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Crossley ER, Fedorova L, Mulyar O, Freeman R, Khuder S, Fedorov A. Computational identification of ultra-conserved elements in the human genome: a hypothesis on homologous DNA pairing. NAR Genom Bioinform 2024; 6:lqae074. [PMID: 38962254 PMCID: PMC11217675 DOI: 10.1093/nargab/lqae074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/29/2024] [Accepted: 06/19/2024] [Indexed: 07/05/2024] Open
Abstract
Thousands of prolonged sequences of human ultra-conserved non-coding elements (UCNEs) share only one common feature: peculiarities in the unique composition of their dinucleotides. Here we investigate whether the numerous weak signals emanating from these dinucleotide arrangements can be used for computational identification of UCNEs within the human genome. For this purpose, we analyzed 4272 UCNE sequences, encompassing 1 393 448 nucleotides, alongside equally sized control samples of randomly selected human genomic sequences. Our research identified nine different features of dinucleotide arrangements that enable differentiation of UCNEs from the rest of the genome. We employed these nine features, implementing three Machine Learning techniques - Support Vector Machine, Random Forest, and Artificial Neural Networks - to classify UCNEs, achieving an accuracy rate of 82-84%, with specific conditions allowing for over 90% accuracy. Notably, the strongest feature for UCNE identification was the frequency ratio between GpC dinucleotides and the sum of GpG and CpC dinucleotides. Additionally, we investigated the entire pool of 31 046 SNPs located within UCNEs for their representation in the ClinVar database, which catalogs human SNPs with known phenotypic effects. The presence of UCNE-associated SNPs in ClinVar aligns with the expectation of a random distribution, emphasizing the enigmatic nature of UCNE phenotypic manifestation.
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Affiliation(s)
- Emily R Crossley
- Program of Bioinformatics and Proteomics/Genomics, University of Toledo, Toledo, OH 43606, USA
| | | | | | | | - Sadik Khuder
- Program of Bioinformatics and Proteomics/Genomics, University of Toledo, Toledo, OH 43606, USA
- Department of Medicine, University of Toledo, Toledo, OH 43606, USA
| | - Alexei Fedorov
- Program of Bioinformatics and Proteomics/Genomics, University of Toledo, Toledo, OH 43606, USA
- CRI Genetics LLC, Santa Monica, CA 90404, USA
- Department of Medicine, University of Toledo, Toledo, OH 43606, USA
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2
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Wang J, Wang M, Moshiri A, Harris RA, Raveendran M, Nguyen T, Kim S, Young L, Wang K, Wiseman R, O'Connor DH, Johnson Z, Martinez M, Montague MJ, Sayers K, Lyke M, Vallender E, Stout T, Li Y, Thomasy SM, Rogers J, Chen R. Genetic diversity of 1,845 rhesus macaques improves genetic variation interpretation and identifies disease models. Nat Commun 2024; 15:5658. [PMID: 38969634 PMCID: PMC11226599 DOI: 10.1038/s41467-024-49922-6] [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: 12/06/2023] [Accepted: 06/25/2024] [Indexed: 07/07/2024] Open
Abstract
Understanding and treating human diseases require valid animal models. Leveraging the genetic diversity in rhesus macaque populations across eight primate centers in the United States, we conduct targeted-sequencing on 1845 individuals for 374 genes linked to inherited human retinal and neurodevelopmental diseases. We identify over 47,000 single nucleotide variants, a substantial proportion of which are shared with human populations. By combining rhesus and human allele frequencies with established variant prediction methods, we develop a machine learning-based score that outperforms established methods in predicting missense variant pathogenicity. Remarkably, we find a marked number of loss-of-function variants and putative deleterious variants, which may lead to the development of rhesus disease models. Through phenotyping of macaques carrying a pathogenic OPA1:p.A8S variant, we identify a genetic model of autosomal dominant optic atrophy. Finally, we present a public website housing variant and genotype data from over two thousand rhesus macaques.
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Affiliation(s)
- Jun Wang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Meng Wang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Ala Moshiri
- Department of Ophthalmology & Vision Science, School of Medicine, UC Davis, Sacramento, California, USA
| | - R Alan Harris
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Tracy Nguyen
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California-Davis, Davis, California, USA
| | - Soohyun Kim
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California-Davis, Davis, California, USA
| | - Laura Young
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California-Davis, Davis, California, USA
| | - Keqing Wang
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Roger Wiseman
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - David H O'Connor
- Wisconsin National Primate Research Center, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Zach Johnson
- Emory National Primate Research Center, Emory University, Atlanta, Georgia, USA
| | - Melween Martinez
- Caribbean Primate Research Center, University of Puerto Rico, Punta Santiago, Humacao, Puerto Rico
| | - Michael J Montague
- Department of Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ken Sayers
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Martha Lyke
- Southwest National Primate Research Center, Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Eric Vallender
- Tulane National Primate Research Center, Tulane university, Covington, Louisiana, USA
| | - Tim Stout
- Department of Ophthalmology, Cullen Eye Institute, Baylor College of Medicine, Houston, Texas, USA
| | - Yumei Li
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Sara M Thomasy
- Department of Ophthalmology & Vision Science, School of Medicine, UC Davis, Sacramento, California, USA
- Department of Surgical and Radiological Sciences, School of Veterinary Medicine, University of California-Davis, Davis, California, USA
- California National Primate Research Center, University of California-Davis, Davis, California, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Rui Chen
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA.
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.
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3
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Akhter G, Ahmed I, Ahmad SM. Genomic analysis and phylogenetic characterization of Himalayan snow trout, Schizothorax esocinus based on mitochondrial protein-coding genes. Mol Biol Rep 2024; 51:659. [PMID: 38748061 DOI: 10.1007/s11033-024-09622-2] [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: 02/17/2024] [Accepted: 05/07/2024] [Indexed: 06/22/2024]
Abstract
BACKGROUND Mitochondrial DNA (mtDNA) has become a significant tool for exploring genetic diversity and delineating evolutionary links across diverse taxa. Within the group of cold-water fish species that are native to the Indian Himalayan region, Schizothorax esocinus holds particular importance due to its ecological significance and is potentially vulnerable to environmental changes. This research aims to clarify the phylogenetic relationships within the Schizothorax genus by utilizing mitochondrial protein-coding genes. METHODS Standard protocols were followed for the isolation of DNA from S. esocinus. For the amplification of mtDNA, overlapping primers were used, and then subsequent sequencing was performed. The genetic features were investigated by the application of bioinformatic approaches. These approaches covered the evaluation of nucleotide composition, codon usage, selective pressure using nonsynonymous substitution /synonymous substitution (Ka/Ks) ratios, and phylogenetic analysis. RESULTS The study specifically examined the 13 protein-coding genes of Schizothorax species which belongs to the Schizothoracinae subfamily. Nucleotide composition analysis showed a bias towards A + T content, consistent with other cyprinid fish species, suggesting evolutionary conservation. Relative Synonymous Codon Usage highlighted leucine as the most frequent (5.18%) and cysteine as the least frequent (0.78%) codon. The positive AT-skew and the predominantly negative GC-skew indicated the abundance of A and C. Comparative analysis revealed significant conservation of amino acids in multiple genes. The majority of amino acids were hydrophobic rather than polar. The purifying selection was revealed by the genetic distance and Ka/Ks ratios. Phylogenetic study revealed a significant genetic divergence between S. esocinus and other Schizothorax species with interspecific K2P distances ranging from 0.00 to 8.87%, with an average of 5.76%. CONCLUSION The present study provides significant contributions to the understanding of mitochondrial genome diversity and genetic evolution mechanisms in Schizothoracinae, hence offering vital insights for the development of conservation initiatives aimed at protecting freshwater fish species.
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Affiliation(s)
- G Akhter
- Fish Nutrition Research Laboratory, Department of Zoology, University of Kashmir, Hazratbal, Srinagar, Jammu and Kashmir, 190 006, India
| | - I Ahmed
- Fish Nutrition Research Laboratory, Department of Zoology, University of Kashmir, Hazratbal, Srinagar, Jammu and Kashmir, 190 006, India.
| | - S M Ahmad
- Division of Biotechnology, Faculty of Veterinary Sciences & Animal Husbandry, Sher-E-Kashmir University of Agricultural Sciences and Technology, Srinagar, India.
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4
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Fan WTL, Wakeley J. Latent mutations in the ancestries of alleles under selection. Theor Popul Biol 2024:S0040-5809(24)00041-8. [PMID: 38697365 DOI: 10.1016/j.tpb.2024.04.008] [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: 06/02/2023] [Revised: 04/23/2024] [Accepted: 04/29/2024] [Indexed: 05/05/2024]
Abstract
We consider a single genetic locus with two alleles A1 and A2 in a large haploid population. The locus is subject to selection and two-way, or recurrent, mutation. Assuming the allele frequencies follow a Wright-Fisher diffusion and have reached stationarity, we describe the asymptotic behaviors of the conditional gene genealogy and the latent mutations of a sample with known allele counts, when the count n1 of allele A1 is fixed, and when either or both the sample size n and the selection strength |α| tend to infinity. Our study extends previous work under neutrality to the case of non-neutral rare alleles, asserting that when selection is not too strong relative to the sample size, even if it is strongly positive or strongly negative in the usual sense (α→-∞ or α→+∞), the number of latent mutations of the n1 copies of allele A1 follows the same distribution as the number of alleles in the Ewens sampling formula. On the other hand, very strong positive selection relative to the sample size leads to neutral gene genealogies with a single ancient latent mutation. We also demonstrate robustness of our asymptotic results against changing population sizes, when one of |α| or n is large.
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Affiliation(s)
- Wai-Tong Louis Fan
- Department of Mathematics, Indiana University, 831 East 3rd St, Bloomington, 47405, IN, USA; Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Ave, Cambridge, 02138, MA, USA.
| | - John Wakeley
- Department of Organismic and Evolutionary Biology, Harvard University, 16 Divinity Ave, Cambridge, 02138, MA, USA.
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5
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Buffalo V, Kern AD. A quantitative genetic model of background selection in humans. PLoS Genet 2024; 20:e1011144. [PMID: 38507461 PMCID: PMC10984650 DOI: 10.1371/journal.pgen.1011144] [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: 09/17/2023] [Revised: 04/01/2024] [Accepted: 01/19/2024] [Indexed: 03/22/2024] Open
Abstract
Across the human genome, there are large-scale fluctuations in genetic diversity caused by the indirect effects of selection. This "linked selection signal" reflects the impact of selection according to the physical placement of functional regions and recombination rates along chromosomes. Previous work has shown that purifying selection acting against the steady influx of new deleterious mutations at functional portions of the genome shapes patterns of genomic variation. To date, statistical efforts to estimate purifying selection parameters from linked selection models have relied on classic Background Selection theory, which is only applicable when new mutations are so deleterious that they cannot fix in the population. Here, we develop a statistical method based on a quantitative genetics view of linked selection, that models how polygenic additive fitness variance distributed along the genome increases the rate of stochastic allele frequency change. By jointly predicting the equilibrium fitness variance and substitution rate due to both strong and weakly deleterious mutations, we estimate the distribution of fitness effects (DFE) and mutation rate across three geographically distinct human samples. While our model can accommodate weaker selection, we find evidence of strong selection operating similarly across all human samples. Although our quantitative genetic model of linked selection fits better than previous models, substitution rates of the most constrained sites disagree with observed divergence levels. We find that a model incorporating selective interference better predicts observed divergence in conserved regions, but overall our results suggest uncertainty remains about the processes generating fitness variation in humans.
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Affiliation(s)
- Vince Buffalo
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, United States of America
- Institute of Ecology and Evolution and Department of Biology, University of Oregon, Eugene, Oregon, United States of America
| | - Andrew D. Kern
- Institute of Ecology and Evolution and Department of Biology, University of Oregon, Eugene, Oregon, United States of America
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6
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Kyriazis CC, Lohmueller KE. Constraining models of dominance for nonsynonymous mutations in the human genome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.25.582010. [PMID: 38463985 PMCID: PMC10925099 DOI: 10.1101/2024.02.25.582010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Dominance is a fundamental parameter in genetics, determining the dynamics of natural selection on deleterious and beneficial mutations, the patterns of genetic variation in natural populations, and the severity of inbreeding depression in a population. Despite this importance, dominance parameters remain poorly known, particularly in humans or other non-model organisms. A key reason for this lack of information about dominance is that it is extremely challenging to disentangle the selection coefficient (s) of a mutation from its dominance coefficient (h). Here, we explore dominance and selection parameters in humans by fitting models to the site frequency spectrum (SFS) for nonsynonymous mutations. When assuming a single dominance coefficient for all nonsynonymous mutations, we find that numerous h values can fit the data, so long as h is greater than ~0.15. Moreover, we also observe that theoretically-predicted models with a negative relationship between h and s can also fit the data well, including models with h=0.05 for strongly deleterious mutations. Finally, we use our estimated dominance and selection parameters to inform simulations revisiting the question of whether the out-of-Africa bottleneck has led to differences in genetic load between African and non-African human populations. These simulations suggest that the relative burden of genetic load in non-African populations depends on the dominance model assumed, with slight increases for more weakly recessive models and slight decreases shown for more strongly recessive models. Moreover, these results also demonstrate that models of partially recessive nonsynonymous mutations can explain the observed severity of inbreeding depression in humans, bridging the gap between molecular population genetics and direct measures of fitness in humans. Our work represents a comprehensive assessment of dominance and deleterious variation in humans, with implications for parameterizing models of deleterious variation in humans and other mammalian species.
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Affiliation(s)
| | - Kirk E. Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, USA
- Interdepartmental Program in Bioinformatics, University of California, Los Angeles, USA
- Department of Human Genetics, David Geffen School of Medicine, Los Angeles, USA
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7
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Lopez Soriano V, Dueñas Rey A, Mukherjee R, Coppieters F, Bauwens M, Willaert A, De Baere E. Multi-omics analysis in human retina uncovers ultraconserved cis-regulatory elements at rare eye disease loci. Nat Commun 2024; 15:1600. [PMID: 38383453 PMCID: PMC10881467 DOI: 10.1038/s41467-024-45381-1] [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: 10/01/2023] [Accepted: 01/19/2024] [Indexed: 02/23/2024] Open
Abstract
Cross-species genome comparisons have revealed a substantial number of ultraconserved non-coding elements (UCNEs). Several of these elements have proved to be essential tissue- and cell type-specific cis-regulators of developmental gene expression. Here, we characterize a set of UCNEs as candidate CREs (cCREs) during retinal development and evaluate the contribution of their genomic variation to rare eye diseases, for which pathogenic non-coding variants are emerging. Integration of bulk and single-cell retinal multi-omics data reveals 594 genes under potential cis-regulatory control of UCNEs, of which 45 are implicated in rare eye disease. Mining of candidate cis-regulatory UCNEs in WGS data derived from the rare eye disease cohort of Genomics England reveals 178 ultrarare variants within 84 UCNEs associated with 29 disease genes. Overall, we provide a comprehensive annotation of ultraconserved non-coding regions acting as cCREs during retinal development which can be targets of non-coding variation underlying rare eye diseases.
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Affiliation(s)
- Victor Lopez Soriano
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Alfredo Dueñas Rey
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | | | - Frauke Coppieters
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Department of Pharmaceutics, Ghent University, Ghent, Belgium
| | - Miriam Bauwens
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Andy Willaert
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Elfride De Baere
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.
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Kyriazis CC, Robinson JA, Lohmueller KE. Using Computational Simulations to Model Deleterious Variation and Genetic Load in Natural Populations. Am Nat 2023; 202:737-752. [PMID: 38033186 PMCID: PMC10897732 DOI: 10.1086/726736] [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] [Indexed: 12/02/2023]
Abstract
AbstractDeleterious genetic variation is abundant in wild populations, and understanding the ecological and conservation implications of such variation is an area of active research. Genomic methods are increasingly used to quantify the impacts of deleterious variation in natural populations; however, these approaches remain limited by an inability to accurately predict the selective and dominance effects of mutations. Computational simulations of deleterious variation offer a complementary tool that can help overcome these limitations, although such approaches have yet to be widely employed. In this perspective article, we aim to encourage ecological and conservation genomics researchers to adopt greater use of computational simulations to aid in deepening our understanding of deleterious variation in natural populations. We first provide an overview of the components of a simulation of deleterious variation, describing the key parameters involved in such models. Next, we discuss several approaches for validating simulation models. Finally, we compare and validate several recently proposed deleterious mutation models, demonstrating that models based on estimates of selection parameters from experimental systems are biased toward highly deleterious mutations. We describe a new model that is supported by multiple orthogonal lines of evidence and provide example scripts for implementing this model (https://github.com/ckyriazis/simulations_review).
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9
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Seplyarskiy V, Koch EM, Lee DJ, Lichtman JS, Luan HH, Sunyaev SR. A mutation rate model at the basepair resolution identifies the mutagenic effect of polymerase III transcription. Nat Genet 2023; 55:2235-2242. [PMID: 38036792 DOI: 10.1038/s41588-023-01562-0] [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: 08/20/2022] [Accepted: 10/06/2023] [Indexed: 12/02/2023]
Abstract
De novo mutations occur at substantially different rates depending on genomic location, sequence context and DNA strand. The success of methods to estimate selection intensity, infer demographic history and map rare disease genes, depends strongly on assumptions about the local mutation rate. Here we present Roulette, a genome-wide mutation rate model at basepair resolution that incorporates known determinants of local mutation rate. Roulette is shown to be more accurate than existing models. We use Roulette to refine the estimates of population growth within Europe by incorporating the full range of human mutation rates. The analysis of significant deviations from the model predictions revealed a tenfold increase in mutation rate in nearly all genes transcribed by polymerase III (Pol III), suggesting a new mutagenic mechanism. We also detected an elevated mutation rate within transcription factor binding sites restricted to sites actively used in testis and residing in promoters.
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Affiliation(s)
- Vladimir Seplyarskiy
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Brigham and Women's Hospital, Division of Genetics, Harvard Medical School, Boston, MA, USA
| | - Evan M Koch
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Brigham and Women's Hospital, Division of Genetics, Harvard Medical School, Boston, MA, USA
| | - Daniel J Lee
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Brigham and Women's Hospital, Division of Genetics, Harvard Medical School, Boston, MA, USA
| | - Joshua S Lichtman
- NGM Biopharmaceuticals Inc., South San Francisco, CA, USA
- Soleil Labs, South San Francisco, CA, USA
| | - Harding H Luan
- NGM Biopharmaceuticals Inc., South San Francisco, CA, USA
- Soleil Labs, South San Francisco, CA, USA
| | - Shamil R Sunyaev
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Brigham and Women's Hospital, Division of Genetics, Harvard Medical School, Boston, MA, USA.
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10
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McCoy RC, Summers MC, McCollin A, Ottolini CS, Ahuja K, Handyside AH. Meiotic and mitotic aneuploidies drive arrest of in vitro fertilized human preimplantation embryos. Genome Med 2023; 15:77. [PMID: 37779206 PMCID: PMC10544495 DOI: 10.1186/s13073-023-01231-1] [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: 12/14/2022] [Accepted: 09/12/2023] [Indexed: 10/03/2023] Open
Abstract
BACKGROUND The high incidence of aneuploidy in early human development, arising either from errors in meiosis or postzygotic mitosis, is the primary cause of pregnancy loss, miscarriage, and stillbirth following natural conception as well as in vitro fertilization (IVF). Preimplantation genetic testing for aneuploidy (PGT-A) has confirmed the prevalence of meiotic and mitotic aneuploidies among blastocyst-stage IVF embryos that are candidates for transfer. However, only about half of normally fertilized embryos develop to the blastocyst stage in vitro, while the others arrest at cleavage to late morula or early blastocyst stages. METHODS To achieve a more complete view of the impacts of aneuploidy, we applied low-coverage sequencing-based PGT-A to a large series (n = 909) of arrested embryos and trophectoderm biopsies. We then correlated observed aneuploidies with abnormalities of the first two cleavage divisions using time-lapse imaging (n = 843). RESULTS The combined incidence of meiotic and mitotic aneuploidies was strongly associated with blastocyst morphological grading, with the proportion ranging from 20 to 90% for the highest to lowest grades, respectively. In contrast, the incidence of aneuploidy among arrested embryos was exceptionally high (94%), dominated by mitotic aneuploidies affecting multiple chromosomes. In turn, these mitotic aneuploidies were strongly associated with abnormal cleavage divisions, such that 51% of abnormally dividing embryos possessed mitotic aneuploidies compared to only 23% of normally dividing embryos. CONCLUSIONS We conclude that the combination of meiotic and mitotic aneuploidies drives arrest of human embryos in vitro, as development increasingly relies on embryonic gene expression at the blastocyst stage.
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Affiliation(s)
- Rajiv C McCoy
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD, 21212, USA.
| | - Michael C Summers
- London Women's Clinic, 113-115 Harley Street, Marylebone, London, W1G 6AP, UK
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, Kent, UK
- Present Address: London Women's Clinic, The Chesterfield, Nuffield Health Clinic, 3 Clifton Hill, Bristol, BS8 1BN, UK
| | - Abeo McCollin
- London Women's Clinic, 113-115 Harley Street, Marylebone, London, W1G 6AP, UK
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, Kent, UK
| | - Christian S Ottolini
- London Women's Clinic, 113-115 Harley Street, Marylebone, London, W1G 6AP, UK
- Department of Maternal and Fetal Medicine, University College London, 86-96 Chenies Mews, London, WC1E 6HX, UK
- Present Address: Juno Genetics Italia, Via Di Quarto Peperino 22, 00188, Rome, Italy
| | - Kamal Ahuja
- London Women's Clinic, 113-115 Harley Street, Marylebone, London, W1G 6AP, UK
| | - Alan H Handyside
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, Kent, UK
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11
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Wade EE, Kyriazis CC, Cavassim MIA, Lohmueller KE. Quantifying the fraction of new mutations that are recessive lethal. Evolution 2023; 77:1539-1549. [PMID: 37074880 PMCID: PMC10309970 DOI: 10.1093/evolut/qpad061] [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: 09/23/2022] [Revised: 03/21/2023] [Accepted: 04/14/2023] [Indexed: 04/20/2023]
Abstract
The presence and impact of recessive lethal mutations have been widely documented in diploid outcrossing species. However, precise estimates of the proportion of new mutations that are recessive lethal remain limited. Here, we evaluate the performance of Fit∂a∂i, a commonly used method for inferring the distribution of fitness effects (DFE), in the presence of lethal mutations. Using simulations, we demonstrate that in both additive and recessive cases, inference of the deleterious nonlethal portion of the DFE is minimally affected by a small proportion (<10%) of lethal mutations. Additionally, we demonstrate that while Fit∂a∂i cannot estimate the fraction of recessive lethal mutations, Fit∂a∂i can accurately infer the fraction of additive lethal mutations. Finally, as an alternative approach to estimate the proportion of mutations that are recessive lethal, we employ models of mutation-selection-drift balance using existing genomic parameters and estimates of segregating recessive lethals for humans and Drosophila melanogaster. In both species, the segregating recessive lethal load can be explained by a very small fraction (<1%) of new nonsynonymous mutations being recessive lethal. Our results refute recent assertions of a much higher proportion of mutations being recessive lethal (4%-5%), while highlighting the need for additional information on the joint distribution of selection and dominance coefficients.
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Affiliation(s)
- Emma E Wade
- Department of Ecology and Evolutionary Biology, University of California–Los Angeles, Los Angeles, CA, United States
- Department of Computer Science and Engineering, Mississippi State University, Starkville, MS, United States
| | - Christopher C Kyriazis
- Department of Ecology and Evolutionary Biology, University of California–Los Angeles, Los Angeles, CA, United States
| | - Maria Izabel A Cavassim
- Department of Ecology and Evolutionary Biology, University of California–Los Angeles, Los Angeles, CA, United States
| | - Kirk E Lohmueller
- Department of Ecology and Evolutionary Biology, University of California–Los Angeles, Los Angeles, CA, United States
- Interdepartmental Program in Bioinformatics, University of California–Los Angeles, Los Angeles, CA, United States
- Department of Human Genetics, David Geffen School of Medicine, University of California–Los Angeles, Los Angeles, CA, United States
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Kyriazis CC, Robinson JA, Nigenda-Morales SF, Beichman AC, Rojas-Bracho L, Robertson KM, Fontaine MC, Wayne RK, Taylor BL, Lohmueller KE, Morin PA. Models based on best-available information support a low inbreeding load and potential for recovery in the vaquita. Heredity (Edinb) 2023; 130:183-187. [PMID: 36941409 PMCID: PMC10076335 DOI: 10.1038/s41437-023-00608-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 03/01/2023] [Accepted: 03/02/2023] [Indexed: 03/23/2023] Open
Affiliation(s)
- Christopher C Kyriazis
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Jacqueline A Robinson
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA.
| | - Sergio F Nigenda-Morales
- Advanced Genomics Unit, National Laboratory of Genomics for Biodiversity (Langebio), Center for Research and Advanced Studies (Cinvestav); Irapuato, Guanajuato, Mexico
| | - Annabel C Beichman
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Kelly M Robertson
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA, USA
| | - Michael C Fontaine
- MIVEGEC, Université de Montpellier, CNRS, IRD, Montpellier, France
- Centre de Recherche en Écologie et Évolution de la Santé (CREES), Montpellier, France
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands
| | - Robert K Wayne
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Barbara L Taylor
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA, USA
| | - Kirk E Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles, CA, USA.
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
| | - Phillip A Morin
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA, USA.
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Long noncoding RNAs in cardiovascular disease. Curr Opin Cardiol 2023; 38:179-192. [PMID: 36930221 PMCID: PMC10090314 DOI: 10.1097/hco.0000000000001041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
PURPOSE OF REVIEW Here, we review recent findings on the role of long noncoding RNAs (lncRNAs) in cardiovascular disease (CVD). In addition, we highlight some of the latest findings in lncRNA biology, providing an outlook for future avenues of lncRNA research in CVD. RECENT FINDINGS Recent publications provide translational evidence from patient studies and animal models for the role of specific lncRNAs in CVD. The molecular effector mechanisms of these lncRNAs are diverse. Overall, cell-type selective modulation of gene expression is the largest common denominator. New methods, such as single-cell profiling and CRISPR/Cas9-screening, reveal additional novel mechanistic principles: For example, many lncRNAs establish RNA-based spatial compartments that concentrate effector proteins. Also, RNA modifications and splicing features can be determinants of lncRNA function. SUMMARY lncRNA research is passing the stage of enumerating lncRNAs or recording simplified on-off expression switches. Mechanistic analyses are starting to reveal overarching principles of how lncRNAs can function. Exploring these principles with decisive genetic testing in vivo remains the ultimate test to discern how lncRNA loci, by RNA motifs or DNA elements, affect CVD pathophysiology.
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Agarwal I, Fuller ZL, Myers SR, Przeworski M. Relating pathogenic loss-of-function mutations in humans to their evolutionary fitness costs. eLife 2023; 12:83172. [PMID: 36648429 PMCID: PMC9937649 DOI: 10.7554/elife.83172] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 01/16/2023] [Indexed: 01/18/2023] Open
Abstract
Causal loss-of-function (LOF) variants for Mendelian and severe complex diseases are enriched in 'mutation intolerant' genes. We show how such observations can be interpreted in light of a model of mutation-selection balance and use the model to relate the pathogenic consequences of LOF mutations at present to their evolutionary fitness effects. To this end, we first infer posterior distributions for the fitness costs of LOF mutations in 17,318 autosomal and 679 X-linked genes from exome sequences in 56,855 individuals. Estimated fitness costs for the loss of a gene copy are typically above 1%; they tend to be largest for X-linked genes, whether or not they have a Y homolog, followed by autosomal genes and genes in the pseudoautosomal region. We compare inferred fitness effects for all possible de novo LOF mutations to those of de novo mutations identified in individuals diagnosed with one of six severe, complex diseases or developmental disorders. Probands carry an excess of mutations with estimated fitness effects above 10%; as we show by simulation, when sampled in the population, such highly deleterious mutations are typically only a couple of generations old. Moreover, the proportion of highly deleterious mutations carried by probands reflects the typical age of onset of the disease. The study design also has a discernible influence: a greater proportion of highly deleterious mutations is detected in pedigree than case-control studies, and for autism, in simplex than multiplex families and in female versus male probands. Thus, anchoring observations in human genetics to a population genetic model allows us to learn about the fitness effects of mutations identified by different mapping strategies and for different traits.
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Affiliation(s)
- Ipsita Agarwal
- Department of Biological Sciences, Columbia UniversityNew YorkUnited States
- Department of Statistics, University of OxfordOxfordUnited Kingdom
| | - Zachary L Fuller
- Department of Biological Sciences, Columbia UniversityNew YorkUnited States
| | - Simon R Myers
- Department of Statistics, University of OxfordOxfordUnited Kingdom
- The Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
| | - Molly Przeworski
- Department of Biological Sciences, Columbia UniversityNew YorkUnited States
- Department of Systems Biology, Columbia UniversityNew YorkUnited States
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