stages and analyzed mutation frequency and mutational spectrum from data gathered using next-generation sequencing (NGS) technology. Our results revealed low spontaneous mutation rates of C. elegans, along with distinct mutagenic effects elicited by the two mutagens. Our data show that the parental worms treated during germ cell mitosis, spermatogenesis, and oogenesis resulted in different mutation frequencies in their offspring, and female germ cells could be very susceptible to mutagen exposure during oogenesis. In summary, our study indicates that the use of C. elegans and its specific chronological hermaphroditism would be a promising way to explore the sensitivities of both male and female germ cells to mutagens.
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Affiliation(s)
- Hua Du
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Rd, Jefferson, AR, 72079, USA
- High Magnetic Field Laboratory, Chinese Academy of Sciences, Hefei, 230031, Anhui, People's Republic of China
| | - Bohu Pan
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, 72079, USA
| | - Alexander W Alund
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Rd, Jefferson, AR, 72079, USA
- Discovery Sciences | Medicine Design, Pfizer Inc., 280 Shennecossett Rd, Groton, CT, 06340, USA
| | - Jian Yan
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Rd, Jefferson, AR, 72079, USA
| | - Ying Chen
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Rd, Jefferson, AR, 72079, USA
| | - Timothy W Robison
- Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Tao Chen
- Division of Genetic and Molecular Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Rd, Jefferson, AR, 72079, USA.
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87
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Bilgrav Saether K, Nilsson D, Thonberg H, Tham E, Ameur A, Eisfeldt J, Lindstrand A. Transposable element insertions in 1000 Swedish individuals. PLoS One 2023; 18:e0289346. [PMID: 37506127 PMCID: PMC10381067 DOI: 10.1371/journal.pone.0289346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 07/09/2023] [Indexed: 07/30/2023] Open
Abstract
The majority of rare diseases are genetic, and regardless of advanced high-throughput genomics-based investigations, 60% of patients remain undiagnosed. A major factor limiting our ability to identify disease-causing alterations is a poor understanding of the morbid and normal human genome. A major genomic contributor of which function and distribution remain largely unstudied are the transposable elements (TE), which constitute 50% of our genome. Here we aim to resolve this knowledge gap and increase the diagnostic yield of rare disease patients investigated with clinical genome sequencing. To this end we characterized TE insertions in 1000 Swedish individuals from the SweGen dataset and 2504 individuals from the 1000 Genomes Project (1KGP), creating seven population-specific TE insertion databases. Of note, 66% of TE insertions in SweGen were present at >1% in the 1KGP databases, proving that most insertions are common across populations. Focusing on the rare TE insertions, we show that even though ~0.7% of those insertions affect protein coding genes, they rarely affect known disease casing genes (<0.1%). Finally, we applied a TE insertion identification workflow on two clinical cases where disease causing TE insertions were suspected and could verify the presence of pathogenic TE insertions in both. Altogether we demonstrate the importance of TE insertion detection and highlight possible clinical implications in rare disease diagnostics.
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Affiliation(s)
- Kristine Bilgrav Saether
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Daniel Nilsson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Håkan Thonberg
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Emma Tham
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Adam Ameur
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Jesper Eisfeldt
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Anna Lindstrand
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
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88
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Hildyard JCW, Piercy RJ. When Size Really Matters: The Eccentricities of Dystrophin Transcription and the Hazards of Quantifying mRNA from Very Long Genes. Biomedicines 2023; 11:2082. [PMID: 37509720 PMCID: PMC10377302 DOI: 10.3390/biomedicines11072082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/10/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
At 2.3 megabases in length, the dystrophin gene is enormous: transcription of a single mRNA requires approximately 16 h. Principally expressed in skeletal muscle, the dystrophin protein product protects the muscle sarcolemma against contraction-induced injury, and dystrophin deficiency results in the fatal muscle-wasting disease, Duchenne muscular dystrophy. This gene is thus of key clinical interest, and therapeutic strategies aimed at eliciting dystrophin restoration require quantitative analysis of its expression. Approaches for quantifying dystrophin at the protein level are well-established, however study at the mRNA level warrants closer scrutiny: measured expression values differ in a sequence-dependent fashion, with significant consequences for data interpretation. In this manuscript, we discuss these nuances of expression and present evidence to support a transcriptional model whereby the long transcription time is coupled to a short mature mRNA half-life, with dystrophin transcripts being predominantly nascent as a consequence. We explore the effects of such a model on cellular transcriptional dynamics and then discuss key implications for the study of dystrophin gene expression, focusing on both conventional (qPCR) and next-gen (RNAseq) approaches.
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Affiliation(s)
- John C. W. Hildyard
- Comparative Neuromuscular Disease Laboratory, Department of Clinical Science and Services, Royal Veterinary College, London NW1 0TU, UK;
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89
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Castro CP, Diehl AG, Boyle AP. Challenges in screening for de novo noncoding variants contributing to genetically complex phenotypes. HGG ADVANCES 2023; 4:100210. [PMID: 37305558 PMCID: PMC10248550 DOI: 10.1016/j.xhgg.2023.100210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 05/15/2023] [Indexed: 06/13/2023] Open
Abstract
Understanding the genetic basis for complex, heterogeneous disorders, such as autism spectrum disorder (ASD), is a persistent challenge in human medicine. Owing to their phenotypic complexity, the genetic mechanisms underlying these disorders may be highly variable across individual patients. Furthermore, much of their heritability is unexplained by known regulatory or coding variants. Indeed, there is evidence that much of the causal genetic variation stems from rare and de novo variants arising from ongoing mutation. These variants occur mostly in noncoding regions, likely affecting regulatory processes for genes linked to the phenotype of interest. However, because there is no uniform code for assessing regulatory function, it is difficult to separate these mutations into likely functional and nonfunctional subsets. This makes finding associations between complex diseases and potentially causal de novo single-nucleotide variants (dnSNVs) a difficult task. To date, most published studies have struggled to find any significant associations between dnSNVs from ASD patients and any class of known regulatory elements. We sought to identify the underlying reasons for this and present strategies for overcoming these challenges. We show that, contrary to previous claims, the main reason for failure to find robust statistical enrichments is not only the number of families sampled, but also the quality and relevance to ASD of the annotations used to prioritize dnSNVs, and the reliability of the set of dnSNVs itself. We present a list of recommendations for designing future studies of this sort that will help researchers avoid common pitfalls.
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Affiliation(s)
- Christopher P. Castro
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Adam G. Diehl
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Alan P. Boyle
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
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90
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Xia QQ, Walker AK, Song C, Wang J, Singh A, Mobley JA, Xuan ZX, Singer JD, Powell CM. Effects of heterozygous deletion of autism-related gene Cullin-3 in mice. PLoS One 2023; 18:e0283299. [PMID: 37428799 PMCID: PMC10332626 DOI: 10.1371/journal.pone.0283299] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 03/05/2023] [Indexed: 07/12/2023] Open
Abstract
Autism Spectrum Disorder (ASD) is a developmental disorder in which children display repetitive behavior, restricted range of interests, and atypical social interaction and communication. CUL3, coding for a Cullin family scaffold protein mediating assembly of ubiquitin ligase complexes through BTB domain substrate-recruiting adaptors, has been identified as a high-risk gene for autism. Although complete knockout of Cul3 results in embryonic lethality, Cul3 heterozygous mice have reduced CUL3 protein, demonstrate comparable body weight, and display minimal behavioral differences including decreased spatial object recognition memory. In measures of reciprocal social interaction, Cul3 heterozygous mice behaved similarly to their wild-type littermates. In area CA1 of hippocampus, reduction of Cul3 significantly increased mEPSC frequency but not amplitude nor baseline evoked synaptic transmission or paired-pulse ratio. Sholl and spine analysis data suggest there is a small yet significant difference in CA1 pyramidal neuron dendritic branching and stubby spine density. Unbiased proteomic analysis of Cul3 heterozygous brain tissue revealed dysregulation of various cytoskeletal organization proteins, among others. Overall, our results suggest that Cul3 heterozygous deletion impairs spatial object recognition memory, alters cytoskeletal organization proteins, but does not cause major hippocampal neuronal morphology, functional, or behavioral abnormalities in adult global Cul3 heterozygous mice.
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Affiliation(s)
- Qiang-qiang Xia
- Department of Neurobiology, University of Alabama at Birmingham Marnix E. Heersink School of Medicine, & Civitan International Research Center, Birmingham, AL, United States of America
| | - Angela K. Walker
- Department of Neurology, University of Texas Southwestern Medical Center, Dallas, TX, United States of America
| | - Chenghui Song
- Department of Neurobiology, University of Alabama at Birmingham Marnix E. Heersink School of Medicine, & Civitan International Research Center, Birmingham, AL, United States of America
| | - Jing Wang
- Department of Neurobiology, University of Alabama at Birmingham Marnix E. Heersink School of Medicine, & Civitan International Research Center, Birmingham, AL, United States of America
| | - Anju Singh
- Department of Neurobiology, University of Alabama at Birmingham Marnix E. Heersink School of Medicine, & Civitan International Research Center, Birmingham, AL, United States of America
| | - James A. Mobley
- Department of Anesthesiology and Perioperative Medicine, University of Alabama at Birmingham Mass Spectrometry & Proteomics Shared Facility, Birmingham, AL, United States of America
| | - Zhong X. Xuan
- Department of Neurobiology, University of Alabama at Birmingham Marnix E. Heersink School of Medicine, & Civitan International Research Center, Birmingham, AL, United States of America
| | - Jeffrey D. Singer
- Department of Biology, Portland State University, Portland, OR, United States of America
| | - Craig M. Powell
- Department of Neurobiology, University of Alabama at Birmingham Marnix E. Heersink School of Medicine, & Civitan International Research Center, Birmingham, AL, United States of America
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91
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Jakkamsetti V, Ma Q, Angulo G, Scudder W, Beutler B, Pascual JM. Genetic influences on motor learning and superperformance mutants revealed by random mutational survey of mouse locomotion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.28.546756. [PMID: 37425744 PMCID: PMC10327015 DOI: 10.1101/2023.06.28.546756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Evolution depends upon genetic variations that influence physiology. As defined in a genetic screen, phenotypic performance may be enhanced or degraded by such mutations. We set out to detect mutations that influence motor function, including motor learning. Thus, we tested the motor effects of 36,444 non-synonymous coding/splicing mutations induced in the germline of C57BL/6J mice with N-ethyl-N-nitrosourea by measuring changes in the performance of repetitive rotarod trials while blinded to genotype. Automated meiotic mapping was used to implicate individual mutations in causation. 32,726 mice bearing all the variant alleles were screened. This was complemented with the simultaneous testing of 1,408 normal mice for reference. 16.3% of autosomal genes were thus rendered detectably hypomorphic or nullified by mutations in homozygosity and motor tested in at least 3 mice. This approach allowed us to identify superperformance mutations in Rif1, Tk1, Fan1 and Mn1. These genes are primarily related, among other less well characterized functions, to nucleic acid biology. We also associated distinct motor learning patterns with groups of functionally related genes. These functional sets included preferentially histone H3 methyltransferase activity for mice that learnt at an accelerated rate relative to the rest of mutant mice. The results allow for an estimation of the fraction of mutations that can modify a behavior influential for evolution such as locomotion. They may also enable, once the loci are further validated and the mechanisms elucidated, the harnessing of the activity of the newly identified genes to enhance motor ability or to counterbalance disability or disease.
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Affiliation(s)
- Vikram Jakkamsetti
- Rare Brain Disorders Program, Department of Neurology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Qian Ma
- Rare Brain Disorders Program, Department of Neurology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Gustavo Angulo
- Rare Brain Disorders Program, Department of Neurology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - William Scudder
- Rare Brain Disorders Program, Department of Neurology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Bruce Beutler
- Center for Genetics of Host Defense, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Immunology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Internal Medicine, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Juan M. Pascual
- Rare Brain Disorders Program, Department of Neurology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Physiology, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Pediatrics, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Eugene McDermott Center for Human Growth & Development / Center for Human Genetics, The University of Texas Southwestern Medical Center, Dallas, Texas, USA
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92
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Gaitanis J, Nie D, Hou T, Frye R. Developmental Regression Followed by Epilepsy and Aggression: A New Syndrome in Autism Spectrum Disorder? J Pers Med 2023; 13:1049. [PMID: 37511662 PMCID: PMC10381960 DOI: 10.3390/jpm13071049] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/20/2023] [Accepted: 06/22/2023] [Indexed: 07/30/2023] Open
Abstract
Autism spectrum disorder (ASD) with regression (ASD-R) involves the loss of previously attained developmental milestones, typically during the first or second year of life. As children age, it is not uncommon for them to develop comorbid conditions such as aggressive behaviors or epilepsy, which can inhibit habilitation in language and social function. In this paper, we hypothesize that aggressive behaviors and epilepsy more commonly develop in patients with ASD-R than in those without a history of regression (ASD-NR). We conducted a retrospective review of non-syndromic patients with ASD over 12 years of age and compared the rates of epilepsy and aggression between ASD-R and ASD-NR patients. Patients with ASD-R, as compared to ASD-NR patients, demonstrated non-significantly higher rates of epilepsy (51.8% vs. 38.1%, p = 0.1335) and aggressive behaviors (73.2% vs. 57.1%, p = 0.0673) when evaluated separately. The rates for combined epilepsy and aggression, however, were statistically significant when comparing ASD-R versus ASD patients (44.5% vs. 23.8%, p = 0.0163). These results suggest that epilepsy with aggression is more common in ASD-R as compared to ASD-NR patients. When considering the impact of epilepsy and aggression on quality of life, these co-morbidities effectively cause a second regression in patients who experienced an earlier regression as toddlers. A larger, prospective trial is recommended to confirm these associations and further define the timeline in which these characteristics develop from early childhood to adolescence.
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Affiliation(s)
- John Gaitanis
- Hasbro Children's Hospital, The Warren Alpert Medical School of Brown University, Providence, RI 02903, USA
| | - Duyu Nie
- Hasbro Children's Hospital, The Warren Alpert Medical School of Brown University, Providence, RI 02903, USA
| | - Tao Hou
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Richard Frye
- Autism Discovery and Treatment Foundation, Phoenix, AZ 85050, USA
- Rossignol Medical Center, Phoenix, AZ 85050, USA
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93
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Sherwood K, Ward JC, Soriano I, Martin L, Campbell A, Rahbari R, Kafetzopoulos I, Sproul D, Green A, Sampson JR, Donaldson A, Ong KR, Heinimann K, Nielsen M, Thomas H, Latchford A, Palles C, Tomlinson I. Germline de novo mutations in families with Mendelian cancer syndromes caused by defects in DNA repair. Nat Commun 2023; 14:3636. [PMID: 37336879 PMCID: PMC10279637 DOI: 10.1038/s41467-023-39248-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Accepted: 05/31/2023] [Indexed: 06/21/2023] Open
Abstract
DNA repair defects underlie many cancer syndromes. We tested whether de novo germline mutations (DNMs) are increased in families with germline defects in polymerase proofreading or base excision repair. A parent with a single germline POLE or POLD1 mutation, or biallelic MUTYH mutations, had 3-4 fold increased DNMs over sex-matched controls. POLE had the largest effect. The DNMs carried mutational signatures of the appropriate DNA repair deficiency. No DNM increase occurred in offspring of MUTYH heterozygous parents. Parental DNA repair defects caused about 20-150 DNMs per child, additional to the ~60 found in controls, but almost all extra DNMs occurred in non-coding regions. No increase in post-zygotic mutations was detected, excepting a child with bi-allelic MUTYH mutations who was excluded from the main analysis; she had received chemotherapy and may have undergone oligoclonal haematopoiesis. Inherited DNA repair defects associated with base pair-level mutations increase DNMs, but phenotypic consequences appear unlikely.
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Affiliation(s)
- Kitty Sherwood
- Cancer Research UK Edinburgh Centre and MRC Human Genetics Unit, Institute of Genomics and Cancer, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Joseph C Ward
- Dept of Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Ignacio Soriano
- Dept of Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Lynn Martin
- Institute of Cancer and Genomic Sciences, University of Birmingham Medical School, Vincent Drive, Edgbaston, Birmingham, B15 2JJ, UK
| | - Archie Campbell
- Centre for Genetics and Experimental Medicine, Institute of Genetics and Cancer, Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Raheleh Rahbari
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Ioannis Kafetzopoulos
- Cancer Research UK Edinburgh Centre and MRC Human Genetics Unit, Institute of Genomics and Cancer, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Duncan Sproul
- Cancer Research UK Edinburgh Centre and MRC Human Genetics Unit, Institute of Genomics and Cancer, Crewe Road, Edinburgh, EH4 2XU, UK
| | - Andrew Green
- Department of Clinical Genetics, Children's Health Ireland and School of Medicine University College, Dublin, Ireland
| | - Julian R Sampson
- Institute of Medical Genetics, Division of Cancer and Genetics, Cardiff University School of Medicine, Cardiff, UK
| | - Alan Donaldson
- Bristol Regional Clinical Genetics Service, St Michael's Hospital, Southwell Street, Bristol, BS2 8EG, UK
| | - Kai-Ren Ong
- West Midlands Regional Genetics Service, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Karl Heinimann
- Institute for Medical Genetics and Pathology, University Hospital Basel, Basel, BS, Switzerland
| | - Maartje Nielsen
- Department of Clinical Genetics, Leiden University Medical Centre, 2333 ZA, Leiden, the Netherlands
| | - Huw Thomas
- St Mark's Hospital, Watford Road, Harrow, HA1 3UJ, UK
| | | | - Claire Palles
- Institute of Cancer and Genomic Sciences, University of Birmingham Medical School, Vincent Drive, Edgbaston, Birmingham, B15 2JJ, UK.
| | - Ian Tomlinson
- Dept of Oncology, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford, OX3 7DQ, UK.
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94
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Feng Y, Cao Z, Xu A, Du H. Evaluation of toxicity and mutagenicity of oxaliplatin on germ cells in an alternative in vivo model Caenorhabditis elegans. Food Chem Toxicol 2023:113902. [PMID: 37331561 DOI: 10.1016/j.fct.2023.113902] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 06/05/2023] [Accepted: 06/15/2023] [Indexed: 06/20/2023]
Abstract
The platinum compound oxaliplatin is a widely used chemotherapeutic drug that shows a broad spectrum of activity in various human tumors. While the treatment-related side effects of oxaliplatin on directly treated individuals have been well-documented, little is known about the influence of oxaliplatin on germ cells and non-exposed progenies. Here we investigated the reproductive toxicity of oxaliplatin in a 3R-compliant in vivo model Caenorhabditis elegans, and evaluated the germ cell mutagenicity of oxaliplatin by using whole genome sequencing. Our results indicated that oxaliplatin treatment significantly disrupts development of spermatids and oocytes. By treating parental worms with oxaliplatin for three successive generations, sequencing data unveiled the clear mutagenic effects of oxaliplatin on germ cells. Analysis of genome-wide mutation spectra showed the preferentially induction of indels by oxaliplatin. In addition, we uncovered the involvement of translesion synthesis polymerase ζ in modulating mutagenic effects of oxaliplatin. These findings suggest that germ cell mutagenicity is worthy of consideration for the health risk assessment of chemotherapeutic drugs, while the combined use of alternative in vivo models and next generation sequencing technology appears to be a promising way for the preliminary safety assessment of various drugs.
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Affiliation(s)
- Yu Feng
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, CAS, Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, CAS, Hefei, 230031, Anhui, PR China; Science Island Branch, Graduate School of USTC, Hefei, 230026, Anhui, PR China
| | - Zhenxiao Cao
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, CAS, Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, CAS, Hefei, 230031, Anhui, PR China; School of Environmental Science and Optoelectronic Technology, University of Science and Technology of China, Hefei, 230026, Anhui, PR China
| | - An Xu
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, CAS, Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, CAS, Hefei, 230031, Anhui, PR China.
| | - Hua Du
- Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, CAS, Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, CAS, Hefei, 230031, Anhui, PR China.
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95
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Blackburn PR, Ebstein F, Hsieh TC, Motta M, Radio FC, Herkert JC, Rinne T, Thiffault I, Rapp M, Alders M, Maas S, Gerard B, Smol T, Vincent-Delorme C, Cogné B, Isidor B, Vincent M, Bachmann-Gagescu R, Rauch A, Joset P, Ferrero GB, Ciolfi A, Husson T, Guerrot AM, Bacino C, Macmurdo C, Thompson SS, Rosenfeld JA, Faivre L, Mau-Them FT, Deb W, Vignard V, Agrawal PB, Madden JA, Goldenberg A, Lecoquierre F, Zech M, Prokisch H, Necpál J, Jech R, Winkelmann J, Koprušáková MT, Konstantopoulou V, Younce JR, Shinawi M, Mighton C, Fung C, Morel C, Ellis JL, DiTroia S, Barth M, Bonneau D, Krapels I, Stegmann S, van der Schoot V, Brunet T, Bußmann C, Mignot C, Courtin T, Ravelli C, Keren B, Ziegler A, Hasadsri L, Pichurin PN, Klee EW, Grand K, Sanchez-Lara PA, Krüger E, Bézieau S, Klinkhammer H, Krawitz PM, Eichler EE, Tartaglia M, Küry S, Wang T. Loss-of-function variants in CUL3 cause a syndromic neurodevelopmental disorder. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.06.13.23290941. [PMID: 37398376 PMCID: PMC10312857 DOI: 10.1101/2023.06.13.23290941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Purpose De novo variants in CUL3 (Cullin-3 ubiquitin ligase) have been strongly associated with neurodevelopmental disorders (NDDs), but no large case series have been reported so far. Here we aimed to collect sporadic cases carrying rare variants in CUL3, describe the genotype-phenotype correlation, and investigate the underlying pathogenic mechanism. Methods Genetic data and detailed clinical records were collected via multi-center collaboration. Dysmorphic facial features were analyzed using GestaltMatcher. Variant effects on CUL3 protein stability were assessed using patient-derived T-cells. Results We assembled a cohort of 35 individuals with heterozygous CUL3 variants presenting a syndromic NDD characterized by intellectual disability with or without autistic features. Of these, 33 have loss-of-function (LoF) and two have missense variants. CUL3 LoF variants in patients may affect protein stability leading to perturbations in protein homeostasis, as evidenced by decreased ubiquitin-protein conjugates in vitro . Specifically, we show that cyclin E1 (CCNE1) and 4E-BP1 (EIF4EBP1), two prominent substrates of CUL3, fail to be targeted for proteasomal degradation in patient-derived cells. Conclusion Our study further refines the clinical and mutational spectrum of CUL3 -associated NDDs, expands the spectrum of cullin RING E3 ligase-associated neuropsychiatric disorders, and suggests haploinsufficiency via LoF variants is the predominant pathogenic mechanism.
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96
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Wang M. Estimating the parental age effect on intelligence with controlling for confounding effects from genotypic differences. PERSONALITY AND INDIVIDUAL DIFFERENCES 2023. [DOI: 10.1016/j.paid.2023.112137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
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97
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Ouisselsat M, Maidoumi S, Elmaouaki A, Lekouch N, Pineau A, Sedki A. Hair Trace Elements and Mineral Content in Moroccan Children with Autism Spectrum Disorder: a Case-Control Study. Biol Trace Elem Res 2023; 201:2701-2710. [PMID: 35896886 DOI: 10.1007/s12011-022-03365-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/16/2022] [Indexed: 11/02/2022]
Abstract
The prevalence of autism spectrum disorder (ASD) around the world continues to increase while the pathophysiology remains insufficiently elucidated. Genetics, environment, and epigenetic changes are often implicated. Abnormal level in trace elements and minerals is among environmental factors assumed to be involved. The purpose of this article is to assess hair concentrations of toxic and essential elements in children with ASD and children with neurotypical development in the city of Marrakech. Two hundred and twenty-seven children (107 with ASD and 120 controls) aged 3 to 14 years old were recruited. The results of analysis by ICP-MS showed a significant decrease in hair levels of copper, zinc, iron, and selenium (25%, 13%, 17%, 11%) of children with ASD. The most significantly reduced concentrations in children with ASD are that of manganese by 34%. Hair aluminum level was significantly elevated by 29% in ASD compared to controls. Multiple linear regression analysis revealed that copper, selenium, and iron content in hair were significantly inversely associated with ASD, similarly, hair aluminum content was significantly associated with ASD. Adjusted model for demographic parameters increased the predictive ability of the model, father's age was a significant predictor. In addition, ASD and gender were significant predictors of hair levels of aluminum, selenium, and manganese.These results support the hypothesis of the disparity of trace elements and minerals levels in children with ASD and highlight the potential interest of micronutrient supplementation in the eventual improvement of ASD symptoms. Future research should explore the pathophysiology of these micronutrient deficiencies.
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Affiliation(s)
- Mariam Ouisselsat
- Laboratory of Water, Biodiversity and Climate Change, Department of Biology, Faculty of Sciences - Semlalia, Cadi Ayyad University, Bd Moulay Abdellah BP, 2390-40001, Marrakech, Morocco.
| | - Sana Maidoumi
- Laboratory of Water, Biodiversity and Climate Change, Department of Biology, Faculty of Sciences - Semlalia, Cadi Ayyad University, Bd Moulay Abdellah BP, 2390-40001, Marrakech, Morocco
| | - Amal Elmaouaki
- Laboratory of Water, Biodiversity and Climate Change, Department of Biology, Faculty of Sciences - Semlalia, Cadi Ayyad University, Bd Moulay Abdellah BP, 2390-40001, Marrakech, Morocco
| | - Nadra Lekouch
- Laboratory of Water, Biodiversity and Climate Change, Department of Biology, Faculty of Sciences - Semlalia, Cadi Ayyad University, Bd Moulay Abdellah BP, 2390-40001, Marrakech, Morocco
| | - Alain Pineau
- Mineral Element Dosing Centre, UFR of Pharmaceutical and Biological Sciences, University of Nantes, 9, rue Bias, 44035 - 44000, Nantes Cedex 1, France
| | - Azeddine Sedki
- Laboratory of Water, Biodiversity and Climate Change, Department of Biology, Faculty of Sciences - Semlalia, Cadi Ayyad University, Bd Moulay Abdellah BP, 2390-40001, Marrakech, Morocco
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98
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Zemet R, Du H, Gambin T, Lupski JR, Liu P, Stankiewicz P. SNV/indel hypermutator phenotype in biallelic RAD51C variant: Fanconi anemia. Hum Genet 2023; 142:721-733. [PMID: 37031326 PMCID: PMC10996436 DOI: 10.1007/s00439-023-02550-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 03/24/2023] [Indexed: 04/10/2023]
Abstract
We previously reported a fetus with Fanconi anemia (FA), complementation group O due to compound heterozygous variants involving RAD51C. Interestingly, the trio exome sequencing analysis also detected eight apparent de novo mosaic variants with variant allele fraction (VAF) ranging between 11.5 and 37%. Here, using whole genome sequencing and a 'home-brew' variant filtering pipeline and DeepMosaic module, we investigated the number and signature of de novo heterozygous and mosaic variants and the hypothesis of a rare phenomenon of hypermutation. Eight-hundred-thirty apparent de novo SNVs and 21 de novo indels had VAFs below 37.41% and were considered postzygotic somatic mosaic variants. The VAFs showed a bimodal distribution, with one component having an average VAF of 25% (range: 18.7-37.41%) (n = 446), representing potential postzygotic first mitotic events, and the other component with an average VAF of 12.5% (range 9.55-18.69%) (n = 384), describing potential second mitotic events. No increased rate of CNV formation was observed. The mutational pattern analysis for somatic single base substitution showed SBS40, SBS5, and SBS3 as the top recognized signatures. SBS3 is a known signature associated with homologous recombination-based DNA damage repair error. Our data demonstrate that biallelic RAD51C variants show evidence for defective genomic DNA damage repair and thereby result in a hypermutator phenotype with the accumulation of postzygotic de novo mutations, at least in the prenatal period. This 'genome hypermutator phenomenon' might contribute to the observed hematological manifestations and the predisposition to tumors in patients with FA. We propose that other FA groups should be investigated for genome-wide de novo variants.
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Affiliation(s)
- Roni Zemet
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Haowei Du
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Tomasz Gambin
- Institute of Computer Science, Warsaw University of Technology, Warsaw, Poland
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Baylor Genetics, Houston, TX, USA.
| | - Paweł Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
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99
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Wang T, Liu L, Fan T, Xia K, Sun Z. Shared and divergent contribution of vitamin A and oxytocin to the aetiology of autism spectrum disorder. Comput Struct Biotechnol J 2023; 21:3109-3123. [PMID: 38213898 PMCID: PMC10782014 DOI: 10.1016/j.csbj.2023.05.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 05/15/2023] [Accepted: 05/15/2023] [Indexed: 01/13/2024] Open
Abstract
Rare genetic variations contribute to the heterogeneity of autism spectrum disorder (ASD) and the responses to various interventions for ASD probands. However, the associated molecular underpinnings remain unclear. Herein, we estimated the association between rare genetic variations in 410 vitamin A (VA)-related genes (VARGs) and ASD aetiology using publicly available de novo mutations (DNMs), rare inherited variants, and copy number variations (CNVs) from about 50,000 ASD probands and 20,000 normal controls (discovery and validation cohorts). Additionally, given the functional relevance of VA and oxytocin, we systematically compared the similarities and differences between VA and oxytocin with respect to ASD aetiology and evaluated their potential for clinical applications. Functional DNMs and pathogenic CNVs in VARGs contributed to ASD pathogenesis in the discovery and validation cohorts. Additionally, 324 potential VA-related biomarkers were identified, 243 of which were shared with previously identified oxytocin-related biomarkers, while 81 were unique VA biomarkers. Moreover, multivariable logistic regression analysis revealed that both VA- and oxytocin-related biomarkers were able to predict ASD aetiology for individuals carrying functional DNM in corresponding biomarkers with an average precision of 0.94. As well as, convergent and divergent functions were also identified between VA- and oxytocin-related biomarkers. The findings of this study provide a basis for future studies aimed at understanding the pathophysiological mechanisms underlying ASD while also defining a set of potential molecular biomarkers for adjuvant diagnosis and intervention in ASD.
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Affiliation(s)
- Tao Wang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Kaifu District, Changsha, Hunan 410078, China
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Liqiu Liu
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Tianda Fan
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Kaifu District, Changsha, Hunan 410078, China
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325025, China
| | - Kun Xia
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Kaifu District, Changsha, Hunan 410078, China
- CAS Center for Excellence in Brain Science and Intelligences Technology (CEBSIT), Shanghai 200031, China
- Hengyang Medical School, University of South China, Hengyang, Hunan 410078, China
| | - Zhongsheng Sun
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang 325025, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Chinese Academy of Sciences, Beijing 100101, China
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100
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Hagenbeek FA, Hirzinger JS, Breunig S, Bruins S, Kuznetsov DV, Schut K, Odintsova VV, Boomsma DI. Maximizing the value of twin studies in health and behaviour. Nat Hum Behav 2023:10.1038/s41562-023-01609-6. [PMID: 37188734 DOI: 10.1038/s41562-023-01609-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 04/19/2023] [Indexed: 05/17/2023]
Abstract
In the classical twin design, researchers compare trait resemblance in cohorts of identical and non-identical twins to understand how genetic and environmental factors correlate with resemblance in behaviour and other phenotypes. The twin design is also a valuable tool for studying causality, intergenerational transmission, and gene-environment correlation and interaction. Here we review recent developments in twin studies, recent results from twin studies of new phenotypes and recent insights into twinning. We ask whether the results of existing twin studies are representative of the general population and of global diversity, and we conclude that stronger efforts to increase representativeness are needed. We provide an updated overview of twin concordance and discordance for major diseases and mental disorders, which conveys a crucial message: genetic influences are not as deterministic as many believe. This has important implications for public understanding of genetic risk prediction tools, as the accuracy of genetic predictions can never exceed identical twin concordance rates.
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Affiliation(s)
- Fiona A Hagenbeek
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands.
- Amsterdam Public Health Research Institute, Amsterdam, the Netherlands.
| | - Jana S Hirzinger
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Sophie Breunig
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Department of Psychology & Neuroscience, University of Colorado Boulder, Boulder, CO, USA
- Institute for Behavioral Genetics, University of Colorado Boulder, Boulder, CO, USA
| | - Susanne Bruins
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Public Health Research Institute, Amsterdam, the Netherlands
| | - Dmitry V Kuznetsov
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Faculty of Sociology, Bielefeld University, Bielefeld, Germany
| | - Kirsten Schut
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Nightingale Health Plc, Helsinki, Finland
| | - Veronika V Odintsova
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- Amsterdam Reproduction & Development (AR&D) Research Institute, Amsterdam, the Netherlands
- Department of Psychiatry, University Medical Center of Groningen, University of Groningen, Groningen, the Netherlands
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands.
- Amsterdam Public Health Research Institute, Amsterdam, the Netherlands.
- Amsterdam Reproduction & Development (AR&D) Research Institute, Amsterdam, the Netherlands.
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