101
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Weghorn D, Balick DJ, Cassa C, Kosmicki JA, Daly MJ, Beier DR, Sunyaev SR. Applicability of the Mutation-Selection Balance Model to Population Genetics of Heterozygous Protein-Truncating Variants in Humans. Mol Biol Evol 2020; 36:1701-1710. [PMID: 31004148 DOI: 10.1093/molbev/msz092] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The fate of alleles in the human population is believed to be highly affected by the stochastic force of genetic drift. Estimation of the strength of natural selection in humans generally necessitates a careful modeling of drift including complex effects of the population history and structure. Protein-truncating variants (PTVs) are expected to evolve under strong purifying selection and to have a relatively high per-gene mutation rate. Thus, it is appealing to model the population genetics of PTVs under a simple deterministic mutation-selection balance, as has been proposed earlier (Cassa et al. 2017). Here, we investigated the limits of this approximation using both computer simulations and data-driven approaches. Our simulations rely on a model of demographic history estimated from 33,370 individual exomes of the Non-Finnish European subset of the ExAC data set (Lek et al. 2016). Additionally, we compared the African and European subset of the ExAC study and analyzed de novo PTVs. We show that the mutation-selection balance model is applicable to the majority of human genes, but not to genes under the weakest selection.
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Affiliation(s)
- Donate Weghorn
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA.,Centre for Genomic Regulation and Universitat Pompeu Fabra, Barcelona, Spain
| | - Daniel J Balick
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA
| | - Christopher Cassa
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA
| | - Jack A Kosmicki
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - Mark J Daly
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA.,Program in Medical and Population Genetics, Broad Institute, Cambridge, MA
| | - David R Beier
- Center for Developmental Biology and Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA.,Department of Pediatrics, University of Washington School of Medicine, Seattle, WA
| | - Shamil R Sunyaev
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA
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102
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Franaszczyk M, Truszkowska G, Chmielewski P, Rydzanicz M, Kosinska J, Rywik T, Biernacka A, Spiewak M, Kostrzewa G, Stepien-Wojno M, Stawinski P, Bilinska M, Krajewski P, Zielinski T, Lutynska A, Bilinska ZT, Ploski R. Analysis of De Novo Mutations in Sporadic Cardiomyopathies Emphasizes Their Clinical Relevance and Points to Novel Candidate Genes. J Clin Med 2020; 9:jcm9020370. [PMID: 32013205 PMCID: PMC7073782 DOI: 10.3390/jcm9020370] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 01/22/2020] [Accepted: 01/24/2020] [Indexed: 02/06/2023] Open
Abstract
The vast majority of cardiomyopathies have an autosomal dominant inheritance; hence, genetic testing is typically offered to patients with a positive family history. A de novo mutation is a new germline mutation not inherited from either parent. The purpose of our study was to search for de novo mutations in patients with cardiomyopathy and no evidence of the disease in the family. Using next-generation sequencing, we analyzed cardiomyopathy genes in 12 probands. In 8 (66.7%), we found de novo variants in known cardiomyopathy genes (TTN, DSP, SCN5A, TNNC1, TPM1, CRYAB, MYH7). In the remaining probands, the analysis was extended to whole exome sequencing in a trio (proband and parents). We found de novo variants in genes that, so far, were not associated with any disease (TRIB3, SLC2A6), a possible disease-causing biallelic genotype (APOBEC gene family), and a de novo mosaic variant without strong evidence of pathogenicity (UNC45A). The high prevalence of de novo mutations emphasizes that genetic screening is also indicated in cases of sporadic cardiomyopathy. Moreover, we have identified novel cardiomyopathy candidate genes that are likely to affect immunological function and/or reaction to stress that could be especially relevant in patients with disease onset associated with infection/infestation.
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Affiliation(s)
- Maria Franaszczyk
- Molecular Biology Laboratory, Department of Medical Biology, Institute of Cardiology, 04-628 Warsaw, Poland; (M.F.)
| | - Grazyna Truszkowska
- Molecular Biology Laboratory, Department of Medical Biology, Institute of Cardiology, 04-628 Warsaw, Poland; (M.F.)
| | - Przemyslaw Chmielewski
- Unit for Screening Studies in Inherited Cardiovascular Diseases, Institute of Cardiology, 04-628 Warsaw, Poland
| | - Malgorzata Rydzanicz
- Department of Medical Genetics, Medical University of Warsaw, 02-106 Warsaw, Poland
| | - Joanna Kosinska
- Department of Medical Genetics, Medical University of Warsaw, 02-106 Warsaw, Poland
| | - Tomasz Rywik
- Department of Heart Failure and Transplantology, Institute of Cardiology, 04-628 Warsaw, Poland
| | - Anna Biernacka
- Postgraduate School of Molecular Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland
| | - Mateusz Spiewak
- Magnetic Resonance Unit, Department of Radiology, Institute of Cardiology, 04-628 Warsaw, Poland
| | - Grazyna Kostrzewa
- Department of Forensic Medicine, Medical University of Warsaw, 02-007 Warsaw, Poland
| | - Malgorzata Stepien-Wojno
- Unit for Screening Studies in Inherited Cardiovascular Diseases, Institute of Cardiology, 04-628 Warsaw, Poland
| | - Piotr Stawinski
- Department of Medical Genetics, Medical University of Warsaw, 02-106 Warsaw, Poland
| | - Maria Bilinska
- Department of Arrhythmia, Institute of Cardiology, 04-628 Warsaw, Poland
| | - Pawel Krajewski
- Department of Forensic Medicine, Medical University of Warsaw, 02-007 Warsaw, Poland
| | - Tomasz Zielinski
- Department of Heart Failure and Transplantology, Institute of Cardiology, 04-628 Warsaw, Poland
| | - Anna Lutynska
- Department of Medical Biology, Institute of Cardiology, 04-628 Warsaw, Poland
| | - Zofia T. Bilinska
- Unit for Screening Studies in Inherited Cardiovascular Diseases, Institute of Cardiology, 04-628 Warsaw, Poland
- Correspondence: (Z.T.B.); (R.P.); Tel.: +48-223434710 (Z.T.B.); +48-225720695 (R.P.)
| | - Rafal Ploski
- Department of Medical Genetics, Medical University of Warsaw, 02-106 Warsaw, Poland
- Correspondence: (Z.T.B.); (R.P.); Tel.: +48-223434710 (Z.T.B.); +48-225720695 (R.P.)
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103
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Seiden AH, Richter F, Patel N, Rodriguez OL, Deikus G, Shah H, Smith M, Roberts A, King EC, Sebra RP, Sharp AJ, Gelb BD. Elucidation of de novo small insertion/deletion biology with parent-of-origin phasing. Hum Mutat 2020; 41:800-806. [PMID: 31898844 DOI: 10.1002/humu.23971] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 11/24/2019] [Accepted: 12/24/2019] [Indexed: 12/30/2022]
Abstract
The mechanisms underlying de novo insertion/deletion (indel) genesis, such as polymerase slippage, have been hypothesized but not well characterized in the human genome. We implemented two methodological improvements, which were leveraged to dissect indel mutagenesis. We assigned de novo variants to parent-of-origin (i.e., phasing) with low-coverage long-read whole-genome sequencing, achieving better phasing compared to short-read sequencing (medians of 84% and 23%, respectively). We then wrote an application programming interface to classify indels into three subtypes according to sequence context. Across three cohorts with different phasing methods (Ntrios = 540, all cohorts), we observed that one de novo indel subtype, change in copy count (CCC), was significantly correlated with father's (p = 7.1 × 10-4 ) but not mother's (p = .45) age at conception. We replicated this effect in three cohorts without de novo phasing (ppaternal = 1.9 × 10-9 , pmaternal = .61; Ntrios = 3,391, all cohorts). Although this is consistent with polymerase slippage during spermatogenesis, the percentage of variance explained by paternal age was low, and we did not observe an association with replication timing. These results suggest that spermatogenesis-specific events have a minor role in CCC indel mutagenesis, one not observed for other indel subtypes nor for maternal age in general. These results have implications for indel modeling in evolution and disease.
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Affiliation(s)
- Allison H Seiden
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Felix Richter
- Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Nihir Patel
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Oscar L Rodriguez
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York.,Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Gintaras Deikus
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.,Icahn Institute for Data Science and Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Hardik Shah
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.,Icahn Institute for Data Science and Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Melissa Smith
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.,Icahn Institute for Data Science and Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Amy Roberts
- Division of Genetics, Department of Pediatrics and Department of Cardiology, Boston Children's Hospital, Boston, Massachusetts
| | - Eileen C King
- Division of Biostatistics and Epidemiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Robert P Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.,Icahn Institute for Data Science and Genomics Technology, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Andrew J Sharp
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Bruce D Gelb
- Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York.,Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.,Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York
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104
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Parrott A, Khoury PR, Shikany AR, Lorts A, Villa CR, Miller EM. Investigation of de novo variation in pediatric cardiomyopathy. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2020; 184:116-123. [PMID: 31912959 DOI: 10.1002/ajmg.c.31764] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 12/23/2019] [Accepted: 12/27/2019] [Indexed: 12/20/2022]
Abstract
Pediatric cardiomyopathies can be caused by variants in genes encoding the sarcomere and cytoskeleton in cardiomyocytes. Variants are typically inherited in an autosomal dominant manner with variable expressivity. De novo variants have been reported, however their overall frequency is largely unknown. We sought to determine the rate of de novo, pathogenic and likely pathogenic (P/LP) variants in children with a diagnosis of hypertrophic, dilated, or restrictive cardiomyopathy (HCM, DCM, or RCM), and to compare disease outcomes between individuals with and without a de novo variant. A retrospective record review identified 126 individuals with HCM (55%), DCM (37%), or RCM (8%) ≤18 years of age who had genetic testing. Overall, 50 (40%) had positive genetic testing and 18% of P/LP variants occurred de novo. The rate of de novo variation in those with RCM (80%) was higher than in those with HCM (9%) or DCM (20%). There was evidence of germline mosaicism in one family with RCM. Individuals with de novo variants were more likely than those without to have a history of arrhythmia (p = .049), sudden cardiac arrest (p = .024), hospitalization (p = .041), and cardiac transplantation (p = .030). The likelihood of de novo variation and impact on family risk and screening should be integrated into genetic counseling.
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Affiliation(s)
- Ashley Parrott
- The Heart Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Philip R Khoury
- The Heart Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Amy R Shikany
- The Heart Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Angela Lorts
- The Heart Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Chet R Villa
- The Heart Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Erin M Miller
- The Heart Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
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105
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Castellano D, Eyre-Walker A, Munch K. Impact of Mutation Rate and Selection at Linked Sites on DNA Variation across the Genomes of Humans and Other Homininae. Genome Biol Evol 2020; 12:3550-3561. [PMID: 31596481 PMCID: PMC6944223 DOI: 10.1093/gbe/evz215] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/03/2019] [Indexed: 12/23/2022] Open
Abstract
DNA diversity varies across the genome of many species. Variation in diversity across a genome might arise from regional variation in the mutation rate, variation in the intensity and mode of natural selection, and regional variation in the recombination rate. We show that both noncoding and nonsynonymous diversity are positively correlated to a measure of the mutation rate and the recombination rate and negatively correlated to the density of conserved sequences in 50 kb windows across the genomes of humans and nonhuman homininae. Interestingly, we find that although noncoding diversity is equally affected by these three genomic variables, nonsynonymous diversity is mostly dominated by the density of conserved sequences. The positive correlation between diversity and our measure of the mutation rate seems to be largely a direct consequence of regions with higher mutation rates having more diversity. However, the positive correlation with recombination rate and the negative correlation with the density of conserved sequences suggest that selection at linked sites also affect levels of diversity. This is supported by the observation that the ratio of the number of nonsynonymous to noncoding polymorphisms is negatively correlated to a measure of the effective population size across the genome. We show these patterns persist even when we restrict our analysis to GC-conservative mutations, demonstrating that the patterns are not driven by GC biased gene conversion. In conclusion, our comparative analyses describe how recombination rate, gene density, and mutation rate interact to produce the patterns of DNA diversity that we observe along the hominine genomes.
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Affiliation(s)
- David Castellano
- Bioinformatics Research Centre, Aarhus University, Denmark
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona, Spain
| | - Adam Eyre-Walker
- School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Kasper Munch
- Bioinformatics Research Centre, Aarhus University, Denmark
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106
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Marchetti F, Douglas GR, Yauk CL. A Return to the Origin of the EMGS: Rejuvenating the Quest for Human Germ Cell Mutagens and Determining the Risk to Future Generations. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2020; 61:42-54. [PMID: 31472026 DOI: 10.1002/em.22327] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 08/21/2019] [Accepted: 08/28/2019] [Indexed: 05/23/2023]
Abstract
Fifty years ago, the Environmental Mutagen Society (now Environmental Mutagenesis and Genomics Society) was founded with a laser-focus on germ cell mutagenesis and the protection of "our most vital assets"-the sperm and egg genomes. Yet, five decades on, despite the fact that many agents have been demonstrated to induce inherited changes in the offspring of exposed laboratory rodents, there is no consensus on whether human germ cell mutagens exist. We argue that it is time to reevaluate the available data and conclude that we already have evidence for the existence of environmental exposures that impact human germ cells. What is missing are definite data to demonstrate a significant increase in de novo mutations in the offspring of exposed parents. We believe that with over two decades of research advancing knowledge and technologies in genomics, we are at the cusp of generating data to conclusively show that environmental exposures cause heritable de novo changes in the human offspring. We call on the research community to harness our technologies, synergize our efforts, and return to our Founders' original focus. The next 50 years must involve collaborative work between clinicians, epidemiologists, genetic toxicologists, genomics experts and bioinformaticians to precisely define how environmental exposures impact germ cell genomes. It is time for the research and regulatory communities to prepare to interpret the coming outpouring of data and develop a framework for managing, communicating and mitigating the risk of exposure to human germ cell mutagens. Environ. Mol. Mutagen. 61:42-54, 2020. © 2019 Her Majesty the Queen in Right of Canada.
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Affiliation(s)
- Francesco Marchetti
- Environmental Health Science Research Bureau, Health Canada, Ottawa, Ontario, Canada
| | - George R Douglas
- Environmental Health Science Research Bureau, Health Canada, Ottawa, Ontario, Canada
| | - Carole L Yauk
- Environmental Health Science Research Bureau, Health Canada, Ottawa, Ontario, Canada
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107
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Guo C, Zhao Z, Chen D, He S, Sun N, Li Z, Liu J, Zhang D, Zhang J, Li J, Zhang M, Ge J, Liu X, Zhang X, Fan Z. Detection of Clinically Relevant Genetic Variants in Chinese Patients With Nanophthalmos by Trio-Based Whole-Genome Sequencing Study. Invest Ophthalmol Vis Sci 2019; 60:2904-2913. [PMID: 31266062 DOI: 10.1167/iovs.18-26275] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose Nanophthalmos is a rare genetic disorder commonly characterized by a short axial length (AL) and severe hyperopia. Mutations that have been identified through Mendelian genetic analysis can only explain a fraction of nanophthalmic cases. We investigate the clinically relevant genetic variants in nanophthalmos by whole-genome sequencing (WGS), including de novo mutations (DNMs) and inherited mutations. Methods Clinically relevant genetic variants of 11 trios (11 nanophthalmic probands and their unaffected parents) from the Zhongshan Ophthalmic Center, China, were analyzed by WGS. We further screened three trios and 10 sporadic cases to identify the MYRF mutations. Results In two of 11 trios, without evidence of the presence of deleterious inherited autosomal variants, two DNMs of MYRF (c.789delC, p.S264fs and c.789dupC, p.S264fs) were identified in the probands. These loss-of-function DNMs were predicted to result in premature stop codons and protein structure damage in both probands. In addition, deleterious inherited genetic variants in PRSS56 and MFRP were found in eight probands of the other nine trios. Expanded screening found an additional MYRF DNM (c.1433G>C, p.R478P) in one trio and a stop-gain MYRF mutation (c.2956C>T, p.R986X) in one sporadic case, suggesting the recurrence of MYRF mutations in nanophthalmic patients. Conclusions This is the first trio-based WGS study for nanophthalmos, revealing the potential role of DNMs in MYRF and rare inherited genetic variants in PRSS56 and MFRP. The underlying mechanism of MYRF in the development of nanophthalmos needs to be further investigated.
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Affiliation(s)
- Congcong Guo
- State Key Laboratory of Ophthalmology, Department of Glaucoma, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Zhenni Zhao
- State Key Laboratory of Ophthalmology, Department of Glaucoma, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Denghui Chen
- State Key Laboratory of Ophthalmology, Department of Glaucoma, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Shuxiang He
- Guangzhou KingMed Diagnostics, Guangzhou, China
| | - Nannan Sun
- State Key Laboratory of Ophthalmology, Department of Glaucoma, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Zhongwen Li
- State Key Laboratory of Ophthalmology, Department of Glaucoma, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Jiafan Liu
- State Key Laboratory of Ophthalmology, Department of Glaucoma, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Dandan Zhang
- State Key Laboratory of Ophthalmology, Department of Glaucoma, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Jiamin Zhang
- State Key Laboratory of Ophthalmology, Department of Glaucoma, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Jianlong Li
- State Key Laboratory of Ophthalmology, Department of Glaucoma, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Miao Zhang
- State Key Laboratory of Ophthalmology, Department of Glaucoma, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Jian Ge
- State Key Laboratory of Ophthalmology, Department of Glaucoma, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Xing Liu
- State Key Laboratory of Ophthalmology, Department of Glaucoma, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Xiaoling Zhang
- Section of Biomedical Genetics, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, United States.,Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, United States
| | - Zhigang Fan
- State Key Laboratory of Ophthalmology, Department of Glaucoma, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
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108
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Goldmann JM, Veltman JA, Gilissen C. De Novo Mutations Reflect Development and Aging of the Human Germline. Trends Genet 2019; 35:828-839. [PMID: 31610893 DOI: 10.1016/j.tig.2019.08.005] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 08/15/2019] [Accepted: 08/28/2019] [Indexed: 01/19/2023]
Abstract
Human germline de novo mutations (DNMs) are both a driver of evolution and an important cause of genetic diseases. In the past few years, whole-genome sequencing (WGS) of parent-offspring trios has facilitated the large-scale detection and study of human DNMs, which has led to exciting discoveries. The overarching theme of all of these studies is that the DNMs of an individual are a complex mixture of mutations that arise through different biological processes acting at different times during human development and life.
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Affiliation(s)
- J M Goldmann
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA Nijmegen, The Netherlands
| | - J A Veltman
- Institute of Genetic Medicine, International Centre for Life, Newcastle University, Newcastle upon Tyne, UK; Department of Human Genetics, Donders Centre for Neuroscience, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA Nijmegen, The Netherlands
| | - C Gilissen
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA Nijmegen, The Netherlands.
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109
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V. Barroso G, Puzović N, Dutheil JY. Inference of recombination maps from a single pair of genomes and its application to ancient samples. PLoS Genet 2019; 15:e1008449. [PMID: 31725722 PMCID: PMC6879166 DOI: 10.1371/journal.pgen.1008449] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 11/26/2019] [Accepted: 09/30/2019] [Indexed: 12/11/2022] Open
Abstract
Understanding the causes and consequences of recombination landscape evolution is a fundamental goal in genetics that requires recombination maps from across the tree of life. Such maps can be obtained from population genomic datasets, but require large sample sizes. Alternative methods are therefore necessary to research organisms where such datasets cannot be generated easily, such as non-model or ancient species. Here we extend the sequentially Markovian coalescent model to jointly infer demography and the spatial variation in recombination rate. Using extensive simulations and sequence data from humans, fruit-flies and a fungal pathogen, we demonstrate that iSMC accurately infers recombination maps under a wide range of scenarios-remarkably, even from a single pair of unphased genomes. We exploit this possibility and reconstruct the recombination maps of ancient hominins. We report that the ancient and modern maps are correlated in a manner that reflects the established phylogeny of Neanderthals, Denisovans, and modern human populations.
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Affiliation(s)
- Gustavo V. Barroso
- Max Planck Institute for Evolutionary Biology, Department of Evolutionary Genetics, August-Thienemann-Straße , Plön–GERMANY
| | - Nataša Puzović
- Max Planck Institute for Evolutionary Biology, Department of Evolutionary Genetics, August-Thienemann-Straße , Plön–GERMANY
| | - Julien Y. Dutheil
- Max Planck Institute for Evolutionary Biology, Department of Evolutionary Genetics, August-Thienemann-Straße , Plön–GERMANY
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110
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White TJH. Brain Development and Stochastic Processes During Prenatal and Early Life: You Can't Lose It if You've Never Had It; But It's Better to Have It and Lose It, Than Never to Have Had It at All. J Am Acad Child Adolesc Psychiatry 2019; 58:1042-1050. [PMID: 31327672 DOI: 10.1016/j.jaac.2019.02.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 02/04/2019] [Accepted: 02/22/2019] [Indexed: 11/29/2022]
Abstract
Brain development, although largely driven by genetic processes, also is influenced by environmental factors. However, there has been little discussion in the psychiatric literature on the role of stochastic, or chance, events that take place during neurodevelopment. Studies suggest that the brain capitalizes on and regulates the extent of stochastic processes during development. Furthermore, because neurodevelopment is influenced by environmental factors, there is emerging evidence that fostering those positive environmental factors during prenatal and early life could optimize neurodevelopment and provide greater resilience, including those potentially resulting from stochastic processes. Evidence for the role of environmental factors in optimizing early brain development is supported by work in large population-based studies of child development, randomized control trials in high-risk populations, and early-life adoption studies. The public health message is that creating an environment that fosters optimal brain development during prenatal and early life could prevent psychopathology and provide the developing brain the best chance against negative stochastic processes and potential stressors that are inevitable later in life.
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Affiliation(s)
- Tonya J H White
- Erasmus University Medical Centre, Rotterdam, The Netherlands.
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111
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Sasani TA, Pedersen BS, Gao Z, Baird L, Przeworski M, Jorde LB, Quinlan AR. Large, three-generation human families reveal post-zygotic mosaicism and variability in germline mutation accumulation. eLife 2019; 8:e46922. [PMID: 31549960 PMCID: PMC6759356 DOI: 10.7554/elife.46922] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Accepted: 08/13/2019] [Indexed: 12/27/2022] Open
Abstract
The number of de novo mutations (DNMs) found in an offspring's genome increases with both paternal and maternal age. But does the rate of mutation accumulation in human gametes differ across families? Using sequencing data from 33 large, three-generation CEPH families, we observed significant variability in parental age effects on DNM counts across families, ranging from 0.19 to 3.24 DNMs per year. Additionally, we found that ~3% of DNMs originated following primordial germ cell specification in a parent, and differed from non-mosaic germline DNMs in their mutational spectra. We also discovered that nearly 10% of candidate DNMs in the second generation were post-zygotic, and present in both somatic and germ cells; these gonosomal mutations occurred at equivalent frequencies on both parental haplotypes. Our results demonstrate that rates of germline mutation accumulation vary among families with similar ancestry, and confirm that post-zygotic mosaicism is a substantial source of human DNM.
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Affiliation(s)
- Thomas A Sasani
- Department of Human GeneticsUniversity of UtahSalt Lake CityUnited States
| | - Brent S Pedersen
- Department of Human GeneticsUniversity of UtahSalt Lake CityUnited States
| | - Ziyue Gao
- Howard Hughes Medical Institute and Department of GeneticsStanford UniversityStanfordUnited States
| | - Lisa Baird
- Department of Human GeneticsUniversity of UtahSalt Lake CityUnited States
| | - Molly Przeworski
- Department of Biological SciencesColumbia UniversityNew York CityUnited States
- Department of Systems BiologyColumbia UniversityNew York CityUnited States
| | - Lynn B Jorde
- Department of Human GeneticsUniversity of UtahSalt Lake CityUnited States
- USTAR Center for Genetic DiscoveryUniversity of UtahSalt Lake CityUnited States
| | - Aaron R Quinlan
- Department of Human GeneticsUniversity of UtahSalt Lake CityUnited States
- USTAR Center for Genetic DiscoveryUniversity of UtahSalt Lake CityUnited States
- Department of Biomedical InformaticsUniversity of UtahSalt Lake CityUnited States
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112
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Fisher E, Schweiger R, Rosset S. Efficient Construction of Test Inversion Confidence Intervals Using Quantile Regression. J Comput Graph Stat 2019. [DOI: 10.1080/10618600.2019.1647215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Eyal Fisher
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Regev Schweiger
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Saharon Rosset
- Department of Statistics, Tel Aviv University, Tel Aviv, Israel
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113
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Amos W. Flanking heterozygosity influences the relative probability of different base substitutions in humans. ROYAL SOCIETY OPEN SCIENCE 2019; 6:191018. [PMID: 31598319 PMCID: PMC6774961 DOI: 10.1098/rsos.191018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 08/30/2019] [Indexed: 06/10/2023]
Abstract
Understanding when, where and which mutations are mostly likely to occur impacts many areas of evolutionary biology, from genetic diseases to phylogenetic reconstruction. Africans and non-African humans differ in the mutability of different triplet base combinations. Africans and non-Africans also differ in mutation rate, possibly because heterozygosity is mutagenic, such that diversity lost when humans expanded out of Africa also lowered the mutation rate. I show that these phenomena are linked: as flanking heterozygosity increases, some triplets become progressively more mutable while others become less so. Africans and non-African show near-identical patterns of dependence on heterozygosity. Thus, the striking differences in triplet mutation frequency between Africans and non-Africans, at least in part, seem to be an emergent property, driven by the way changes in heterozygosity 'out of Africa' have differentially impacted the mutability of different triplets. As heterozygosity decreased, the mutation spectrum outside Africa became enriched for triplet mutations that are favoured by low heterozygosity while those favoured by high heterozygosity became relatively rarer.
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114
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Signatures of replication timing, recombination, and sex in the spectrum of rare variants on the human X chromosome and autosomes. Proc Natl Acad Sci U S A 2019; 116:17916-17924. [PMID: 31427530 PMCID: PMC6731651 DOI: 10.1073/pnas.1900714116] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The sources of human germline mutations are poorly understood. Part of the difficulty is that mutations occur very rarely, and so direct pedigree-based approaches remain limited in the numbers that they can examine. To address this problem, we consider the spectrum of low-frequency variants in a dataset (Genome Aggregation Database, gnomAD) of 13,860 human X chromosomes and autosomes. X-autosome differences are reflective of germline sex differences and have been used extensively to learn about male versus female mutational processes; what is less appreciated is that they also reflect chromosome-level biochemical features that differ between the X and autosomes. We tease these components apart by comparing the mutation spectrum in multiple genomic compartments on the autosomes and between the X and autosomes. In so doing, we are able to ascribe specific mutation patterns to replication timing and recombination and to identify differences in the types of mutations that accrue in males and females. In particular, we identify C > G as a mutagenic signature of male meiotic double-strand breaks on the X, which may result from late repair. Our results show how biochemical processes of damage and repair in the germline interact with sex-specific life history traits to shape mutation patterns on both the X chromosome and autosomes.
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115
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Ruzzo EK, Pérez-Cano L, Jung JY, Wang LK, Kashef-Haghighi D, Hartl C, Singh C, Xu J, Hoekstra JN, Leventhal O, Leppä VM, Gandal MJ, Paskov K, Stockham N, Polioudakis D, Lowe JK, Prober DA, Geschwind DH, Wall DP. Inherited and De Novo Genetic Risk for Autism Impacts Shared Networks. Cell 2019; 178:850-866.e26. [PMID: 31398340 PMCID: PMC7102900 DOI: 10.1016/j.cell.2019.07.015] [Citation(s) in RCA: 255] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 04/08/2019] [Accepted: 07/11/2019] [Indexed: 02/08/2023]
Abstract
We performed a comprehensive assessment of rare inherited variation in autism spectrum disorder (ASD) by analyzing whole-genome sequences of 2,308 individuals from families with multiple affected children. We implicate 69 genes in ASD risk, including 24 passing genome-wide Bonferroni correction and 16 new ASD risk genes, most supported by rare inherited variants, a substantial extension of previous findings. Biological pathways enriched for genes harboring inherited variants represent cytoskeletal organization and ion transport, which are distinct from pathways implicated in previous studies. Nevertheless, the de novo and inherited genes contribute to a common protein-protein interaction network. We also identified structural variants (SVs) affecting non-coding regions, implicating recurrent deletions in the promoters of DLG2 and NR3C2. Loss of nr3c2 function in zebrafish disrupts sleep and social function, overlapping with human ASD-related phenotypes. These data support the utility of studying multiplex families in ASD and are available through the Hartwell Autism Research and Technology portal.
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Affiliation(s)
- Elizabeth K Ruzzo
- Department of Psychiatry and Biobehavioral Sciences, Semel Institue, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Laura Pérez-Cano
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Jae-Yoon Jung
- Department of Pediatrics, Division of Systems Medicine, Stanford University, Stanford, CA, USA; Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Lee-Kai Wang
- Department of Psychiatry and Biobehavioral Sciences, Semel Institue, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Dorna Kashef-Haghighi
- Department of Pediatrics, Division of Systems Medicine, Stanford University, Stanford, CA, USA; Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Chris Hartl
- Bioinformatics IDP, University of California, Los Angeles, Los Angeles, CA, USA
| | - Chanpreet Singh
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Jin Xu
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Jackson N Hoekstra
- Department of Psychiatry and Biobehavioral Sciences, Semel Institue, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Olivia Leventhal
- Department of Psychiatry and Biobehavioral Sciences, Semel Institue, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Virpi M Leppä
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Michael J Gandal
- Department of Psychiatry and Biobehavioral Sciences, Semel Institue, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Kelley Paskov
- Department of Pediatrics, Division of Systems Medicine, Stanford University, Stanford, CA, USA; Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Nate Stockham
- Department of Pediatrics, Division of Systems Medicine, Stanford University, Stanford, CA, USA; Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Damon Polioudakis
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Jennifer K Lowe
- Department of Psychiatry and Biobehavioral Sciences, Semel Institue, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - David A Prober
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Daniel H Geschwind
- Department of Psychiatry and Biobehavioral Sciences, Semel Institue, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Center for Autism Research and Treatment, Semel Institute, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA; Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.
| | - Dennis P Wall
- Department of Pediatrics, Division of Systems Medicine, Stanford University, Stanford, CA, USA; Department of Biomedical Data Science, Stanford University, Stanford, CA, USA.
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116
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Yang J, Adli M. Mapping and Making Sense of Noncoding Mutations in the Genome. Cancer Res 2019; 79:4309-4314. [PMID: 31387922 DOI: 10.1158/0008-5472.can-19-0905] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 04/30/2019] [Accepted: 05/21/2019] [Indexed: 11/16/2022]
Abstract
Whole-genome sequencing efforts of tumors and normal tissues have identified numerous genetic mutations, both somatic and germline, that do not overlap with coding genomic sequences. Attributing a functional role to these noncoding mutations and characterizing them using experimental methods has been more challenging compared with coding mutations. In this review, we provide a brief introduction to the world of noncoding mutations. We discuss recent progress in identifying noncoding mutations and the analytic and experimental approaches utilized to interpret their functional roles. We also highlight the potential mechanisms by which a noncoding mutation may exert its effect and discuss future challenges and opportunities.
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Affiliation(s)
- Jiekun Yang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Mazhar Adli
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, Virginia.
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117
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Zondervan-Zwijnenburg MAJ, Veldkamp SAM, Neumann A, Barzeva SA, Nelemans SA, van Beijsterveldt CEM, Branje SJT, Hillegers MHJ, Meeus WHJ, Tiemeier H, Hoijtink HJA, Oldehinkel AJ, Boomsma DI. Parental Age and Offspring Childhood Mental Health: A Multi-Cohort, Population-Based Investigation. Child Dev 2019; 91:964-982. [PMID: 31364163 PMCID: PMC7317448 DOI: 10.1111/cdev.13267] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 02/06/2019] [Accepted: 02/22/2019] [Indexed: 01/07/2023]
Abstract
To examine the contributions of maternal and paternal age on offspring externalizing and internalizing problems, this study analyzed problem behaviors at age 10-12 years from four Dutch population-based cohorts (N = 32,892) by a multiple informant design. Bayesian evidence synthesis was used to combine results across cohorts with 50% of the data analyzed for discovery and 50% for confirmation. There was evidence of a robust negative linear relation between parental age and externalizing problems as reported by parents. In teacher-reports, this relation was largely explained by parental socio-economic status. Parental age had limited to no association with internalizing problems. Thus, in this large population-based study, either a beneficial or no effect of advanced parenthood on child problem behavior was observed.
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118
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Somatic and Germline Mutation Periodicity Follow the Orientation of the DNA Minor Groove around Nucleosomes. Cell 2019; 175:1074-1087.e18. [PMID: 30388444 DOI: 10.1016/j.cell.2018.10.004] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 08/27/2018] [Accepted: 10/01/2018] [Indexed: 12/11/2022]
Abstract
Mutation rates along the genome are highly variable and influenced by several chromatin features. Here, we addressed how nucleosomes, the most pervasive chromatin structure in eukaryotes, affect the generation of mutations. We discovered that within nucleosomes, the somatic mutation rate across several tumor cohorts exhibits a strong 10 base pair (bp) periodicity. This periodic pattern tracks the alternation of the DNA minor groove facing toward and away from the histones. The strength and phase of the mutation rate periodicity are determined by the mutational processes active in tumors. We uncovered similar periodic patterns in the genetic variation among human and Arabidopsis populations, also detectable in their divergence from close species, indicating that the same principles underlie germline and somatic mutation rates. We propose that differential DNA damage and repair processes dependent on the minor groove orientation in nucleosome-bound DNA contribute to the 10-bp periodicity in AT/CG content in eukaryotic genomes.
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119
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Supek F, Lehner B. Scales and mechanisms of somatic mutation rate variation across the human genome. DNA Repair (Amst) 2019; 81:102647. [PMID: 31307927 DOI: 10.1016/j.dnarep.2019.102647] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Cancer genome sequencing has revealed that somatic mutation rates vary substantially across the human genome and at scales from megabase-sized domains to individual nucleotides. Here we review recent work that has both revealed the major mutation biases that operate across the genome and the molecular mechanisms that cause them. The default mutation rate landscape in mammalian genomes results in active genes having low mutation rates because of a combination of factors that increase DNA repair: early DNA replication, transcription, active chromatin modifications and accessible chromatin. Therefore, either an increase in the global mutation rate or a redistribution of mutations from inactive to active DNA can increase the rate at which consequential mutations are acquired in active genes. Several environmental carcinogens and intrinsic mechanisms operating in tumor cells likely cause cancer by this second mechanism: by specifically increasing the mutation rate in active regions of the genome.
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Affiliation(s)
- Fran Supek
- Genome Data Science, Institut de Recerca Biomedica (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain.
| | - Ben Lehner
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain; Systems Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Doctor Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
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120
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Goncearenco A, Rager SL, Li M, Sang QX, Rogozin IB, Panchenko AR. Exploring background mutational processes to decipher cancer genetic heterogeneity. Nucleic Acids Res 2019; 45:W514-W522. [PMID: 28472504 PMCID: PMC5793731 DOI: 10.1093/nar/gkx367] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 04/21/2017] [Indexed: 01/08/2023] Open
Abstract
Much remains unknown about the progression and heterogeneity of mutational processes in different cancers and their diagnostic and clinical potential. A growing body of evidence supports mutation rate dependence on the local DNA sequence context for various types of mutations. We propose several tools for the analysis of cancer context-dependent mutations, which are implemented in an online computational framework MutaGene. The framework explores DNA context-dependent mutational patterns and underlying somatic cancer mutagenesis, analyzes mutational profiles of cancer samples, identifies the combinations of underlying mutagenic processes including those related to infidelity of DNA replication and repair machinery, and various other endogenous and exogenous mutagenic factors. As a result, the combination of mutagenic processes can be identified in any query sample with subsequent comparison to mutational profiles derived from malignant and benign samples. In addition, mutagen or cancer-specific mutational background models are applied to calculate expected DNA and protein site mutability to decouple relative contributions of mutagenesis and selection in carcinogenesis, thus elucidating the site-specific driving events in cancer. MutaGene is freely available at https://www.ncbi.nlm.nih.gov/projects/mutagene/.
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Affiliation(s)
| | - Stephanie L Rager
- National Center for Biotechnology Information, NIH, Bethesda, MD 20894, USA.,Columbia University, School of Engineering and Applied Science, New York, NY 10027, USA
| | - Minghui Li
- National Center for Biotechnology Information, NIH, Bethesda, MD 20894, USA
| | - Qing-Xiang Sang
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
| | - Igor B Rogozin
- National Center for Biotechnology Information, NIH, Bethesda, MD 20894, USA
| | - Anna R Panchenko
- National Center for Biotechnology Information, NIH, Bethesda, MD 20894, USA
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121
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Konrad A, Brady MJ, Bergthorsson U, Katju V. Mutational Landscape of Spontaneous Base Substitutions and Small Indels in Experimental Caenorhabditis elegans Populations of Differing Size. Genetics 2019; 212:837-854. [PMID: 31110155 PMCID: PMC6614903 DOI: 10.1534/genetics.119.302054] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 05/16/2019] [Indexed: 02/08/2023] Open
Abstract
Experimental investigations into the rates and fitness effects of spontaneous mutations are fundamental to our understanding of the evolutionary process. To gain insights into the molecular and fitness consequences of spontaneous mutations, we conducted a mutation accumulation (MA) experiment at varying population sizes in the nematode Caenorhabditis elegans, evolving 35 lines in parallel for 409 generations at three population sizes (N = 1, 10, and 100 individuals). Here, we focus on nuclear SNPs and small insertion/deletions (indels) under minimal influence of selection, as well as their accrual rates in larger populations under greater selection efficacy. The spontaneous rates of base substitutions and small indels are 1.84 (95% C.I. ± 0.14) × 10-9 substitutions and 6.84 (95% C.I. ± 0.97) × 10-10 changes/site/generation, respectively. Small indels exhibit a deletion bias with deletions exceeding insertions by threefold. Notably, there was no correlation between the frequency of base substitutions, nonsynonymous substitutions, or small indels with population size. These results contrast with our previous analysis of mitochondrial DNA mutations and nuclear copy-number changes in these MA lines, and suggest that nuclear base substitutions and small indels are under less stringent purifying selection compared to the former mutational classes. A transition bias was observed in exons as was a near universal base substitution bias toward A/T. Strongly context-dependent base substitutions, where 5'-Ts and 3'-As increase the frequency of A/T → T/A transversions, especially at the boundaries of A or T homopolymeric runs, manifest as higher mutation rates in (i) introns and intergenic regions relative to exons, (ii) chromosomal cores vs. arms and tips, and (iii) germline-expressed genes.
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Affiliation(s)
- Anke Konrad
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77845
| | - Meghan J Brady
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77845
| | - Ulfar Bergthorsson
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77845
| | - Vaishali Katju
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas 77845
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122
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Huang YF, Siepel A. Estimation of allele-specific fitness effects across human protein-coding sequences and implications for disease. Genome Res 2019; 29:1310-1321. [PMID: 31249063 PMCID: PMC6673719 DOI: 10.1101/gr.245522.118] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 06/20/2019] [Indexed: 12/16/2022]
Abstract
A central challenge in human genomics is to understand the cellular, evolutionary, and clinical significance of genetic variants. Here, we introduce a unified population-genetic and machine-learning model, called Linear Allele-Specific Selection InferencE (LASSIE), for estimating the fitness effects of all observed and potential single-nucleotide variants, based on polymorphism data and predictive genomic features. We applied LASSIE to 51 high-coverage genome sequences annotated with 33 genomic features and constructed a map of allele-specific selection coefficients across all protein-coding sequences in the human genome. This map is generally consistent with previous inferences of the bulk distribution of fitness effects but reveals pervasive weak negative selection against synonymous mutations. In addition, the estimated selection coefficients are highly predictive of inherited pathogenic variants and cancer driver mutations, outperforming state-of-the-art variant prioritization methods. By contrasting our estimated model with ultrahigh coverage ExAC exome-sequencing data, we identified 1118 genes under unusually strong negative selection, which tend to be exclusively expressed in the central nervous system or associated with autism spectrum disorder, as well as 773 genes under unusually weak selection, which tend to be associated with metabolism. This combination of classical population genetic theory with modern machine-learning and large-scale genomic data is a powerful paradigm for the study of both human evolution and disease.
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Affiliation(s)
- Yi-Fei Huang
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Adam Siepel
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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123
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Fraser BA, Whiting JR. What can be learned by scanning the genome for molecular convergence in wild populations? Ann N Y Acad Sci 2019; 1476:23-42. [PMID: 31241191 PMCID: PMC7586825 DOI: 10.1111/nyas.14177] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/24/2019] [Accepted: 06/04/2019] [Indexed: 12/11/2022]
Abstract
Convergent evolution, where independent lineages evolve similar phenotypes in response to similar challenges, can provide valuable insight into how selection operates and the limitations it encounters. However, it has only recently become possible to explore how convergent evolution is reflected at the genomic level. The overlapping outlier approach (OOA), where genome scans of multiple independent lineages are used to find outliers that overlap and therefore identify convergently evolving loci, is becoming popular. Here, we present a quantitative analysis of 34 studies that used this approach across many sampling designs, taxa, and sampling intensities. We found that OOA studies with increased biological sampling power within replicates have increased likelihood of finding overlapping, "convergent" signals of adaptation between them. When identifying convergent loci as overlapping outliers, it is tempting to assume that any false-positive outliers derived from individual scans will fail to overlap across replicates, but this cannot be guaranteed. We highlight how population demographics and genomic context can contribute toward both true convergence and false positives in OOA studies. We finish with an exploration of emerging methods that couple genome scans with phenotype and environmental measures, leveraging added information from genome data to more directly test hypotheses of the likelihood of convergent evolution.
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Affiliation(s)
- Bonnie A Fraser
- Department of Biosciences, University of Exeter, Exeter, United Kingdom
| | - James R Whiting
- Department of Biosciences, University of Exeter, Exeter, United Kingdom
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124
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A pilot study of the implementation of pharmacogenomic pharmacist initiated pre-emptive testing in primary care. Eur J Hum Genet 2019; 27:1532-1541. [PMID: 31227807 DOI: 10.1038/s41431-019-0454-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Revised: 05/17/2019] [Accepted: 05/22/2019] [Indexed: 12/23/2022] Open
Abstract
Despite the nationwide availability of pharmacogenomic (PGx) guidelines in electronic medication surveillance systems in The Netherlands, PGx guided prescribing is still uncommon in primary care. We set out to investigate the adoption of pharmacist initiated PGx testing in primary care. Community pharmacists were offered a free PGx test covering 40 variants in 8 genes to test patients receiving an incident prescription (IRx) of a selection of 10 drugs. Results of the PGx test along with predicted phenotypes and a therapeutic recommendation based on the Dutch Pharmacogenetics Working Group (DPWG) guidelines were transferred to the pharmacist and physician. Adoption was defined as the percentage of eligible patients that received genotyping. From November 2014-July 2016, 200 patients were included with an adoption of 18.0%. Of the included patients 57.5% received an IRx for atorvastatin, 14.5% started with simvastatin and 28.0% received an IRx for amitriptyline, (es)citalopram, nortriptyline, or venlafaxine. 90% of the patients carried at least one actionable PGx test result in the selected PGx-panel. In 31.0% of the incident prescriptions a combination between a drug with a known gene-drug interaction and an actionable genotype was present and a therapeutic recommendation was provided. The provided recommendations were accepted by the clinicians in 88.7% of the patients. Pharmacist initiated implementation of PGx in primary care is feasible, and the frequency of actionable gene-drug interactions for the selected drugs is high.
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125
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Beal MA, Meier MJ, Williams A, Rowan-Carroll A, Gagné R, Lindsay SJ, Fitzgerald T, Hurles ME, Marchetti F, Yauk CL. Paternal exposure to benzo(a)pyrene induces genome-wide mutations in mouse offspring. Commun Biol 2019; 2:228. [PMID: 31240266 PMCID: PMC6586636 DOI: 10.1038/s42003-019-0476-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 05/23/2019] [Indexed: 01/14/2023] Open
Abstract
Understanding the effects of environmental exposures on germline mutation rates has been a decades-long pursuit in genetics. We used next-generation sequencing and comparative genomic hybridization arrays to investigate genome-wide mutations in the offspring of male mice exposed to benzo(a)pyrene (BaP), a common environmental pollutant. We demonstrate that offspring developing from sperm exposed during the mitotic or post-mitotic phases of spermatogenesis have significantly more de novo single nucleotide variants (1.8-fold; P < 0.01) than controls. Both phases of spermatogenesis are susceptible to the induction of heritable mutations, although mutations arising from post-fertilization events are more common after post-mitotic exposure. In addition, the mutation spectra in sperm and offspring of BaP-exposed males are consistent. Finally, we report a significant increase in transmitted copy number duplications (P = 0.001) in BaP-exposed sires. Our study demonstrates that germ cell mutagen exposures induce genome-wide mutations in the offspring that may be associated with adverse health outcomes.
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Affiliation(s)
- Marc A. Beal
- Carleton University, Ottawa, Ontario K1S 5B6 Canada
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario K1A 0K9 Canada
| | - Matthew J. Meier
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario K1A 0K9 Canada
| | - Andrew Williams
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario K1A 0K9 Canada
| | - Andrea Rowan-Carroll
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario K1A 0K9 Canada
| | - Rémi Gagné
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario K1A 0K9 Canada
| | - Sarah J. Lindsay
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Tomas Fitzgerald
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Matthew E. Hurles
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA UK
| | - Francesco Marchetti
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario K1A 0K9 Canada
| | - Carole L. Yauk
- Environmental Health Science and Research Bureau, Healthy Environments and Consumer Safety Branch, Health Canada, Ottawa, Ontario K1A 0K9 Canada
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126
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Laurin-Lemay S, Rodrigue N, Lartillot N, Philippe H. Conditional Approximate Bayesian Computation: A New Approach for Across-Site Dependency in High-Dimensional Mutation-Selection Models. Mol Biol Evol 2019; 35:2819-2834. [PMID: 30203003 DOI: 10.1093/molbev/msy173] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
A key question in molecular evolutionary biology concerns the relative roles of mutation and selection in shaping genomic data. Moreover, features of mutation and selection are heterogeneous along the genome and over time. Mechanistic codon substitution models based on the mutation-selection framework are promising approaches to separating these effects. In practice, however, several complications arise, since accounting for such heterogeneities often implies handling models of high dimensionality (e.g., amino acid preferences), or leads to across-site dependence (e.g., CpG hypermutability), making the likelihood function intractable. Approximate Bayesian Computation (ABC) could address this latter issue. Here, we propose a new approach, named Conditional ABC (CABC), which combines the sampling efficiency of MCMC and the flexibility of ABC. To illustrate the potential of the CABC approach, we apply it to the study of mammalian CpG hypermutability based on a new mutation-level parameter implying dependence across adjacent sites, combined with site-specific purifying selection on amino-acids captured by a Dirichlet process. Our proof-of-concept of the CABC methodology opens new modeling perspectives. Our application of the method reveals a high level of heterogeneity of CpG hypermutability across loci and mild heterogeneity across taxonomic groups; and finally, we show that CpG hypermutability is an important evolutionary factor in rendering relative synonymous codon usage. All source code is available as a GitHub repository (https://github.com/Simonll/LikelihoodFreePhylogenetics.git).
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Affiliation(s)
- Simon Laurin-Lemay
- Robert-Cedergren Center for Bioinformatics and Genomics, Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Nicolas Rodrigue
- Department of Biology, Institute of Biochemistry, and School of Mathematics and Statistics, Carleton University, Ottawa, ON, Canada
| | - Nicolas Lartillot
- Laboratoire de Biométrie et Biologie Évolutive, UMR CNRS 5558, Université Lyon 1, Lyon, France
| | - Hervé Philippe
- Robert-Cedergren Center for Bioinformatics and Genomics, Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada.,Centre de Théorisation et de Modélisation de la Biodiversité, Station d'Écologie Théorique et Expérimentale, UMR CNRS 5321, Moulis, France
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127
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Saxena AS, Salomon MP, Matsuba C, Yeh SD, Baer CF. Evolution of the Mutational Process under Relaxed Selection in Caenorhabditis elegans. Mol Biol Evol 2019; 36:239-251. [PMID: 30445510 DOI: 10.1093/molbev/msy213] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The mutational process varies at many levels, from within genomes to among taxa. Many mechanisms have been linked to variation in mutation, but understanding of the evolution of the mutational process is rudimentary. Physiological condition is often implicated as a source of variation in microbial mutation rate and may contribute to mutation rate variation in multicellular organisms.Deleterious mutations are an ubiquitous source of variation in condition. We test the hypothesis that the mutational process depends on the underlying mutation load in two groups of Caenorhabditis elegans mutation accumulation (MA) lines that differ in their starting mutation loads. "First-order MA" (O1MA) lines maintained under minimal selection for ∼250 generations were divided into high-fitness and low-fitness groups and sets of "second-order MA" (O2MA) lines derived from each O1MA line were maintained for ∼150 additional generations. Genomes of 48 O2MA lines and their progenitors were sequenced. There is significant variation among O2MA lines in base-substitution rate (µbs), but no effect of initial fitness; the indel rate is greater in high-fitness O2MA lines. Overall, µbs is positively correlated with recombination and proximity to short tandem repeats and negatively correlated with 10 bp and 1 kb GC content. However, probability of mutation is sufficiently predicted by the three-nucleotide motif alone. Approximately 90% of the variance in standing nucleotide variation is explained by mutability. Total mutation rate increased in the O2MA lines, as predicted by the "drift barrier" model of mutation rate evolution. These data, combined with experimental estimates of fitness, suggest that epistasis is synergistic.
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Affiliation(s)
| | - Matthew P Salomon
- Department of Biology, University of Florida, Gainesville, FL
- Department of Molecular Oncology, John Wayne Cancer Institute, Santa Monica, CA
| | - Chikako Matsuba
- Department of Biology, University of Florida, Gainesville, FL
- Department of Molecular Oncology, John Wayne Cancer Institute, Santa Monica, CA
| | - Shu-Dan Yeh
- Department of Biology, University of Florida, Gainesville, FL
- Department of Life Sciences, National Central University, Taoyuan, Taiwan
| | - Charles F Baer
- Department of Biology, University of Florida, Gainesville, FL
- University of Florida Genetics Institute
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128
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Hulke ML, Siefert JC, Sansam CL, Koren A. Germline Structural Variations Are Preferential Sites of DNA Replication Timing Plasticity during Development. Genome Biol Evol 2019; 11:1663-1678. [PMID: 31076752 PMCID: PMC6582765 DOI: 10.1093/gbe/evz098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/02/2019] [Indexed: 02/06/2023] Open
Abstract
The DNA replication timing program is modulated throughout development and is also one of the main factors influencing the distribution of mutation rates across the genome. However, the relationship between the mutagenic influence of replication timing and its developmental plasticity remains unexplored. Here, we studied the distribution of copy number variations (CNVs) and single nucleotide polymorphisms across the zebrafish genome in relation to changes in DNA replication timing during embryonic development in this model vertebrate species. We show that CNV sites exhibit strong replication timing plasticity during development, replicating significantly early during early development but significantly late during more advanced developmental stages. Reciprocally, genomic regions that changed their replication timing during development contained a higher proportion of CNVs than developmentally constant regions. Developmentally plastic CNV sites, in particular those that become delayed in their replication timing, were enriched for the clustered protocadherins, a set of genes important for neuronal development that have undergone extensive genetic and epigenetic diversification during zebrafish evolution. In contrast, single nucleotide polymorphism sites replicated consistently early throughout embryonic development, highlighting a unique aspect of the zebrafish genome. Our results uncover a hitherto unrecognized interface between development and evolution.
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Affiliation(s)
- Michelle L Hulke
- Department of Molecular Biology and Genetics, Cornell University
| | - Joseph C Siefert
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation.,Department of Cell Biology, University of Oklahoma Health Sciences Center
| | - Christopher L Sansam
- Cell Cycle and Cancer Biology Research Program, Oklahoma Medical Research Foundation.,Department of Cell Biology, University of Oklahoma Health Sciences Center
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University
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129
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Gao Z, Moorjani P, Sasani TA, Pedersen BS, Quinlan AR, Jorde LB, Amster G, Przeworski M. Overlooked roles of DNA damage and maternal age in generating human germline mutations. Proc Natl Acad Sci U S A 2019; 116:9491-9500. [PMID: 31019089 PMCID: PMC6511033 DOI: 10.1073/pnas.1901259116] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The textbook view that most germline mutations in mammals arise from replication errors is indirectly supported by the fact that there are both more mutations and more cell divisions in the male than in the female germline. When analyzing large de novo mutation datasets in humans, we find multiple lines of evidence that call that view into question. Notably, despite the drastic increase in the ratio of male to female germ cell divisions after the onset of spermatogenesis, even young fathers contribute three times more mutations than young mothers, and this ratio barely increases with parental age. This surprising finding points to a substantial contribution of damage-induced mutations. Indeed, C-to-G transversions and CpG transitions, which together constitute over one-fourth of all base substitution mutations, show genomic distributions and sex-specific age dependencies indicative of double-strand break repair and methylation-associated damage, respectively. Moreover, we find evidence that maternal age at conception influences the mutation rate both because of the accumulation of damage in oocytes and potentially through an influence on the number of postzygotic mutations in the embryo. These findings reveal underappreciated roles of DNA damage and maternal age in the genesis of human germline mutations.
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Affiliation(s)
- Ziyue Gao
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305;
- Department of Genetics, Stanford University, Stanford, CA 94305
| | - Priya Moorjani
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- Center for Computational Biology, University of California, Berkeley, CA 94720
| | - Thomas A Sasani
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Brent S Pedersen
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Aaron R Quinlan
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT 84108
| | - Lynn B Jorde
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Guy Amster
- Department of Biological Sciences, Columbia University, New York, NY 10027
| | - Molly Przeworski
- Department of Biological Sciences, Columbia University, New York, NY 10027;
- Department of Systems Biology, Columbia University, New York, NY 10027
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130
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Uspenskaya NY, Akopov SB, Snezhkov EV, Sverdlov ED. The Rate of Human Germline Mutations—Variable Factor of Evolution and Diseases. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419050144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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131
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Abstract
Mutation provides the ultimate source of all new alleles in populations, including variants that cause disease and fuel adaptation. Recent whole genome sequencing studies have uncovered variation in the mutation rate among individuals and differences in the relative frequency of specific nucleotide changes (the mutation spectrum) between populations. Although parental age is a major driver of differences in overall mutation rate among individuals, the causes of variation in the mutation spectrum remain less well understood. Here, I use high-quality whole genome sequences from 29 inbred laboratory mouse strains to explore the root causes of strain variation in the mutation spectrum. My analysis leverages the unique, mosaic patterns of genetic relatedness among inbred mouse strains to identify strain private variants residing on haplotypes shared between multiple strains due to their recent descent from a common ancestor. I show that these strain-private alleles are strongly enriched for recent de novo mutations and lack signals of widespread purifying selection, suggesting their faithful recapitulation of the spontaneous mutation landscape in single strains. The spectrum of strain-private variants varies significantly among inbred mouse strains reared under standardized laboratory conditions. This variation is not solely explained by strain differences in age at reproduction, raising the possibility that segregating genetic differences affect the constellation of new mutations that arise in a given strain. Collectively, these findings imply the action of remarkably precise nucleotide-specific genetic mechanisms for tuning the de novo mutation landscape in mammals and underscore the genetic complexity of mutation rate control.
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132
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Lecoquierre F, Duffourd Y, Vitobello A, Bruel AL, Urteaga B, Coubes C, Garret P, Nambot S, Chevarin M, Jouan T, Moutton S, Tran-Mau-Them F, Philippe C, Sorlin A, Faivre L, Thauvin-Robinet C. Variant recurrence in neurodevelopmental disorders: the use of publicly available genomic data identifies clinically relevant pathogenic missense variants. Genet Med 2019; 21:2504-2511. [DOI: 10.1038/s41436-019-0518-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 04/12/2019] [Indexed: 12/19/2022] Open
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133
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Neininger K, Marschall T, Helms V. SNP and indel frequencies at transcription start sites and at canonical and alternative translation initiation sites in the human genome. PLoS One 2019; 14:e0214816. [PMID: 30978217 PMCID: PMC6461226 DOI: 10.1371/journal.pone.0214816] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 03/20/2019] [Indexed: 11/30/2022] Open
Abstract
Single-nucleotide polymorphisms (SNPs) are the most common form of genetic variation in humans and drive phenotypic variation. Due to evolutionary conservation, SNPs and indels (insertion and deletions) are depleted in functionally important sequence elements. Recently, population-scale sequencing efforts such as the 1000 Genomes Project and the Genome of the Netherlands Project have catalogued large numbers of sequence variants. Here, we present a systematic analysis of the polymorphisms reported by these two projects in different coding and non-coding genomic elements of the human genome (intergenic regions, CpG islands, promoters, 5’ UTRs, coding exons, 3’ UTRs, introns, and intragenic regions). Furthermore, we were especially interested in the distribution of SNPs and indels in direct vicinity to the transcription start site (TSS) and translation start site (CSS). Thereby, we discovered an enrichment of dinucleotides CpG and CpA and an accumulation of SNPs at base position −1 relative to the TSS that involved primarily CpG and CpA dinucleotides. Genes having a CpG dinucleotide at TSS position -1 were enriched in the functional GO terms “Phosphoprotein”, “Alternative splicing”, and “Protein binding”. Focusing on the CSS, we compared SNP patterns in the flanking regions of canonical and alternative AUG and near-cognate start sites where we considered alternative starts previously identified by experimental ribosome profiling. We observed similar conservation patterns of canonical and alternative translation start sites, which underlines the importance of alternative translation mechanisms for cellular function.
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Affiliation(s)
- Kerstin Neininger
- Center for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
- Graduate School of Computer Science, Saarland University, 66123 Saarbrücken, Germany
| | - Tobias Marschall
- Center for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
- Max Planck Institute for Informatics, 66123 Saarbrücken, Germany
| | - Volkhard Helms
- Center for Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
- * E-mail:
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134
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Vadgama N, Pittman A, Simpson M, Nirmalananthan N, Murray R, Yoshikawa T, De Rijk P, Rees E, Kirov G, Hughes D, Fitzgerald T, Kristiansen M, Pearce K, Cerveira E, Zhu Q, Zhang C, Lee C, Hardy J, Nasir J. De novo single-nucleotide and copy number variation in discordant monozygotic twins reveals disease-related genes. Eur J Hum Genet 2019; 27:1121-1133. [PMID: 30886340 DOI: 10.1038/s41431-019-0376-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 02/18/2019] [Accepted: 03/01/2019] [Indexed: 01/11/2023] Open
Abstract
Recent studies have demonstrated genetic differences between monozygotic (MZ) twins. To test the hypothesis that early post-twinning mutational events associate with phenotypic discordance, we investigated a cohort of 13 twin pairs (n = 26) discordant for various clinical phenotypes using whole-exome sequencing and screened for copy number variation (CNV). We identified a de novo variant in PLCB1, a gene involved in the hydrolysis of lipid phosphorus in milk from dairy cows, associated with lactase non-persistence, and a variant in the mitochondrial complex I gene MT-ND5 associated with amyotrophic lateral sclerosis (ALS). We also found somatic variants in multiple genes (TMEM225B, KBTBD3, TUBGCP4, TFIP11) in another MZ twin pair discordant for ALS. Based on the assumption that discordance between twins could be explained by a common variant with variable penetrance or expressivity, we screened the twin samples for known pathogenic variants that are shared and identified a rare deletion overlapping ARHGAP11B, in the twin pair manifesting with either schizotypal personality disorder or schizophrenia. Parent-offspring trio analysis was implemented for two twin pairs to assess potential association of variants of parental origin with susceptibility to disease. We identified a de novo variant in RASD2 shared by 8-year-old male twins with a suspected diagnosis of autism spectrum disorder (ASD) manifesting as different traits. A de novo CNV duplication was also identified in these twins overlapping CD38, a gene previously implicated in ASD. In twins discordant for Tourette's syndrome, a paternally inherited stop loss variant was detected in AADAC, a known candidate gene for the disorder.
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Affiliation(s)
- Nirmal Vadgama
- Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Alan Pittman
- Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Michael Simpson
- Division of Genetics and Molecular Medicine, King's College London, London, UK
| | | | - Robin Murray
- Institute of Psychiatry, Psychology, and Neuroscience, King's College, London, UK
| | - Takeo Yoshikawa
- RIKEN Brain Science Institute, Wako, Saitama, 351-0198, Japan
| | - Peter De Rijk
- Applied Molecular Genomics Group, University of Antwerp, Antwerp, Belgium
| | - Elliott Rees
- Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - George Kirov
- Centre for Neuropsychiatric Genetics and Genomics, Institute of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Deborah Hughes
- Institute of Neurology, University College London, London, WC1N 3BG, UK
| | | | - Mark Kristiansen
- UCL Great Ormond Street Institute of Child Health, London, WC1N 1EH, UK
| | - Kerra Pearce
- UCL Great Ormond Street Institute of Child Health, London, WC1N 1EH, UK
| | - Eliza Cerveira
- Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Qihui Zhu
- Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Chengsheng Zhang
- Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Charles Lee
- Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - John Hardy
- Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Jamal Nasir
- Cell Biology and Genetics Research Centre, St. George's University of London, London, UK. .,Molecular Biosciences Research Group, University of Northampton, Northampton, NN1 5PH, UK.
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135
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Gallego-Martinez A, Requena T, Roman-Naranjo P, Lopez-Escamez JA. Excess of Rare Missense Variants in Hearing Loss Genes in Sporadic Meniere Disease. Front Genet 2019; 10:76. [PMID: 30828346 PMCID: PMC6385525 DOI: 10.3389/fgene.2019.00076] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 01/28/2019] [Indexed: 12/25/2022] Open
Abstract
Meniere's disease (MD) is a clinical spectrum of rare disorders characterized by vertigo attacks, associated with sensorineural hearing loss (SNHL) and tinnitus involving low to medium frequencies. Although it shows familial aggregation with incomplete phenotypic forms and variable expressivity, most cases are considered sporadic. The aim of this study was to investigate the burden for rare variation in SNHL genes in patients with sporadic MD. We conducted a targeted-sequencing study including SNHL and familial MD genes in 890 MD patients to compare the frequency of rare variants in cases using three independent public datasets as controls. Patients with sporadic MD showed a significant enrichment of missense variants in SNHL genes that was not found in the controls. The list of genes includes GJB2, USH1G, SLC26A4, ESRRB, and CLDN14. A rare synonymous variant with unknown significance was found in the MARVELD2 gene in several unrelated patients with MD. There is a burden of rare variation in certain SNHL genes in sporadic MD. Furthermore, the interaction of common and rare variants in SNHL genes may have an additive effect on MD phenotype. This study will contribute to design a gene panel for the genetic diagnosis of MD.
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Affiliation(s)
- Alvaro Gallego-Martinez
- Otology and Neurotology Group CTS 495, Department of Genomic Medicine, Centre for Genomics and Oncological Research (GENyO), Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
| | - Teresa Requena
- Otology and Neurotology Group CTS 495, Department of Genomic Medicine, Centre for Genomics and Oncological Research (GENyO), Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
| | - Pablo Roman-Naranjo
- Otology and Neurotology Group CTS 495, Department of Genomic Medicine, Centre for Genomics and Oncological Research (GENyO), Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
| | - Jose A. Lopez-Escamez
- Otology and Neurotology Group CTS 495, Department of Genomic Medicine, Centre for Genomics and Oncological Research (GENyO), Pfizer, University of Granada, Andalusian Regional Government, Granada, Spain
- Department of Otolaryngology, Instituto de Investigación Biosanitaria (ibs. GRANADA), Hospital Universitario Virgen de las Nieves, Universidad de Granada, Granada, Spain
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136
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Eyal O, Berkenstadt M, Reznik-Wolf H, Poran H, Ziv-Baran T, Greenbaum L, Yonath H, Pras E. Prenatal diagnosis for de novo mutations: Experience from a tertiary center over a 10-year period. Mol Genet Genomic Med 2019; 7:e00573. [PMID: 30693677 PMCID: PMC6465671 DOI: 10.1002/mgg3.573] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 12/05/2018] [Accepted: 12/05/2018] [Indexed: 11/07/2022] Open
Abstract
Background This study summarizes the results of prenatal diagnosis due to a history of de novo mutation in a previous pregnancy, in a tertiary center in Israel, over a 10‐year period. Methods We sorted all cases of de novo mutations from a pool of 2,260 pregnancies for which prenatal molecular diagnosis was applied, between the years 2008 and 2017. We identified 122 molecular prenatal diagnosis performed for de novo mutations, in 90 women. Results While the total number of yearly prenatal diagnoses stayed stable, a linear increase was detected in the number of cases for which the procedure was done due to a previous de novo mutation: from 3 cases in 2008 to 24 cases in 2017. The most common diseases were Rett syndrome (19), neurofibromatosis Type‐1 (12) and Tuberous sclerosis (5). Recurrence occurred in 3 of the 90 women (3.3%) and hotspot mutations were identified in two genes accounting for 11 cases. We did not find a difference in paternal age at first occurrence of the de novo mutation between the study group and the control group. Conclusion The large increase in the annual number of prenatal diagnoses performed due to a previous pregnancy with a de novo mutation reflects the growing understanding regarding the role of these mutations in the pathogenesis of genetic diseases.
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Affiliation(s)
- Ori Eyal
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Michal Berkenstadt
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Haike Reznik-Wolf
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Hana Poran
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Tomer Ziv-Baran
- Sackler Faculty of Medicine, School of Public Health, Tel-Aviv University, Tel-Aviv, Israel
| | - Lior Greenbaum
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Hagit Yonath
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Elon Pras
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
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137
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Audano PA, Sulovari A, Graves-Lindsay TA, Cantsilieris S, Sorensen M, Welch AE, Dougherty ML, Nelson BJ, Shah A, Dutcher SK, Warren WC, Magrini V, McGrath SD, Li YI, Wilson RK, Eichler EE. Characterizing the Major Structural Variant Alleles of the Human Genome. Cell 2019; 176:663-675.e19. [PMID: 30661756 PMCID: PMC6438697 DOI: 10.1016/j.cell.2018.12.019] [Citation(s) in RCA: 285] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 09/01/2018] [Accepted: 12/12/2018] [Indexed: 12/17/2022]
Abstract
In order to provide a comprehensive resource for human structural variants (SVs), we generated long-read sequence data and analyzed SVs for fifteen human genomes. We sequence resolved 99,604 insertions, deletions, and inversions including 2,238 (1.6 Mbp) that are shared among all discovery genomes with an additional 13,053 (6.9 Mbp) present in the majority, indicating minor alleles or errors in the reference. Genotyping in 440 additional genomes confirms the most common SVs in unique euchromatin are now sequence resolved. We report a ninefold SV bias toward the last 5 Mbp of human chromosomes with nearly 55% of all VNTRs (variable number of tandem repeats) mapping to this portion of the genome. We identify SVs affecting coding and noncoding regulatory loci improving annotation and interpretation of functional variation. These data provide the framework to construct a canonical human reference and a resource for developing advanced representations capable of capturing allelic diversity.
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Affiliation(s)
- Peter A Audano
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Arvis Sulovari
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Tina A Graves-Lindsay
- McDonnell Genome Institute, Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Stuart Cantsilieris
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Melanie Sorensen
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - AnneMarie E Welch
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Max L Dougherty
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Bradley J Nelson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Ankeeta Shah
- Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, IL 60637, USA
| | - Susan K Dutcher
- McDonnell Genome Institute, Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Wesley C Warren
- McDonnell Genome Institute, Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA
| | - Vincent Magrini
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH 43205, USA; The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Sean D McGrath
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH 43205, USA
| | - Yang I Li
- Section of Genetic Medicine, University of Chicago, Chicago, IL 60637, USA; Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Richard K Wilson
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH 43205, USA; The Ohio State University College of Medicine, Columbus, OH 43210, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.
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138
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Halldorsson BV, Palsson G, Stefansson OA, Jonsson H, Hardarson MT, Eggertsson HP, Gunnarsson B, Oddsson A, Halldorsson GH, Zink F, Gudjonsson SA, Frigge ML, Thorleifsson G, Sigurdsson A, Stacey SN, Sulem P, Masson G, Helgason A, Gudbjartsson DF, Thorsteinsdottir U, Stefansson K. Characterizing mutagenic effects of recombination through a sequence-level genetic map. Science 2019; 363:363/6425/eaau1043. [DOI: 10.1126/science.aau1043] [Citation(s) in RCA: 156] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 05/16/2018] [Accepted: 12/07/2018] [Indexed: 12/14/2022]
Abstract
Genetic diversity arises from recombination and de novo mutation (DNM). Using a combination of microarray genotype and whole-genome sequence data on parent-child pairs, we identified 4,531,535 crossover recombinations and 200,435 DNMs. The resulting genetic map has a resolution of 682 base pairs. Crossovers exhibit a mutagenic effect, with overrepresentation of DNMs within 1 kilobase of crossovers in males and females. In females, a higher mutation rate is observed up to 40 kilobases from crossovers, particularly for complex crossovers, which increase with maternal age. We identified 35 loci associated with the recombination rate or the location of crossovers, demonstrating extensive genetic control of meiotic recombination, and our results highlight genes linked to the formation of the synaptonemal complex as determinants of crossovers.
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139
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Katju V, Bergthorsson U. Old Trade, New Tricks: Insights into the Spontaneous Mutation Process from the Partnering of Classical Mutation Accumulation Experiments with High-Throughput Genomic Approaches. Genome Biol Evol 2019; 11:136-165. [PMID: 30476040 PMCID: PMC6330053 DOI: 10.1093/gbe/evy252] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/22/2018] [Indexed: 12/17/2022] Open
Abstract
Mutations spawn genetic variation which, in turn, fuels evolution. Hence, experimental investigations into the rate and fitness effects of spontaneous mutations are central to the study of evolution. Mutation accumulation (MA) experiments have served as a cornerstone for furthering our understanding of spontaneous mutations for four decades. In the pregenomic era, phenotypic measurements of fitness-related traits in MA lines were used to indirectly estimate key mutational parameters, such as the genomic mutation rate, new mutational variance per generation, and the average fitness effect of mutations. Rapidly emerging next-generating sequencing technology has supplanted this phenotype-dependent approach, enabling direct empirical estimates of the mutation rate and a more nuanced understanding of the relative contributions of different classes of mutations to the standing genetic variation. Whole-genome sequencing of MA lines bears immense potential to provide a unified account of the evolutionary process at multiple levels-the genetic basis of variation, and the evolutionary dynamics of mutations under the forces of selection and drift. In this review, we have attempted to synthesize key insights into the spontaneous mutation process that are rapidly emerging from the partnering of classical MA experiments with high-throughput sequencing, with particular emphasis on the spontaneous rates and molecular properties of different mutational classes in nuclear and mitochondrial genomes of diverse taxa, the contribution of mutations to the evolution of gene expression, and the rate and stability of transgenerational epigenetic modifications. Future advances in sequencing technologies will enable greater species representation to further refine our understanding of mutational parameters and their functional consequences.
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Affiliation(s)
- Vaishali Katju
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843-4458
| | - Ulfar Bergthorsson
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 77843-4458
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140
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Seplyarskiy VB, Akkuratov EE, Akkuratova N, Andrianova MA, Nikolaev SI, Bazykin GA, Adameyko I, Sunyaev SR. Error-prone bypass of DNA lesions during lagging-strand replication is a common source of germline and cancer mutations. Nat Genet 2019; 51:36-41. [PMID: 30510240 PMCID: PMC6317876 DOI: 10.1038/s41588-018-0285-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 10/17/2018] [Indexed: 12/11/2022]
Abstract
Studies in experimental systems have identified a multitude of mutational mechanisms including DNA replication infidelity and DNA damage followed by inefficient repair or replicative bypass. However, the relative contributions of these mechanisms to human germline mutation remain unknown. Here, we show that error-prone damage bypass on the lagging strand plays a major role in human mutagenesis. Transcription-coupled DNA repair removes lesions on the transcribed strand; lesions on the non-transcribed strand are preferentially converted into mutations. In human polymorphism we detect a striking similarity between mutation types predominant on the non-transcribed strand and on the strand lagging during replication. Moreover, damage-induced mutations in cancers accumulate asymmetrically with respect to the direction of replication, suggesting that DNA lesions are resolved asymmetrically. We experimentally demonstrate that replication delay greatly attenuates the mutagenic effect of ultraviolet irradiation, confirming that replication converts DNA damage into mutations. We estimate that at least 10% of human mutations arise due to DNA damage.
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Affiliation(s)
- Vladimir B Seplyarskiy
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Moscow, Russia
| | - Evgeny E Akkuratov
- Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
- Science for Life Laboratory, Department of Applied Physics, Royal Institute of Technology, Stockholm, Sweden
| | - Natalia Akkuratova
- Institute of Translational Biomedicine, St. Petersburg State University, St. Petersburg, Russia
| | | | - Sergey I Nikolaev
- Inserm U981, Gustave Roussy Cancer Campus, Université Paris Saclay, Villejuif, France
- Department of Dermatology and Venereology, Université Paris 7, St. Louis Hospital, Paris, France
| | - Georgii A Bazykin
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Moscow, Russia
- Skolkovo Institute of Science and Technology, Skolkovo, Russia
| | - Igor Adameyko
- Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden
- Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Shamil R Sunyaev
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
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141
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Cioppi F, Casamonti E, Krausz C. Age-Dependent De Novo Mutations During Spermatogenesis and Their Consequences. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1166:29-46. [DOI: 10.1007/978-3-030-21664-1_2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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142
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Role of gene body methylation in acclimatization and adaptation in a basal metazoan. Proc Natl Acad Sci U S A 2018; 115:13342-13346. [PMID: 30530646 DOI: 10.1073/pnas.1813749115] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Gene body methylation (GBM) has been hypothesized to modulate responses to environmental change, including transgenerational plasticity, but the evidence thus far has been lacking. Here we show that coral fragments reciprocally transplanted between two distant reefs respond predominantly by increase or decrease in genome-wide GBM disparity: The range of methylation levels between lowly and highly methylated genes becomes either wider or narrower. Remarkably, at a broad functional level this simple adjustment correlated very well with gene expression change, reflecting a shifting balance between expressions of environmentally responsive and housekeeping genes. In our experiment, corals in a lower-quality habitat up-regulated genes involved in environmental responses, while corals in a higher-quality habitat invested more in housekeeping genes. Transplanted fragments showing closer GBM match to local corals attained higher fitness characteristics, which supports GBM's role in acclimatization. Fixed differences in GBM between populations did not align with plastic GBM changes and were mostly observed in genes with elevated F ST, which suggests that they arose predominantly through genetic divergence. However, we cannot completely rule out transgenerational inheritance of acquired GBM states.
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143
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Roberts R. Mendelian Randomization Studies Promise to Shorten the Journey to FDA Approval. JACC Basic Transl Sci 2018; 3:690-703. [PMID: 30456340 PMCID: PMC6234613 DOI: 10.1016/j.jacbts.2018.08.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 07/19/2018] [Accepted: 08/06/2018] [Indexed: 12/11/2022]
Abstract
There has been a dearth of new drugs approved for cardiovascular disorders. The cost is prohibitive, averaging to $2.5 billion, and requiring 12.5 years. This is in large part due to the high failure rate, with only 5% approval by the Food and Drug Administration. Despite preclinical studies showing potential safety and efficacy, most fail when they go to clinical trials phase I to III. One cause for failure is the drug target, often discovered to be a biomarker rather than causative for the disease. Mendelian randomization (MR) studies would determine whether the drug target is causative and could save millions of dollars and time, and prevent unnecessary exposure to adverse drug effects. This was demonstrated in 3 clinical trials that were negative with 2 drugs, veraspladib and darapladib. MR studies during the trials showed the targets of secretory and lipoprotein-associated phospholipids A2 are not causative for coronary artery disease and predicted negative results. The requirement for MR studies is a genetic risk variant with altered function, randomized at conception that remains fixed throughout one’s lifetime. It is not confounded by dietary, lifestyle, or socioeconomic factors. It is more sensitive than randomized controlled trials because exposure to the risk factor is fixed for a lifetime. MR studies showed plasma high-density lipoprotein cholesterol is not a causative target of coronary artery disease, and neither is uric acid, C-reactive protein, and others. MR studies are highly sensitive in determining whether drug targets are causative, and are relatively easy, inexpensive, and not time consuming. It is recommended that drug targets undergo MR studies before proceeding to randomized controlled trials.
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Affiliation(s)
- Robert Roberts
- Department of Medicine, University of Arizona College of Medicine, Phoenix, Arizona
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144
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Dantas-Torres F. Species Concepts: What about Ticks? Trends Parasitol 2018; 34:1017-1026. [PMID: 30343986 DOI: 10.1016/j.pt.2018.09.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 09/19/2018] [Accepted: 09/25/2018] [Indexed: 11/19/2022]
Abstract
Since ancient times, philosophers and taxonomists have tried to classify forms of life. This is what taxonomy is about: the science of identifying, naming, classifying, and describing organisms. In this article I address the issue of the species concept in tick taxonomy. While the typological species concept is still the most widely used, the biological and phylogenetic species concepts are growing in popularity among tick taxonomists. The integrative approach is increasingly being used, but the question is how to define a tick species when using this approach, particularly if data are incongruent. The adoption of an integrative species concept is discussed, in light of recent advances in our understanding of the genetics, morphology, and biology of ticks.
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Affiliation(s)
- Filipe Dantas-Torres
- Laboratory of Immunoparasitology, Department of Immunology, Aggeu Magalhães Institute, Oswaldo Cruz Foundation (Fiocruz), 50740-465 Recife, Pernambuco, Brazil.
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145
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Family-based germline sequencing in children with cancer. Oncogene 2018; 38:1367-1380. [PMID: 30305723 PMCID: PMC6755997 DOI: 10.1038/s41388-018-0520-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 08/22/2018] [Accepted: 09/04/2018] [Indexed: 12/12/2022]
Abstract
The discovery of cancer-predisposing syndromes (CPSs) using next-generation sequencing (NGS) technologies is of increasing importance in pediatric oncology with regard to diagnosis, treatment, surveillance, family counselling and research. Recent studies indicate that a considerable percentage of childhood cancers are associated with CPSs. However, the ratio of CPSs that are caused by inherited vs. de novo mutations (DNMs), the risk of recurrence, and even the total number of genes, which should be considered as a true cancer-predisposing gene, are still unknown. In contrast to sequencing only single index patients, family-based NGS of the germline is a very powerful tool for providing unique insights into inheritance patterns (e.g., DNMs, parental mosaicism) and types of aberrations (e.g., SNV, CNV, indels, SV). Furthermore, functional perturbations of key cancer pathways (e.g., TP53, FA/BRCA) by at least two co-inherited heterozygous digenic mutations from each parent and currently unrecognized rare variants and unmeasured genetic interactions between common and rare variants may be a widespread genetic phenomenon in the germline of affected children. Therefore, family-based trio sequencing has the potential to reveal a striking new landscape of inheritance in childhood cancer and to facilitate the integration and efforts of individualized treatment strategies, including personalized and preventive medicine and cancer surveillance programs. Consequently, cancer genetics is becoming an increasingly common approach in modern oncology, so trio-sequencing should also be routinely integrated into pediatric oncology.
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146
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Thomas GWC, Wang RJ, Puri A, Harris RA, Raveendran M, Hughes DST, Murali SC, Williams LE, Doddapaneni H, Muzny DM, Gibbs RA, Abee CR, Galinski MR, Worley KC, Rogers J, Radivojac P, Hahn MW. Reproductive Longevity Predicts Mutation Rates in Primates. Curr Biol 2018; 28:3193-3197.e5. [PMID: 30270182 DOI: 10.1016/j.cub.2018.08.050] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 07/26/2018] [Accepted: 08/22/2018] [Indexed: 12/30/2022]
Abstract
Mutation rates vary between species across several orders of magnitude, with larger organisms having the highest per-generation mutation rates. Hypotheses for this pattern typically invoke physiological or population-genetic constraints imposed on the molecular machinery preventing mutations [1]. However, continuing germline cell division in multicellular eukaryotes means that organisms with longer generation times and of larger size will leave more mutations to their offspring simply as a byproduct of their increased lifespan [2, 3]. Here, we deeply sequence the genomes of 30 owl monkeys (Aotus nancymaae) from six multi-generation pedigrees to demonstrate that paternal age is the major factor determining the number of de novo mutations in this species. We find that owl monkeys have an average mutation rate of 0.81 × 10-8 per site per generation, roughly 32% lower than the estimate in humans. Based on a simple model of reproductive longevity that does not require any changes to the mutational machinery, we show that this is the expected mutation rate in owl monkeys. We further demonstrate that our model predicts species-specific mutation rates in other primates, including study-specific mutation rates in humans based on the average paternal age. Our results suggest that variation in life history traits alone can explain variation in the per-generation mutation rate among primates, and perhaps among a wide range of multicellular organisms.
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Affiliation(s)
- Gregg W C Thomas
- Department of Biology, Indiana University, 107 S. Indiana Avenue, Bloomington, IN 47405, USA; Department of Computer Science, Indiana University, 107 S. Indiana Avenue, Bloomington, IN 47405, USA.
| | - Richard J Wang
- Department of Biology, Indiana University, 107 S. Indiana Avenue, Bloomington, IN 47405, USA
| | - Arthi Puri
- Department of Computer Science, Indiana University, 107 S. Indiana Avenue, Bloomington, IN 47405, USA
| | - R Alan Harris
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Daniel S T Hughes
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Shwetha C Murali
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Lawrence E Williams
- Keeling Center for Comparative Medicine and Research, University of Texas, MD Anderson Cancer Center, 650 Cool Water Drive, Bastrop, TX 78602, USA
| | - Harsha Doddapaneni
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Donna M Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Christian R Abee
- Keeling Center for Comparative Medicine and Research, University of Texas, MD Anderson Cancer Center, 650 Cool Water Drive, Bastrop, TX 78602, USA
| | - Mary R Galinski
- Emory Vaccine Center, Yerkes National Primate Research Center, Emory University, 201 Dowman Drive, Atlanta, GA, USA; Division of Infectious Diseases, Department of Medicine, Emory University, 201 Dowman Drive, Atlanta, GA, USA
| | - Kim C Worley
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Jeffrey Rogers
- Human Genome Sequencing Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Predrag Radivojac
- Department of Computer Science, Indiana University, 107 S. Indiana Avenue, Bloomington, IN 47405, USA
| | - Matthew W Hahn
- Department of Biology, Indiana University, 107 S. Indiana Avenue, Bloomington, IN 47405, USA; Department of Computer Science, Indiana University, 107 S. Indiana Avenue, Bloomington, IN 47405, USA.
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147
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Liu Z, Zhang N, Zhang Y, Du Y, Zhang T, Li Z, Wu J, Wang X. Prioritized High-Confidence Risk Genes for Intellectual Disability Reveal Molecular Convergence During Brain Development. Front Genet 2018; 9:349. [PMID: 30279698 PMCID: PMC6153320 DOI: 10.3389/fgene.2018.00349] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 08/09/2018] [Indexed: 01/09/2023] Open
Abstract
Dissecting the genetic susceptibility to intellectual disability (ID) based on de novo mutations (DNMs) will aid our understanding of the neurobiological and genetic basis of ID. In this study, we identify 63 high-confidence ID genes with q-values < 0.1 based on four background DNM rates and coding DNM data sets from multiple sequencing cohorts. Bioinformatic annotations revealed a higher burden of these 63 ID genes in FMRP targets and CHD8 targets, and these genes show evolutionary constraint against functional genetic variation. Moreover, these ID risk genes were preferentially expressed in the cortical regions from the early fetal to late mid-fetal stages. In particular, a genome-wide weighted co-expression network analysis suggested that ID genes tightly converge onto two biological modules (M1 and M2) during human brain development. Functional annotations showed specific enrichment of chromatin modification and transcriptional regulation for M1 and synaptic function for M2, implying the divergent etiology of the two modules. In addition, we curated 12 additional strong ID risk genes whose molecular interconnectivity with known ID genes (q-values < 0.3) was greater than random. These findings further highlight the biological convergence of ID risk genes and help improve our understanding of the genetic architecture of ID.
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Affiliation(s)
- Zhenwei Liu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Na Zhang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Yu Zhang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Yaoqiang Du
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Tao Zhang
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Zhongshan Li
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Jinyu Wu
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, China
| | - Xiaobing Wang
- Department of Rheumatology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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148
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Carlson J, Locke AE, Flickinger M, Zawistowski M, Levy S, Myers RM, Boehnke M, Kang HM, Scott LJ, Li JZ, Zöllner S. Extremely rare variants reveal patterns of germline mutation rate heterogeneity in humans. Nat Commun 2018; 9:3753. [PMID: 30218074 PMCID: PMC6138700 DOI: 10.1038/s41467-018-05936-5] [Citation(s) in RCA: 80] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 07/30/2018] [Indexed: 12/30/2022] Open
Abstract
A detailed understanding of the genome-wide variability of single-nucleotide germline mutation rates is essential to studying human genome evolution. Here, we use ~36 million singleton variants from 3560 whole-genome sequences to infer fine-scale patterns of mutation rate heterogeneity. Mutability is jointly affected by adjacent nucleotide context and diverse genomic features of the surrounding region, including histone modifications, replication timing, and recombination rate, sometimes suggesting specific mutagenic mechanisms. Remarkably, GC content, DNase hypersensitivity, CpG islands, and H3K36 trimethylation are associated with both increased and decreased mutation rates depending on nucleotide context. We validate these estimated effects in an independent dataset of ~46,000 de novo mutations, and confirm our estimates are more accurate than previously published results based on ancestrally older variants without considering genomic features. Our results thus provide the most refined portrait to date of the factors contributing to genome-wide variability of the human germline mutation rate.
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Affiliation(s)
- Jedidiah Carlson
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Adam E Locke
- McDonnell Genome Institute & Department of Medicine, Washington University, St. Louis, MO, 63108, USA
| | - Matthew Flickinger
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Matthew Zawistowski
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Shawn Levy
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, 35806, USA
| | - Michael Boehnke
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Hyun Min Kang
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Laura J Scott
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jun Z Li
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA.
- Department of Human Genetics, University of Michigan, Ann Arbor, MI, 48109, USA.
| | - Sebastian Zöllner
- Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA.
- Department of Psychiatry, University of Michigan, Ann Arbor, MI, 48109, USA.
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149
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Pouyet F, Aeschbacher S, Thiéry A, Excoffier L. Background selection and biased gene conversion affect more than 95% of the human genome and bias demographic inferences. eLife 2018; 7:e36317. [PMID: 30125248 PMCID: PMC6177262 DOI: 10.7554/elife.36317] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 08/17/2018] [Indexed: 12/15/2022] Open
Abstract
Disentangling the effect on genomic diversity of natural selection from that of demography is notoriously difficult, but necessary to properly reconstruct the history of species. Here, we use high-quality human genomic data to show that purifying selection at linked sites (i.e. background selection, BGS) and GC-biased gene conversion (gBGC) together affect as much as 95% of the variants of our genome. We find that the magnitude and relative importance of BGS and gBGC are largely determined by variation in recombination rate and base composition. Importantly, synonymous sites and non-transcribed regions are also affected, albeit to different degrees. Their use for demographic inference can lead to strong biases. However, by conditioning on genomic regions with recombination rates above 1.5 cM/Mb and mutation types (C↔G, A↔T), we identify a set of SNPs that is mostly unaffected by BGS or gBGC, and that avoids these biases in the reconstruction of human history.
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Affiliation(s)
- Fanny Pouyet
- Computational and Molecular Population Genetics, Institute of Ecology and EvolutionUniversity of BernBernSwitzerland
- Swiss Institute of BioinformaticsLausanneSwitzerland
| | - Simon Aeschbacher
- Computational and Molecular Population Genetics, Institute of Ecology and EvolutionUniversity of BernBernSwitzerland
- Swiss Institute of BioinformaticsLausanneSwitzerland
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZurichZurichSwitzerland
| | - Alexandre Thiéry
- Computational and Molecular Population Genetics, Institute of Ecology and EvolutionUniversity of BernBernSwitzerland
- Swiss Institute of BioinformaticsLausanneSwitzerland
| | - Laurent Excoffier
- Computational and Molecular Population Genetics, Institute of Ecology and EvolutionUniversity of BernBernSwitzerland
- Swiss Institute of BioinformaticsLausanneSwitzerland
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150
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Pranckėnienė L, Jakaitienė A, Ambrozaitytė L, Kavaliauskienė I, Kučinskas V. Insights Into de novo Mutation Variation in Lithuanian Exome. Front Genet 2018; 9:315. [PMID: 30154829 PMCID: PMC6102505 DOI: 10.3389/fgene.2018.00315] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 07/24/2018] [Indexed: 01/23/2023] Open
Abstract
In the last decade, one of the biggest challenges in genomics research has been to distinguish definitive pathogenic variants from all likely pathogenic variants identified by next-generation sequencing. This task is particularly complex because of our lack of knowledge regarding overall genome variation and pathogenicity of the variants. Therefore, obtaining sufficient information about genome variants in the general population is necessary as such data could be used for the interpretation of de novo mutations (DNMs) in the context of patient's phenotype in cases of sporadic genetic disease. In this study, data from whole-exome sequencing of the general population in Lithuania were directly examined. In total, 84 (VarScan) and 95 (VarSeqTM) DNMs were identified and validated using different algorithms. Thirty-nine of these mutations were considered likely to be pathogenic based on gene function, evolutionary conservation, and mutation impact. The mutation rate estimated per position pair per generation was 2.74 × 10-8 [95% CI: 2.24 × 10-8-3.35 × 10-8] (VarScan) and 2.4 × 10-8 [95% CI: 1.96 × 10-8-2.99 × 10-8] (VarSeqTM), with 1.77 × 10-8 [95% CI: 6.03 × 10-9-5.2 × 10-8] de novo indels per position per generation. The rate of germline DNMs in the Lithuanian population and the effects of the genomic and epigenetic context on DNM formation were calculated for the first time in this study, providing a basis for further analysis of DNMs in individuals with genetic diseases. Considering these findings, additional studies in patient groups with genetic diseases with unclear etiology may facilitate our ability to distinguish certain pathogenic or adaptive DNMs from tolerated background DNMs and to reliably identify disease-causing DNMs by their properties through direct observation.
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Affiliation(s)
- Laura Pranckėnienė
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
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