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Isidor B, Julia S, Nizon M, Vincent M. [Should the knowledge be imperative? The key challenge of high throughput genetics]. Med Sci (Paris) 2017; 33:1001-1002. [PMID: 29200400 DOI: 10.1051/medsci/20173311019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Bertrand Isidor
- Service de génétique médicale, Unité de génétique clinique, CHU Hôtel Dieu, 1, place Alexis Ricordeau, 44093 Nantes, France
| | - Sophie Julia
- Service de génétique médicale, Pôle biologie, Institut Fédératif de Biologie (IFB), 330, avenue de Grande-Bretagne, 31059 Toulouse, France
| | - Mathilde Nizon
- Service de génétique médicale, Unité de génétique clinique, CHU Hôtel Dieu, 1, place Alexis Ricordeau, 44093 Nantes, France
| | - Marie Vincent
- Service de génétique médicale, Unité de génétique clinique, CHU Hôtel Dieu, 1, place Alexis Ricordeau, 44093 Nantes, France
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152
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Repair of UV-Induced DNA Damage Independent of Nucleotide Excision Repair Is Masked by MUTYH. Mol Cell 2017; 68:797-807.e7. [PMID: 29149600 DOI: 10.1016/j.molcel.2017.10.021] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 09/05/2017] [Accepted: 10/17/2017] [Indexed: 02/05/2023]
Abstract
DNA lesions caused by UV damage are thought to be repaired solely by the nucleotide excision repair (NER) pathway in human cells. Patients carrying mutations within genes functioning in this pathway display a range of pathologies, including an increased susceptibility to cancer, premature aging, and neurological defects. There are currently no curative therapies available. Here we performed a high-throughput chemical screen for agents that could alleviate the cellular sensitivity of NER-deficient cells to UV-induced DNA damage. This led to the identification of the clinically approved anti-diabetic drug acetohexamide, which promoted clearance of UV-induced DNA damage without the accumulation of chromosomal aberrations, hence promoting cellular survival. Acetohexamide exerted this protective function by antagonizing expression of the DNA glycosylase, MUTYH. Together, our data reveal the existence of an NER-independent mechanism to remove UV-induced DNA damage and prevent cell death.
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153
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Dougherty M, Lazar J, Klein JC, Diaz K, Gobillot T, Grunblatt E, Hasle N, Lawrence D, Maurano M, Nelson M, Olson G, Srivatsan S, Shendure J, Keene CD, Bird T, Horwitz MS, Marshall DA. Genome sequencing in a case of Niemann-Pick type C. Cold Spring Harb Mol Case Stud 2017; 2:a001222. [PMID: 27900365 PMCID: PMC5111003 DOI: 10.1101/mcs.a001222] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Adult-onset Niemann–Pick disease type C (NPC) is an infrequent presentation of a rare neurovisceral lysosomal lipid storage disorder caused by autosomal recessive mutations in NPC1 (∼95%) or NPC2 (∼5%). Our patient was diagnosed at age 33 when he presented with a 10-yr history of difficulties in judgment, concentration, speech, and coordination. A history of transient neonatal jaundice and splenomegaly with bone marrow biopsy suggesting a lipid storage disorder pointed to NPC; biochemical (“variant” level cholesterol esterification) and ultrastructural studies in adulthood confirmed the diagnosis. Genetic testing revealed two different missense mutations in the NPC1 gene—V950M and N1156S. Symptoms progressed over >20 yr to severe ataxia and spasticity, dementia, and dysphagia with aspiration leading to death. Brain autopsy revealed mild atrophy of the cerebrum and cerebellum. Microscopic examination showed diffuse gray matter deposition of balloon neurons, mild white matter loss, extensive cerebellar Purkinje cell loss with numerous “empty baskets,” and neurofibrillary tangles predominantly in the hippocampal formation and transentorhinal cortex. We performed whole-genome sequencing to examine whether the patient harbored variants outside of the NPC1 locus that could have contributed to his late-onset phenotype. We focused analysis on genetic modifiers in pathways related to lipid metabolism, longevity, and neurodegenerative disease. We identified no rare coding variants in any of the pathways examined nor was the patient enriched for genome-wide association study (GWAS) single-nucleotide polymorphisms (SNPs) associated with longevity or altered lipid metabolism. In light of these findings, this case provides support for the V950M variant being sufficient for adult-onset NPC disease.
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Affiliation(s)
- Max Dougherty
- University of Washington School of Medicine, Seattle, Washington 98195, USA;; Medical Scientist Training Program (MSTP), University of Washington, Seattle, Washington 98195, USA;; Department of Genome Sciences, University of Washington, Seattle, Washington 98105, USA
| | - John Lazar
- University of Washington School of Medicine, Seattle, Washington 98195, USA;; Medical Scientist Training Program (MSTP), University of Washington, Seattle, Washington 98195, USA;; Department of Genome Sciences, University of Washington, Seattle, Washington 98105, USA
| | - Jason C Klein
- University of Washington School of Medicine, Seattle, Washington 98195, USA;; Medical Scientist Training Program (MSTP), University of Washington, Seattle, Washington 98195, USA;; Department of Genome Sciences, University of Washington, Seattle, Washington 98105, USA
| | - Karina Diaz
- University of Washington School of Medicine, Seattle, Washington 98195, USA;; Medical Scientist Training Program (MSTP), University of Washington, Seattle, Washington 98195, USA
| | - Theodore Gobillot
- University of Washington School of Medicine, Seattle, Washington 98195, USA;; Medical Scientist Training Program (MSTP), University of Washington, Seattle, Washington 98195, USA
| | - Eli Grunblatt
- University of Washington School of Medicine, Seattle, Washington 98195, USA;; Medical Scientist Training Program (MSTP), University of Washington, Seattle, Washington 98195, USA
| | - Nicholas Hasle
- University of Washington School of Medicine, Seattle, Washington 98195, USA;; Medical Scientist Training Program (MSTP), University of Washington, Seattle, Washington 98195, USA
| | - Daniel Lawrence
- University of Washington School of Medicine, Seattle, Washington 98195, USA;; Medical Scientist Training Program (MSTP), University of Washington, Seattle, Washington 98195, USA
| | - Megan Maurano
- University of Washington School of Medicine, Seattle, Washington 98195, USA;; Medical Scientist Training Program (MSTP), University of Washington, Seattle, Washington 98195, USA
| | - Maria Nelson
- University of Washington School of Medicine, Seattle, Washington 98195, USA;; Medical Scientist Training Program (MSTP), University of Washington, Seattle, Washington 98195, USA
| | - Gregory Olson
- University of Washington School of Medicine, Seattle, Washington 98195, USA;; Medical Scientist Training Program (MSTP), University of Washington, Seattle, Washington 98195, USA
| | - Sanjay Srivatsan
- University of Washington School of Medicine, Seattle, Washington 98195, USA;; Medical Scientist Training Program (MSTP), University of Washington, Seattle, Washington 98195, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington 98105, USA;; Howard Hughes Medical Institute, Seattle, Washington 98195, USA
| | - C Dirk Keene
- Department of Pathology, University of Washington, Seattle, Washington 98195, USA
| | - Thomas Bird
- Department of Neurology, University of Washington, Seattle, Washington 98105, USA;; Department of Medicine, University of Washington, Seattle, Washington 98195, USA
| | - Marshall S Horwitz
- Department of Pathology, University of Washington, Seattle, Washington 98195, USA
| | - Desiree A Marshall
- Department of Pathology, University of Washington, Seattle, Washington 98195, USA
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154
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Zlotogora J, Patrinos GP, Meiner V. Ashkenazi Jewish genomic variants: integrating data from the Israeli National Genetic Database and gnomAD. Genet Med 2017; 20:867-871. [PMID: 29144512 DOI: 10.1038/gim.2017.193] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Accepted: 10/03/2017] [Indexed: 01/07/2023] Open
Abstract
PURPOSE The aim of the study was to compare the data for mutations related to clinical disorders reported among Ashkenazi Jewish patients in the Israeli National Genetic Database (INGD) with variants included in the Genome Aggregation Database (gnomAD). METHODS We extracted data for mutations claimed to cause disorders reported among Ashkenazi Jews from the INGD and searched gnomAD for each of them. We compared the allele frequency of each variant in Ashkenazi Jews with that of other delineated populations. RESULTS Of the 58 INGD-reported mutations related to autosomal-dominant disorders, 19 were present in gnomAD (32.8%). Of the 309 mutations related to autosomal-recessive disorders, 240 (77.7%) were variants found in gnomAD. Of these variants, 202 (84.2%) were documented among one or more Ashkenazi individuals. At this point in the INGD, there are 168 Ashkenazi assumed founder mutations in 128 different genes corresponding to 111 autosomal-recessive disorders. CONCLUSION Integration of information on mutations among Ashkenazi Jews extracted from the INGD with their population frequency recorded in gnomAD is important for effective straightforward molecular diagnosis as well as for targeted carrier screening either for reproductive decision-making or for implementation of disease-modifying behavior.
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Affiliation(s)
- Joël Zlotogora
- Faculty of Medicine, Hebrew University, Jerusalem, Israel.
| | - George P Patrinos
- Department of Pharmacy, University of Patras School of Health Sciences, Patras, Greece.,Department of Bioinformatics, Faculty of Medicine and Health Sciences, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Vardiella Meiner
- Faculty of Medicine, Hebrew University, Jerusalem, Israel.,Department of Genetics and Metabolic Diseases, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
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155
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Veitia RA, Caburet S, Birchler JA. Mechanisms of Mendelian dominance. Clin Genet 2017; 93:419-428. [PMID: 28755412 DOI: 10.1111/cge.13107] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 07/24/2017] [Accepted: 07/26/2017] [Indexed: 01/12/2023]
Abstract
Genetic dominance has long been considered as a qualitative reflection of interallelic interactions. Dominance arises from many multiple sources whose unifying theme is the existence of non-linear relationships between the genotypic and phenotypic values. One of the clearest examples are dominant negative mutations (DNMs) in which a defective subunit poisons a macromolecular complex. Dominance can also be due to the presence of a heterozygous null allele, as is the case of haploinsufficiency. Dominance can also be influenced by epistatic (interloci) interactions. For instance, a pre-existing genetic variant can make possible the expression of a pathogenic variant in a seemingly "dominant" fashion. Such interactions, which can make an individual more or less sensitive to a particular pathogenic variant, will also be discussed here.
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Affiliation(s)
- R A Veitia
- Institut Jacques Monod, CNRS-UMR 7592, Paris Cedex 13, France.,Université Paris Diderot, Paris, France
| | - S Caburet
- Institut Jacques Monod, CNRS-UMR 7592, Paris Cedex 13, France.,Université Paris Diderot, Paris, France
| | - J A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, Missouri
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156
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Levin A, Tonelli M, Bonventre J, Coresh J, Donner JA, Fogo AB, Fox CS, Gansevoort RT, Heerspink HJL, Jardine M, Kasiske B, Köttgen A, Kretzler M, Levey AS, Luyckx VA, Mehta R, Moe O, Obrador G, Pannu N, Parikh CR, Perkovic V, Pollock C, Stenvinkel P, Tuttle KR, Wheeler DC, Eckardt KU. Global kidney health 2017 and beyond: a roadmap for closing gaps in care, research, and policy. Lancet 2017; 390:1888-1917. [PMID: 28434650 DOI: 10.1016/s0140-6736(17)30788-2] [Citation(s) in RCA: 578] [Impact Index Per Article: 82.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 02/09/2017] [Accepted: 02/15/2017] [Indexed: 12/18/2022]
Abstract
The global nephrology community recognises the need for a cohesive plan to address the problem of chronic kidney disease (CKD). In July, 2016, the International Society of Nephrology hosted a CKD summit of more than 85 people with diverse expertise and professional backgrounds from around the globe. The purpose was to identify and prioritise key activities for the next 5-10 years in the domains of clinical care, research, and advocacy and to create an action plan and performance framework based on ten themes: strengthen CKD surveillance; tackle major risk factors for CKD; reduce acute kidney injury-a special risk factor for CKD; enhance understanding of the genetic causes of CKD; establish better diagnostic methods in CKD; improve understanding of the natural course of CKD; assess and implement established treatment options in patients with CKD; improve management of symptoms and complications of CKD; develop novel therapeutic interventions to slow CKD progression and reduce CKD complications; and increase the quantity and quality of clinical trials in CKD. Each group produced a prioritised list of goals, activities, and a set of key deliverable objectives for each of the themes. The intended users of this action plan are clinicians, patients, scientists, industry partners, governments, and advocacy organisations. Implementation of this integrated comprehensive plan will benefit people who are at risk for or affected by CKD worldwide.
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Affiliation(s)
- Adeera Levin
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada.
| | - Marcello Tonelli
- Department of Medicine, University of Calgary, Calgary, AB, Canada
| | - Joseph Bonventre
- Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Josef Coresh
- Johns Hopkins University Bloomberg School of Public Health, George W Comstock Center for Public Health Research and Prevention, Baltimore, MD, USA; Johns Hopkins University School of Medicine, Welch Center for Prevention, Epidemiology and Clinical Research, Baltimore, MD, USA
| | - Jo-Ann Donner
- International Society of Nephrology, Brussels, Belgium
| | - Agnes B Fogo
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Ron T Gansevoort
- Department of Internal Medicine, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Hiddo J L Heerspink
- Department of Clinical Pharmacy and Pharmacology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Meg Jardine
- The George Institute for Global Health, Sydney, NSW, Australia; Concord Repatriation General Hospital, Concord, NSW, Australia
| | - Bertram Kasiske
- Hennepin County Medical Center, Minneapolis, MN, USA; University of Minnesota, Minneapolis, MN, USA
| | - Anna Köttgen
- Division of Genetic Epidemiology, Faculty of Medicine and Medical Center, University of Freiburg, Freiburg, Germany
| | - Matthias Kretzler
- Department of Internal Medicine and Department of ComputationalMedicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Andrew S Levey
- Tufts Medical Center, Tufts University School of Medicine, Boston, MA, USA
| | - Valerie A Luyckx
- Institute of Biomedical Ethics and Klinik für Nephrologie University Hospital, University of Zurich, Zurich, Switzerland
| | - Ravindra Mehta
- Department of Medicine, University of California, San Diego, CA, USA
| | - Orson Moe
- Department of Internal Medicine and Charles and Jane Pak Center of Mineral Metabolism and Clinical Research, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Gregorio Obrador
- Faculty of Health Sciences, Universidad Panamericana, Mexico City, Mexico
| | - Neesh Pannu
- Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Chirag R Parikh
- Program of Applied Translational Research, Department of Medicine, Yale University, New Haven, CT, USA; Veterans Affairs Medical Center, West Haven, CT, USA
| | - Vlado Perkovic
- The George Institute for Global Health, Sydney, NSW, Australia; University of Sydney, Sydney, NSW, Australia
| | - Carol Pollock
- Kolling Institute of Medical Research, University of Sydney, Sydney, NSW, Australia
| | - Peter Stenvinkel
- Division of Renal Medicine, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Katherine R Tuttle
- Providence Medical Research Center, Providence Health Care Kidney Research Institute, Nephrology Division and Institute for Translational Health Sciences, University of Washington, Spokane, WA, USA
| | - David C Wheeler
- Centre for Nephrology, Royal Free Hospital, University College London, London, UK
| | - Kai-Uwe Eckardt
- Department of Nephrology and Hypertension, University of Erlangen-Nürnberg, Erlangen, Germany
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157
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Hebert E, Borngräber F, Schmidt A, Rakovic A, Brænne I, Weissbach A, Hampf J, Vollstedt EJ, Größer L, Schaake S, Müller M, Manzoor H, Jabusch HC, Alvarez-Fischer D, Kasten M, Kostic VS, Gasser T, Zeuner KE, Kim HJ, Jeon B, Bauer P, Altenmüller E, Klein C, Lohmann K. Functional Characterization of Rare RAB12 Variants and Their Role in Musician's and Other Dystonias. Genes (Basel) 2017; 8:genes8100276. [PMID: 29057844 PMCID: PMC5664126 DOI: 10.3390/genes8100276] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 10/16/2017] [Accepted: 10/17/2017] [Indexed: 01/07/2023] Open
Abstract
Mutations in RAB (member of the Ras superfamily) genes are increasingly recognized as cause of a variety of disorders including neurological conditions. While musician’s dystonia (MD) and writer’s dystonia (WD) are task-specific movement disorders, other dystonias persistently affect postures as in cervical dystonia. Little is known about the underlying etiology. Next-generation sequencing revealed a rare missense variant (c.586A>G; p.Ile196Val) in RAB12 in two of three MD/WD families. Next, we tested 916 additional dystonia patients; 512 Parkinson’s disease patients; and 461 healthy controls for RAB12 variants and identified 10 additional carriers of rare missense changes among dystonia patients (1.1%) but only one carrier in non-dystonic individuals (0.1%; p = 0.005). The detected variants among index patients comprised p.Ile196Val (n = 6); p.Ala174Thr (n = 3); p.Gly13Asp; p.Ala148Thr; and p.Arg181Gln in patients with MD; cervical dystonia; or WD. Two relatives of MD patients with WD also carried p.Ile196Val. The two variants identified in MD patients (p.Ile196Val; p.Gly13Asp) were characterized on endogenous levels in patient-derived fibroblasts and in two RAB12-overexpressing cell models. The ability to hydrolyze guanosine triphosphate (GTP), so called GTPase activity, was increased in mutants compared to wildtype. Furthermore, subcellular distribution of RAB12 in mutants was altered in fibroblasts. Soluble Transferrin receptor 1 levels were reduced in the blood of all three tested p.Ile196Val carriers. In conclusion, we demonstrate an enrichment of missense changes among dystonia patients. Functional characterization revealed altered enzyme activity and lysosomal distribution in mutants suggesting a contribution of RAB12 variants to MD and other dystonias.
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Affiliation(s)
- Eva Hebert
- Institute of Neurogenetics, University of Luebeck, 23538 Luebeck, Germany.
| | - Friederike Borngräber
- Institute of Neurogenetics, University of Luebeck, 23538 Luebeck, Germany.
- Kurt Singer Institute for Music Physiology and Musicians' Health, Hanns Eisler School of Music Berlin, 10595 Berlin, Germany.
- Berlin Center for Musicians' Medicine, Charité-University Medicine Berlin, 10117 Berlin, Germany.
| | - Alexander Schmidt
- Institute of Neurogenetics, University of Luebeck, 23538 Luebeck, Germany.
- Kurt Singer Institute for Music Physiology and Musicians' Health, Hanns Eisler School of Music Berlin, 10595 Berlin, Germany.
- Berlin Center for Musicians' Medicine, Charité-University Medicine Berlin, 10117 Berlin, Germany.
| | - Aleksandar Rakovic
- Institute of Neurogenetics, University of Luebeck, 23538 Luebeck, Germany.
| | - Ingrid Brænne
- Institute for Integrative and Experimental Genomics, University of Luebeck, 23538 Luebeck, Germany.
| | - Anne Weissbach
- Institute of Neurogenetics, University of Luebeck, 23538 Luebeck, Germany.
| | - Jennie Hampf
- Institute of Neurogenetics, University of Luebeck, 23538 Luebeck, Germany.
| | | | - Leopold Größer
- Department of Dermatology, University of Regensburg, 93053 Regensburg, Germany.
| | - Susen Schaake
- Institute of Neurogenetics, University of Luebeck, 23538 Luebeck, Germany.
| | - Michaela Müller
- Institute for Integrative and Experimental Genomics, University of Luebeck, 23538 Luebeck, Germany.
| | - Humera Manzoor
- Institute of Neurogenetics, University of Luebeck, 23538 Luebeck, Germany.
- School of Biological Sciences, University of the Punjab, Quaid-i-Azam Campus, Lahore 54590, Pakistan.
| | | | | | - Meike Kasten
- Institute of Neurogenetics, University of Luebeck, 23538 Luebeck, Germany.
- Department of Psychiatry and Psychotherapy, University of Lübeck, 23538 Lubeck, Germany.
| | - Vladimir S Kostic
- Department of Neurodegenerative Diseases, Clinical Center of Serbia, 11000 Belgrade, Serbia.
| | - Thomas Gasser
- Department of Neurology, University of Tübingen, 72076 Tubingen, Germany.
| | - Kirsten E Zeuner
- Department of Neurology, University of Kiel, 24105 Kiel, Germany.
| | - Han-Joon Kim
- Department of Neurology, Movement Disorder Center, Seoul National University Hospital, Seoul 03080, Korea.
| | - Beomseok Jeon
- Department of Neurology, Movement Disorder Center, Seoul National University Hospital, Seoul 03080, Korea.
| | | | - Eckart Altenmüller
- Institute of Music Physiology and Musician's Medicine, Hanover University of Music, Drama and Media, 30175 Hanover, Germany.
| | - Christine Klein
- Institute of Neurogenetics, University of Luebeck, 23538 Luebeck, Germany.
| | - Katja Lohmann
- Institute of Neurogenetics, University of Luebeck, 23538 Luebeck, Germany.
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158
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Abstract
Gene essentiality is a founding concept of genetics with important implications in both fundamental and applied research. Multiple screens have been performed over the years in bacteria, yeasts, animals and more recently in human cells to identify essential genes. A mounting body of evidence suggests that gene essentiality, rather than being a static and binary property, is both context dependent and evolvable in all kingdoms of life. This concept of a non-absolute nature of gene essentiality changes our fundamental understanding of essential biological processes and could directly affect future treatment strategies for cancer and infectious diseases.
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159
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Golden A. From phenologs to silent suppressors: Identifying potential therapeutic targets for human disease. Mol Reprod Dev 2017; 84:1118-1132. [PMID: 28834577 DOI: 10.1002/mrd.22880] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 08/04/2017] [Indexed: 12/16/2022]
Abstract
Orthologous phenotypes, or phenologs, are seemingly unrelated phenotypes generated by mutations in a conserved set of genes. Phenologs have been widely observed and accepted by those who study model organisms, and allow one to study a set of genes in a model organism to learn more about the function of those genes in other organisms, including humans. At the cellular and molecular level, these conserved genes likely function in a very similar mode, but are doing so in different tissues or cell types and can result in different phenotypic effects. For example, the RAS-RAF-MEK-MAPK pathway in animals is a highly conserved signaling pathway that animals adopted for numerous biological processes, such as vulval induction in Caenorhabditis elegans and cell proliferation in mammalian cells; but this same gene set has been co-opted to function in a variety of cellular contexts. In this review, I give a few examples of how suppressor screens in model organisms (with a emphasis on C. elegans) can identify new genes that function in a conserved pathway in many other organisms. I also demonstrate how the identification of such genes can lead to important insights into mammalian biology. From such screens, an occasional silent suppressor that does not cause a phenotype on its own is found; such suppressors thus make for good candidates as therapeutic targets.
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Affiliation(s)
- Andy Golden
- Laboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland
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160
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Kesselheim A, Ashton E, Bockenhauer D. Potential and pitfalls in the genetic diagnosis of kidney diseases. Clin Kidney J 2017; 10:581-585. [PMID: 28980668 PMCID: PMC5622903 DOI: 10.1093/ckj/sfx075] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 06/13/2017] [Indexed: 12/14/2022] Open
Abstract
Next-generation sequencing has dramatically decreased the cost of gene sequencing, facilitating the simultaneous analysis of multiple genes at the same time; obtaining a genetic result for an individual patient has become much easier. The article by Ars and Torra in this issue of the Clinical Kidney Journal provides examples of the ever-increasing ability to understand a given patient's disease on the molecular level, so that in some cases not only the causative variants in a disease gene are identified, but also potential modifiers in other genes. Yet, with increased sequencing, a large number of variants are discovered that are difficult to interpret. These so-called 'variants of uncertain significance' raise important questions: when and how can pathogenicity be clearly attributed? This is of critical importance, as there are potentially serious consequences attached: decisions about various forms of treatment and even about life and death, such as termination of pregnancy, may hinge on the answer to these questions. Geneticists, thus, need to use the utmost care in the interpretation of identified variants and clinicians must be aware of this problem. We here discuss the potential of genetics to facilitate personalized treatment, but also the pitfalls and how to deal with them.
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Affiliation(s)
- Anne Kesselheim
- Centre for Nephrology, University College London, London, UK
| | - Emma Ashton
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
- North East Thames Regional Genetics Service, Molecular Genetics, London, UK
| | - Detlef Bockenhauer
- Centre for Nephrology, University College London, London, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
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161
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Lacaze P, Ryan J, Woods R, Winship I, McNeil J. Pathogenic variants in the healthy elderly: unique ethical and practical challenges. JOURNAL OF MEDICAL ETHICS 2017; 43:714-722. [PMID: 28341755 PMCID: PMC5629947 DOI: 10.1136/medethics-2016-103967] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 12/20/2016] [Accepted: 02/06/2017] [Indexed: 05/06/2023]
Abstract
: Genetic research into ageing, longevity and late-onset disease is becoming increasingly common. Yet, there is a paucity of knowledge related to clinical actionability and the return of pathogenic variants to otherwise healthy elderly individuals. Whether or not genetic research in the elderly should be managed differently from standard practices adapted for younger populations has not yet been defined. In this article, we provide an overview of ethical and practical challenges in preparing for a genetic study of over 14 000 healthy Australians aged 70 years or older enrolled in the ASPirin in Reducing Events in the Elderly (ASPREE) Healthy Ageing Biobank. At the time of consent, all participants in this study were free of life-threatening illness, cardiovascular disease or cognitive impairment. ASPREE is thus a cohort of healthy elderly individuals with seemingly minimal burden of genetic disease recruited without ascertainment bias. The cohort presents a unique opportunity to address the penetrance of known pathogenic variants in a population without disease symptoms; however, it also raises a number of ethical concerns regarding the interpretation and disclosure of variants with known clinical actionability. Some of the challenges include (a) how to manage the interpretation, disclosure and actioning of pathogenic variants found in otherwise healthy elderly adults without disease symptoms, (b) whether or not to disclose findings for the benefit of family members rather than elderly consented donors themselves, (c) how to manage the return of genetic findings to the elderly individuals who are now in severe cognitive decline or terminal illness, (d) how to ensure quality of information and clinical service upon disclosure of results to this demographic and (e) how to prepare for the insurance implications of disclosing genetic information under Australian law. We discuss these and other dilemmas and propose a defensible plan of management. TRIAL REGISTRATION NUMBER ISRCTN83772183.
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Affiliation(s)
- Paul Lacaze
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, ASPREE - Monash University, Melbourne, Victoria, Australia
| | - Joanne Ryan
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, ASPREE - Monash University, Melbourne, Victoria, Australia
| | - Robyn Woods
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, ASPREE - Monash University, Melbourne, Victoria, Australia
| | - Ingrid Winship
- Genetic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Melbourne, Victoria, Australia
- Department of Medicine, University of Melbourne, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - John McNeil
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, ASPREE - Monash University, Melbourne, Victoria, Australia
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Amorim CEG, Gao Z, Baker Z, Diesel JF, Simons YB, Haque IS, Pickrell J, Przeworski M. The population genetics of human disease: The case of recessive, lethal mutations. PLoS Genet 2017; 13:e1006915. [PMID: 28957316 PMCID: PMC5619689 DOI: 10.1371/journal.pgen.1006915] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2016] [Accepted: 07/09/2017] [Indexed: 01/08/2023] Open
Abstract
Do the frequencies of disease mutations in human populations reflect a simple balance between mutation and purifying selection? What other factors shape the prevalence of disease mutations? To begin to answer these questions, we focused on one of the simplest cases: recessive mutations that alone cause lethal diseases or complete sterility. To this end, we generated a hand-curated set of 417 Mendelian mutations in 32 genes reported to cause a recessive, lethal Mendelian disease. We then considered analytic models of mutation-selection balance in infinite and finite populations of constant sizes and simulations of purifying selection in a more realistic demographic setting, and tested how well these models fit allele frequencies estimated from 33,370 individuals of European ancestry. In doing so, we distinguished between CpG transitions, which occur at a substantially elevated rate, and three other mutation types. Intriguingly, the observed frequency for CpG transitions is slightly higher than expectation but close, whereas the frequencies observed for the three other mutation types are an order of magnitude higher than expected, with a bigger deviation from expectation seen for less mutable types. This discrepancy is even larger when subtle fitness effects in heterozygotes or lethal compound heterozygotes are taken into account. In principle, higher than expected frequencies of disease mutations could be due to widespread errors in reporting causal variants, compensation by other mutations, or balancing selection. It is unclear why these factors would have a greater impact on disease mutations that occur at lower rates, however. We argue instead that the unexpectedly high frequency of disease mutations and the relationship to the mutation rate likely reflect an ascertainment bias: of all the mutations that cause recessive lethal diseases, those that by chance have reached higher frequencies are more likely to have been identified and thus to have been included in this study. Beyond the specific application, this study highlights the parameters likely to be important in shaping the frequencies of Mendelian disease alleles. What determines the frequencies of disease mutations in human populations? To begin to answer this question, we focus on one of the simplest cases: mutations that cause completely recessive, lethal Mendelian diseases. We first review theory about what to expect from mutation and selection in a population of finite size and generate predictions based on simulations using a plausible demographic scenario of recent human evolution. For a highly mutable type of mutation, transitions at CpG sites, we find that the predictions are close to the observed frequencies of recessive lethal disease mutations. For less mutable types, however, predictions substantially under-estimate the observed frequency. We discuss possible explanations for the discrepancy and point to a complication that, to our knowledge, is not widely appreciated: that there exists ascertainment bias in disease mutation discovery. Specifically, we suggest that alleles that have been identified to date are likely the ones that by chance have reached higher frequencies and are thus more likely to have been mapped. More generally, our study highlights the factors that influence the frequencies of Mendelian disease alleles.
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Affiliation(s)
- Carlos Eduardo G. Amorim
- Department of Biological Sciences, Columbia University, New York, NY, United States of America
- CAPES Foundation, Ministry of Education of Brazil, Brasília, DF, Brazil
- * E-mail:
| | - Ziyue Gao
- Howard Hughes Medical Institution, Stanford University, Stanford, CA, United States of America
| | - Zachary Baker
- Department of Systems Biology, Columbia University, New York, NY, United States of America
| | | | - Yuval B. Simons
- Department of Biological Sciences, Columbia University, New York, NY, United States of America
| | - Imran S. Haque
- Counsyl, 180 Kimball Way, South San Francisco, CA, United States of America
| | - Joseph Pickrell
- Department of Biological Sciences, Columbia University, New York, NY, United States of America
- New York Genome Center, New York, NY, United States of America
| | - Molly Przeworski
- Department of Biological Sciences, Columbia University, New York, NY, United States of America
- Department of Systems Biology, Columbia University, New York, NY, United States of America
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163
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Obrador GT, Schultheiss UT, Kretzler M, Langham RG, Nangaku M, Pecoits-Filho R, Pollock C, Rossert J, Correa-Rotter R, Stenvinkel P, Walker R, Yang CW, Fox CS, Köttgen A. Genetic and environmental risk factors for chronic kidney disease. Kidney Int Suppl (2011) 2017; 7:88-106. [PMID: 30675423 DOI: 10.1016/j.kisu.2017.07.004] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
In order to change the current state of chronic kidney disease knowledge and therapeutics, a fundamental improvement in the understanding of genetic and environmental causes of chronic kidney disease is essential. This article first provides an overview of the existing knowledge gaps in our understanding of the genetic and environmental causes of chronic kidney disease, as well as their interactions. The second part of the article formulates goals that should be achieved in order to close these gaps, along with suggested timelines and stakeholders that are to be involved. A better understanding of genetic and environmental factors and their interactions that influence kidney function in healthy and diseased conditions can provide novel insights into renal physiology and pathophysiology and result in the identification of novel therapeutic or preventive targets to tackle the global public health care problem of chronic kidney disease.
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Affiliation(s)
- Gregorio T Obrador
- Department of Epidemiology, Biostatistics and Public Health, Universidad Panamericana School of Medicine, Mexico City, Mexico
| | - Ulla T Schultheiss
- Institute of Genetic Epidemiology, Medical Center and Faculty of Medicine-University of Freiburg, Freiburg, Germany.,Renal Division, Department of Medicine IV, Medical Center-University of Freiburg, Faculty of Medicine, Freiburg, Germany
| | - Matthias Kretzler
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Robyn G Langham
- Monash Rural Health, Monash University, Clayton VIC, Australia
| | - Masaomi Nangaku
- Department of Hemodialysis and Apheresis, Division of Nephrology and Endocrinology, University of Tokyo Graduate School of Medicine, Tokyo, Japan
| | - Roberto Pecoits-Filho
- Department of Internal Medicine, School of Medicine, Pontificia Universidade Catolica do Paraná, Curitiba, Brazil
| | - Carol Pollock
- Kolling Institute of Medical Research, University of Sydney, Sydney, NSW, Australia
| | | | - Ricardo Correa-Rotter
- Department of Nephrology and Mineral Metabolism, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zuibrán, Mexico City, Mexico
| | - Peter Stenvinkel
- Division of Renal Medicine, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Robert Walker
- Department of Medicine, University of Otago, Dunedin, New Zealand
| | - Chih-Wei Yang
- Kidney Research Center, Department of Nephrology, Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Caroline S Fox
- Genetics and Pharmacogenomics, Merck Research Laboratories, Boston, Massachusetts, USA
| | - Anna Köttgen
- Institute of Genetic Epidemiology, Medical Center and Faculty of Medicine-University of Freiburg, Freiburg, Germany
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164
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Cheng SJ, Shi FY, Liu H, Ding Y, Jiang S, Liang N, Gao G. Accurately annotate compound effects of genetic variants using a context-sensitive framework. Nucleic Acids Res 2017; 45:e82. [PMID: 28158838 PMCID: PMC5449550 DOI: 10.1093/nar/gkx041] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 01/24/2017] [Indexed: 02/07/2023] Open
Abstract
In genomics, effectively identifying the biological effects of genetic variants is crucial. Current methods handle each variant independently, assuming that each variant acts in a context-free manner. However, variants within the same gene may interfere with each other, producing combinational (compound) rather than individual effects. In this work, we introduce COPE, a gene-centric variant annotation tool that integrates the entire sequential context in evaluating the functional effects of intra-genic variants. Applying COPE to the 1000 Genomes dataset, we identified numerous cases of multiple-variant compound effects that frequently led to false-positive and false-negative loss-of-function calls by conventional variant-centric tools. Specifically, 64 disease-causing mutations were identified to be rescued in a specific genomic context, thus potentially contributing to the buffering effects for highly penetrant deleterious mutations. COPE is freely available for academic use at http://cope.cbi.pku.edu.cn.
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Affiliation(s)
- Si-Jin Cheng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Center for Bioinformatics, Peking University, Beijing 100871, People's Republic of China
| | - Fang-Yuan Shi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Center for Bioinformatics, Peking University, Beijing 100871, People's Republic of China
| | - Huan Liu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Center for Bioinformatics, Peking University, Beijing 100871, People's Republic of China
| | - Yang Ding
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Center for Bioinformatics, Peking University, Beijing 100871, People's Republic of China
| | - Shuai Jiang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Center for Bioinformatics, Peking University, Beijing 100871, People's Republic of China
| | - Nan Liang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Center for Bioinformatics, Peking University, Beijing 100871, People's Republic of China
| | - Ge Gao
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Center for Bioinformatics, Peking University, Beijing 100871, People's Republic of China
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165
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Dimitriadou E, Melotte C, Debrock S, Esteki MZ, Dierickx K, Voet T, Devriendt K, de Ravel T, Legius E, Peeraer K, Meuleman C, Vermeesch JR. Principles guiding embryo selection following genome-wide haplotyping of preimplantation embryos. Hum Reprod 2017; 32:687-697. [PMID: 28158716 DOI: 10.1093/humrep/dex011] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 01/13/2017] [Indexed: 12/17/2022] Open
Abstract
STUDY QUESTION How to select and prioritize embryos during PGD following genome-wide haplotyping? SUMMARY ANSWER In addition to genetic disease-specific information, the embryo selected for transfer is based on ranking criteria including the existence of mitotic and/or meiotic aneuploidies, but not carriership of mutations causing recessive disorders. WHAT IS KNOWN ALREADY Embryo selection for monogenic diseases has been mainly performed using targeted disease-specific assays. Recently, these targeted approaches are being complemented by generic genome-wide genetic analysis methods such as karyomapping or haplarithmisis, which are based on genomic haplotype reconstruction of cell(s) biopsied from embryos. This provides not only information about the inheritance of Mendelian disease alleles but also about numerical and structural chromosome anomalies and haplotypes genome-wide. Reflections on how to use this information in the diagnostic laboratory are lacking. STUDY DESIGN, SIZE, DURATION We present the results of the first 101 PGD cycles (373 embryos) using haplarithmisis, performed in the Centre for Human Genetics, UZ Leuven. The questions raised were addressed by a multidisciplinary team of clinical geneticist, fertility specialists and ethicists. PARTICIPANTS/MATERIALS, SETTING, METHODS Sixty-three couples enrolled in the genome-wide haplotyping-based PGD program. Families presented with either inherited genetic variants causing known disorders and/or chromosomal rearrangements that could lead to unbalanced translocations in the offspring. MAIN RESULTS AND THE ROLE OF CHANCE Embryos were selected based on the absence or presence of the disease allele, a trisomy or other chromosomal abnormality leading to known developmental disorders. In addition, morphologically normal Day 5 embryos were prioritized for transfer based on the presence of other chromosomal imbalances and/or carrier information. LIMITATIONS, REASONS FOR CAUTION Some of the choices made and principles put forward are specific for cleavage-stage-based genetic testing. The proposed guidelines are subject to continuous update based on the accumulating knowledge from the implementation of genome-wide methods for PGD in many different centers world-wide as well as the results of ongoing scientific research. WIDER IMPLICATIONS OF THE FINDINGS Our embryo selection principles have a profound impact on the organization of PGD operations and on the information that is transferred among the genetic unit, the fertility clinic and the patients. These principles are also important for the organization of pre- and post-counseling and influence the interpretation and reporting of preimplantation genotyping results. As novel genome-wide approaches for embryo selection are revolutionizing the field of reproductive genetics, national and international discussions to set general guidelines are warranted. STUDY FUNDING/COMPETING INTEREST(S) The European Union's Research and Innovation funding programs FP7-PEOPLE-2012-IAPP SARM: 324509 and Horizon 2020 WIDENLIFE: 692065 to J.R.V., T.V., E.D. and M.Z.E. J.R.V., T.V. and M.Z.E. have patents ZL910050-PCT/EP2011/060211-WO/2011/157846 ('Methods for haplotyping single cells') with royalties paid and ZL913096-PCT/EP2014/068315-WO/2015/028576 ('Haplotyping and copy-number typing using polymorphic variant allelic frequencies') with royalties paid, licensed to Cartagenia (Agilent technologies). J.R.V. also has a patent ZL91 2076-PCT/EP20 one 3/070858 ('High throughout genotyping by sequencing') with royalties paid. TRIAL REGISTRATION NUMBER N/A.
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Affiliation(s)
- Eftychia Dimitriadou
- Department of Human Genetics, Centre for Human Genetics, University Hospitals Leuven, O&N I Herestraat 49 - box 602, KU Leuven, 3000 Leuven, Belgium
| | - Cindy Melotte
- Department of Human Genetics, Centre for Human Genetics, University Hospitals Leuven, O&N I Herestraat 49 - box 602, KU Leuven, 3000 Leuven, Belgium
| | - Sophie Debrock
- University Hospitals Leuven, Leuven University Fertility Center, Herestraat 49, 3000 Leuven, Belgium
| | - Masoud Zamani Esteki
- Department of Human Genetics, Centre for Human Genetics, University Hospitals Leuven, O&N I Herestraat 49 - box 602, KU Leuven, 3000 Leuven, Belgium
| | - Kris Dierickx
- Centre for Biomedical Ethics and Law, KU Leuven, 3000 Leuven, Belgium
| | - Thierry Voet
- Department of Human Genetics, Centre for Human Genetics, University Hospitals Leuven, O&N I Herestraat 49 - box 602, KU Leuven, 3000 Leuven, Belgium.,Single-cell Genomics Centre, Welcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Koen Devriendt
- Department of Human Genetics, Centre for Human Genetics, University Hospitals Leuven, O&N I Herestraat 49 - box 602, KU Leuven, 3000 Leuven, Belgium
| | - Thomy de Ravel
- Department of Human Genetics, Centre for Human Genetics, University Hospitals Leuven, O&N I Herestraat 49 - box 602, KU Leuven, 3000 Leuven, Belgium
| | - Eric Legius
- Department of Human Genetics, Centre for Human Genetics, University Hospitals Leuven, O&N I Herestraat 49 - box 602, KU Leuven, 3000 Leuven, Belgium
| | - Karen Peeraer
- University Hospitals Leuven, Leuven University Fertility Center, Herestraat 49, 3000 Leuven, Belgium
| | - Christel Meuleman
- University Hospitals Leuven, Leuven University Fertility Center, Herestraat 49, 3000 Leuven, Belgium
| | - Joris Robert Vermeesch
- Department of Human Genetics, Centre for Human Genetics, University Hospitals Leuven, O&N I Herestraat 49 - box 602, KU Leuven, 3000 Leuven, Belgium
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166
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Abstract
The variable penetrance of pathogenic variants (PVs) represents a major challenge to the field of human genetics, often complicating clinical decision-making and risk management. Nonpenetrance, the detection of PVs in the absence of disease manifestation, is a common phenomenon, yet, we know very little about the underlying factors, which may protect some individuals and not others. Placing a new focus on the genomic study of the healthy elderly may be pivotal for advancing our understanding of penetrance. Studying those who remain unaffected late into life, despite harboring known genetic risk variants, could provide important insights into disease mechanisms and ultimately inform clinical care, yet, it has received relatively little attention as a research strategy. The ever increasing use of sequencing technology is further driving the requirement to understand the penetrance of ascertained variants. The ASPREE Biobank of Healthy Ageing provides a unique opportunity to address this area of need. DNA has been collected from a cohort of over 14,000 healthy elderly individuals aged 70 years or older enrolled in an aspirin clinical trial. The ASPREE cohort represents a healthy reference population ascertained without the typical biases of a genetic study. The cohort is depleted of expressed monogenetic disease, yet will contain hundreds of elderly individuals with known PVs in clinically actionable genes. Investigating this population along with other cohorts of the healthy elderly will provide critical new knowledge into the penetrance of actionable variants as a foundation for informing clinical care.
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Affiliation(s)
- Paul Lacaze
- 1 Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
| | - Ingrid Winship
- 2 Genetic Medicine and Family Cancer Clinic, Royal Melbourne Hospital , Melbourne, Australia .,3 Department of Medicine, University of Melbourne , Royal Melbourne Hospital, Melbourne, Australia
| | - John McNeil
- 1 Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
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167
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Abstract
This commentary will focus on how we can use our knowledge about the complexity of human disease and its pathogenesis to identify novel approaches to therapy. We know that even for single gene Mendelian disorders, patients with identical mutations often have different presentations and outcomes. This lack of genotype-phenotype correlation led us and others to examine the roles of modifier genes in the context of biological networks. These investigations have utilized vertebrate and invertebrate model organisms. Since one of the goals of research on modifier genes and networks is to identify novel therapeutic targets, the challenges to patient access and compliance because of the high costs of medications for rare genetic diseases must be recognized. A recent article explored protective modifiers, including plastin 3 (PLS3) and coronin 1C (CORO1C), in spinal muscular atrophy (SMA). SMA is an autosomal recessive deficit of survival motor neuron protein (SMN) caused by mutations in SMN1. However, the severity of SMA is determined primarily by the number of SMN2 copies, and this results in significant phenotypic variability. PLS3 was upregulated in siblings who were asymptomatic compared with those who had SMA2 or SMA3, but identical homozygous SMN1 deletions and equal numbers of SMN2 copies. CORO1C was identified by interrogation of the PLS3 interactome. Overexpression of these proteins rescued endocytosis in SMA models. In addition, antisense RNA for upregulation of SMN2 protein expression is being developed as another way of modifying the SMA phenotype. These investigations suggest the practical application of protective modifiers to rescue SMA phenotypes. Other examples of the potential therapeutic value of novel protective modifiers will be discussed, including in Duchenne muscular dystrophy and glycerol kinase deficiency. This work shows that while we live in an exciting era of genomic sequencing, a functional understanding of biology, the impact of its disruption, and possibilities for its repair have never been more important as we search for new therapies.
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Affiliation(s)
- Edward R B McCabe
- March of Dimes Foundation, United States; Department of Pediatrics, David Geffen School of Medicine at UCLA, United States.
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168
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Torkamani A, Andersen KG, Steinhubl SR, Topol EJ. High-Definition Medicine. Cell 2017; 170:828-843. [PMID: 28841416 DOI: 10.1016/j.cell.2017.08.007] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 07/10/2017] [Accepted: 08/04/2017] [Indexed: 12/13/2022]
Abstract
The foundation for a new era of data-driven medicine has been set by recent technological advances that enable the assessment and management of human health at an unprecedented level of resolution-what we refer to as high-definition medicine. Our ability to assess human health in high definition is enabled, in part, by advances in DNA sequencing, physiological and environmental monitoring, advanced imaging, and behavioral tracking. Our ability to understand and act upon these observations at equally high precision is driven by advances in genome editing, cellular reprogramming, tissue engineering, and information technologies, especially artificial intelligence. In this review, we will examine the core disciplines that enable high-definition medicine and project how these technologies will alter the future of medicine.
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Affiliation(s)
- Ali Torkamani
- The Scripps Translational Science Institute, La Jolla, CA 92037, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| | - Kristian G Andersen
- The Scripps Translational Science Institute, La Jolla, CA 92037, USA; Department of Immunology and Microbial Science, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Steven R Steinhubl
- The Scripps Translational Science Institute, La Jolla, CA 92037, USA; Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Eric J Topol
- The Scripps Translational Science Institute, La Jolla, CA 92037, USA; Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
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169
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Sgarbieri VC, Pacheco MTB. Healthy human aging: intrinsic and environmental factors. BRAZILIAN JOURNAL OF FOOD TECHNOLOGY 2017. [DOI: 10.1590/1981-6723.00717] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Abstract This review is an attempt to compile current knowledge on concepts and transformations that occur naturally in the human body and that characterize what is defined today as biological aging with quality of life and longevity. Many authors define natural aging as a continuous and uninterrupted process, which occurs in the human body causing structural and functional changes, classified as: cumulative, progressive, intrinsic and deleterious (CUPID). Usually these changes begin early in life and culminate in physical death. Genetic, chemical and biochemical changes lead to progressive degeneration of cells, tissues and organs, body systems and the organism as a whole, leading to loss of structures and functions due to aging. All these changes were discussed in some detail in the review here presented. We concluded that aging is not genetically determined, resulting in the accumulation of cellular and tissue damage, particularly in chromatin and DNA within cells, in addition to structural and bioactive proteins that command the general metabolism. Environmental factors such as feeding (nutrition) and lifestyle were also discussed.
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170
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Vaz-de-Macedo C, Harper J. A closer look at expanded carrier screening from a PGD perspective. Hum Reprod 2017; 32:1951-1956. [DOI: 10.1093/humrep/dex272] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 08/12/2017] [Indexed: 01/28/2023] Open
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171
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Feiglin A, Allen BK, Kohane IS, Kong SW. Comprehensive Analysis of Tissue-wide Gene Expression and Phenotype Data Reveals Tissues Affected in Rare Genetic Disorders. Cell Syst 2017; 5:140-148.e2. [PMID: 28822752 PMCID: PMC5928498 DOI: 10.1016/j.cels.2017.06.016] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 03/21/2017] [Accepted: 06/29/2017] [Indexed: 01/23/2023]
Abstract
Linking putatively pathogenic variants to the tissues they affect is necessary for determining the correct diagnostic workup and therapeutic regime in undiagnosed patients. Here, we explored how gene expression across healthy tissues can be used to infer this link. We integrated 6,665 tissue-wide transcriptomes with genetic disorder knowledge bases covering 3,397 diseases. Receiver-operating characteristics (ROC) analysis using expression levels in each tissue and across tissues indicated significant but modest associations between elevated expression and phenotype for most tissues (maximum area under ROC curve = 0.69). At extreme elevation, associations were marked. Upregulation of disease genes in affected tissues was pronounced for genes associated with autosomal dominant over recessive disorders. Pathways enriched for genes expressed and associated with phenotypes highlighted tissue functionality, including lipid metabolism in spleen and DNA repair in adipose tissue. These results suggest features useful for evaluating the likelihood of particular tissue manifestations in genetic disorders. The web address of an interactive platform integrating these data is provided.
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Affiliation(s)
- Ariel Feiglin
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Bryce K Allen
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Isaac S Kohane
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.
| | - Sek Won Kong
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
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172
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Krier JB, Kalia SS, Green RC. Genomic sequencing in clinical practice: applications, challenges, and opportunities. DIALOGUES IN CLINICAL NEUROSCIENCE 2017. [PMID: 27757064 PMCID: PMC5067147 DOI: 10.31887/dcns.2016.18.3/jkrier] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The development of massively parallel sequencing (or next-generation sequencing) has facilitated a rapid implementation of genomic sequencing in clinical medicine. Genomic sequencing (GS) is now an essential tool for evaluating rare disorders, identifying therapeutic targets in neoplasms, and screening for prenatal aneuploidy. Emerging applications, such as GS for preconception carrier screening and predisposition screening in healthy individuals, are being explored in research settings and utilized by members of the public eager to incorporate genomic information into their health management. The rapid pace of adoption has created challenges for all stakeholders in clinical GS, from standardizing variant interpretation approaches in clinical molecular laboratories to ensuring that nongeneticist clinicians are prepared for new types of clinical information. Clinical GS faces a pivotal moment, as the vast potential of new quantities and types of data enable further clinical innovation and complicated implementation questions continue to be resolved.
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Affiliation(s)
- Joel B Krier
- Genomes2People Research Program, Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA
| | | | - Robert C Green
- Genomes2People Research Program, Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, Massachusetts, USA; Harvard Medical School, Boston, Massachusetts, USA; Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
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173
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Riordan JD, Nadeau JH. From Peas to Disease: Modifier Genes, Network Resilience, and the Genetics of Health. Am J Hum Genet 2017; 101:177-191. [PMID: 28777930 PMCID: PMC5544383 DOI: 10.1016/j.ajhg.2017.06.004] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Phenotypes are rarely consistent across genetic backgrounds and environments, but instead vary in many ways depending on allelic variants, unlinked genes, epigenetic factors, and environmental exposures. In the extreme, individuals carrying the same causal DNA sequence variant but on different backgrounds can be classified as having distinct conditions. Similarly, some individuals that carry disease alleles are nevertheless healthy despite affected family members in the same environment. These genetic background effects often result from the action of so-called "modifier genes" that modulate the phenotypic manifestation of target genes in an epistatic manner. While complicating the prospects for gene discovery and the feasibility of mechanistic studies, such effects are opportunities to gain a deeper understanding of gene interaction networks that provide organismal form and function as well as resilience to perturbation. Here, we review the principles of modifier genetics and assess progress in studies of modifier genes and their targets in both simple and complex traits. We propose that modifier effects emerge from gene interaction networks whose structure and function vary with genetic background and argue that these effects can be exploited as safe and effective ways to prevent, stabilize, and reverse disease and dysfunction.
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Affiliation(s)
- Jesse D Riordan
- Pacific Northwest Research Institute, Seattle, WA 98122, USA.
| | - Joseph H Nadeau
- Pacific Northwest Research Institute, Seattle, WA 98122, USA.
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174
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Abstract
Several recent studies in a number of model systems including zebrafish, Arabidopsis, and mouse have revealed phenotypic differences between knockouts (i.e., mutants) and knockdowns (e.g., antisense-treated animals). These differences have been attributed to a number of reasons including off-target effects of the antisense reagents. An alternative explanation was recently proposed based on a zebrafish study reporting that genetic compensation was observed in egfl7 mutant but not knockdown animals. Dosage compensation was first reported in Drosophila in 1932, and genetic compensation in response to a gene knockout was first reported in yeast in 1969. Since then, genetic compensation has been documented many times in a number of model organisms; however, our understanding of the underlying molecular mechanisms remains limited. In this review, we revisit studies reporting genetic compensation in higher eukaryotes and outline possible molecular mechanisms, which may include both transcriptional and posttranscriptional processes.
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Affiliation(s)
- Mohamed A. El-Brolosy
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Didier Y. R. Stainier
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
- * E-mail:
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175
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Ultra-sensitive Sequencing Identifies High Prevalence of Clonal Hematopoiesis-Associated Mutations throughout Adult Life. Am J Hum Genet 2017; 101:50-64. [PMID: 28669404 DOI: 10.1016/j.ajhg.2017.05.013] [Citation(s) in RCA: 175] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 05/18/2017] [Indexed: 12/13/2022] Open
Abstract
Clonal hematopoiesis results from somatic mutations in hematopoietic stem cells, which give an advantage to mutant cells, driving their clonal expansion and potentially leading to leukemia. The acquisition of clonal hematopoiesis-driver mutations (CHDMs) occurs with normal aging and these mutations have been detected in more than 10% of individuals ≥65 years. We aimed to examine the prevalence and characteristics of CHDMs throughout adult life. We developed a targeted re-sequencing assay combining high-throughput with ultra-high sensitivity based on single-molecule molecular inversion probes (smMIPs). Using smMIPs, we screened more than 100 loci for CHDMs in more than 2,000 blood DNA samples from population controls between 20 and 69 years of age. Loci screened included 40 regions known to drive clonal hematopoiesis when mutated and 64 novel candidate loci. We identified 224 somatic mutations throughout our cohort, of which 216 were coding mutations in known driver genes (DNMT3A, JAK2, GNAS, TET2, and ASXL1), including 196 point mutations and 20 indels. Our assay's improved sensitivity allowed us to detect mutations with variant allele frequencies as low as 0.001. CHDMs were identified in more than 20% of individuals 60 to 69 years of age and in 3% of individuals 20 to 29 years of age, approximately double the previously reported prevalence despite screening a limited set of loci. Our findings support the occurrence of clonal hematopoiesis-associated mutations as a widespread mechanism linked with aging, suggesting that mosaicism as a result of clonal evolution of cells harboring somatic mutations is a universal mechanism occurring at all ages in healthy humans.
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176
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Rehman AU, Friedman TB, Griffith AJ. Unresolved questions regarding human hereditary deafness. Oral Dis 2017; 23:551-558. [PMID: 27259978 PMCID: PMC5136515 DOI: 10.1111/odi.12516] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 05/27/2016] [Accepted: 05/30/2016] [Indexed: 01/18/2023]
Abstract
Human hearing loss is a common neurosensory disorder about which many basic research and clinically relevant questions are unresolved. This review on hereditary deafness focuses on three examples considered at first glance to be uncomplicated, however, upon inspection, are enigmatic and ripe for future research efforts. The three examples of clinical and genetic complexities are drawn from studies of (i) Pendred syndrome/DFNB4 (PDS, OMIM 274600), (ii) Perrault syndrome (deafness and infertility) due to mutations of CLPP (PRTLS3, OMIM 614129), and (iii) the unexplained extensive clinical variability associated with TBC1D24 mutations. At present, it is unknown how different mutations of TBC1D24 cause non-syndromic deafness (DFNB86, OMIM 614617), epilepsy (OMIM 605021), epilepsy with deafness, or DOORS syndrome (OMIM 220500) that is characterized by deafness, onychodystrophy (alteration of toenail or fingernail morphology), osteodystrophy (defective development of bone), mental retardation, and seizures. A comprehensive understanding of the multifaceted roles of each gene associated with human deafness is expected to provide future opportunities for restoration as well as preservation of normal hearing.
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Affiliation(s)
- A U Rehman
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, USA
| | - T B Friedman
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, USA
| | - A J Griffith
- Otolaryngology Branch, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, USA
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177
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van Leeuwen J, Pons C, Boone C, Andrews BJ. Mechanisms of suppression: The wiring of genetic resilience. Bioessays 2017; 39. [PMID: 28582599 DOI: 10.1002/bies.201700042] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Recent analysis of genome sequences has identified individuals that are healthy despite carrying severe disease-associated mutations. A possible explanation is that these individuals carry a second genomic perturbation that can compensate for the detrimental effects of the disease allele, a phenomenon referred to as suppression. In model organisms, suppression interactions are generally divided into two classes: genomic suppressors which are secondary mutations in the genome that bypass a mutant phenotype, and dosage suppression interactions in which overexpression of a suppressor gene rescues a mutant phenotype. Here, we describe the general properties of genomic and dosage suppression, with an emphasis on the budding yeast. We propose that suppression interactions between genetic variants are likely relevant for determining the penetrance of human traits. Consequently, an understanding of suppression mechanisms may guide the discovery of protective variants in healthy individuals that carry disease alleles, which could direct the rational design of new therapeutics.
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Affiliation(s)
- Jolanda van Leeuwen
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Carles Pons
- Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute for Science and Technology, Barcelona, Catalonia, Spain
| | - Charles Boone
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Brenda J Andrews
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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178
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Kammenga JE. The background puzzle: how identical mutations in the same gene lead to different disease symptoms. FEBS J 2017; 284:3362-3373. [PMID: 28390082 DOI: 10.1111/febs.14080] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Revised: 03/31/2017] [Accepted: 04/05/2017] [Indexed: 01/05/2023]
Abstract
Identical disease-causing mutations can lead to different symptoms in different people. The reason for this has been a puzzling problem for geneticists. Differential penetrance and expressivity of mutations has been observed within individuals with different and similar genetic backgrounds. Attempts have been made to uncover the underlying mechanisms that determine differential phenotypic effects of identical mutations through studies of model organisms. From these studies evidence is accumulating that to understand disease mechanism or predict disease prevalence, an understanding of the influence of genetic background is as important as the putative disease-causing mutations of relatively large effect. This review highlights current insights into phenotypic variation due to gene interactions, epigenetics and stochasticity in model organisms, and discusses their importance for understanding the mutational effect on disease symptoms.
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Affiliation(s)
- Jan E Kammenga
- Laboratory of Nematology, Wageningen University, The Netherlands
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179
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Matsui T, Lee JT, Ehrenreich IM. Genetic suppression: Extending our knowledge from lab experiments to natural populations. Bioessays 2017; 39. [PMID: 28471485 DOI: 10.1002/bies.201700023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Many mutations have deleterious phenotypic effects that can be alleviated by suppressor mutations elsewhere in the genome. High-throughput approaches have facilitated the large-scale identification of these suppressors and have helped shed light on core functional mechanisms that give rise to suppression. Following reports that suppression occurs naturally within species, it is important to determine how our understanding of this phenomenon based on lab experiments extends to genetically diverse natural populations. Although suppression is typically mediated by individual genetic changes in lab experiments, recent studies have shown that suppression in natural populations can involve combinations of genetic variants. This difference in complexity suggests that sets of variants can exhibit similar functional effects to individual suppressors found in lab experiments. In this review, we discuss how characterizing the way in which these variants jointly lead to suppression could provide important insights into the genotype-phenotype map that are relevant to evolution and health.
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Affiliation(s)
- Takeshi Matsui
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Jonathan T Lee
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Ian M Ehrenreich
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
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180
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Assessment of the ExAC data set for the presence of individuals with pathogenic genotypes implicated in severe Mendelian pediatric disorders. Genet Med 2017; 19:1300-1308. [PMID: 28471432 PMCID: PMC5729344 DOI: 10.1038/gim.2017.50] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 03/13/2017] [Indexed: 12/26/2022] Open
Abstract
Purpose We analyzed the Exome Aggregation Consortium (ExAC) data set for the presence of individuals with pathogenic genotypes implicated in Mendelian pediatric disorders. Methods ClinVar likely/pathogenic variants supported by at least one peer-reviewed publication were assessed within the ExAC database to identify individuals expected to exhibit a childhood disorder based on concordance with disease inheritance modes: heterozygous (for dominant), homozygous (for recessive) or hemizygous (for X-linked recessive conditions). Variants from 924 genes reported to cause Mendelian childhood disorders were considered. Results We identified ExAC individuals with candidate pathogenic genotypes for 190 previously published likely/pathogenic variants in 128 genes. After curation, we determined that 113 of the variants have sufficient support for pathogenicity and identified 1,717 ExAC individuals (~2.8% of the ExAC population) with corresponding possible/disease-associated genotypes implicated in rare Mendelian disorders, ranging from mild (e.g., due to SCN2A deficiency) to severe pediatric conditions (e.g., due to FGFR1 deficiency). Conclusion Large-scale sequencing projects and data aggregation consortia provide unprecedented opportunities to determine the prevalence of pathogenic genotypes in unselected populations. This knowledge is crucial for understanding the penetrance of disease-associated variants, phenotypic variability, somatic mosaicism, as well as published literature curation for variant classification procedures and predicted clinical outcomes.
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181
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Naslavsky MS, Yamamoto GL, Almeida TF, Ezquina SAM, Sunaga DY, Pho N, Bozoklian D, Sandberg TOM, Brito LA, Lazar M, Bernardo DV, Amaro E, Duarte YAO, Lebrão ML, Passos‐Bueno MR, Zatz M. Exomic variants of an elderly cohort of Brazilians in the ABraOM database. Hum Mutat 2017; 38:751-763. [DOI: 10.1002/humu.23220] [Citation(s) in RCA: 149] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 03/14/2017] [Accepted: 03/19/2017] [Indexed: 01/03/2023]
Affiliation(s)
- Michel Satya Naslavsky
- Human Genome and Stem Cell Research Center Biosciences Institute, University of São Paulo São Paulo Brazil
- Hospital Israelita Albert Einstein São Paulo Brazil
| | - Guilherme Lopes Yamamoto
- Human Genome and Stem Cell Research Center Biosciences Institute, University of São Paulo São Paulo Brazil
- Department of Clinical Genetics Children's Hospital Medical School University of São Paulo São Paulo Brazil
| | - Tatiana Ferreira Almeida
- Human Genome and Stem Cell Research Center Biosciences Institute, University of São Paulo São Paulo Brazil
| | - Suzana A. M. Ezquina
- Human Genome and Stem Cell Research Center Biosciences Institute, University of São Paulo São Paulo Brazil
| | - Daniele Yumi Sunaga
- Human Genome and Stem Cell Research Center Biosciences Institute, University of São Paulo São Paulo Brazil
| | - Nam Pho
- Department of Biomedical Informatics Harvard Medical School Boston Massachusetts
| | - Daniel Bozoklian
- Human Genome and Stem Cell Research Center Biosciences Institute, University of São Paulo São Paulo Brazil
| | | | - Luciano Abreu Brito
- Human Genome and Stem Cell Research Center Biosciences Institute, University of São Paulo São Paulo Brazil
| | - Monize Lazar
- Human Genome and Stem Cell Research Center Biosciences Institute, University of São Paulo São Paulo Brazil
| | - Danilo Vicensotto Bernardo
- Laboratório de Estudos em Antropologia Biológica Bioarqueologia e Evolução Humana, Instituto de Ciências Humanas e da Informação, Universidade Federal do Rio Grande Rio Grande Rio Grande de Sul Brazil
| | - Edson Amaro
- Hospital Israelita Albert Einstein São Paulo Brazil
- Radiology Institute Medical School, University of São Paulo São Paulo Brazil
| | - Yeda A. O. Duarte
- Department of Epidemiology Public Health School University of São Paulo São Paulo Brazil
- School of Nursing University of São Paulo São Paulo Brazil
| | - Maria Lúcia Lebrão
- Department of Epidemiology Public Health School University of São Paulo São Paulo Brazil
| | - Maria Rita Passos‐Bueno
- Human Genome and Stem Cell Research Center Biosciences Institute, University of São Paulo São Paulo Brazil
| | - Mayana Zatz
- Human Genome and Stem Cell Research Center Biosciences Institute, University of São Paulo São Paulo Brazil
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182
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Woodbury-Smith M, Nicolson R, Zarrei M, Yuen RKC, Walker S, Howe J, Uddin M, Hoang N, Buchanan JA, Chrysler C, Thompson A, Szatmari P, Scherer SW. Variable phenotype expression in a family segregating microdeletions of the NRXN1 and MBD5 autism spectrum disorder susceptibility genes. NPJ Genom Med 2017. [PMID: 28649445 PMCID: PMC5482711 DOI: 10.1038/s41525-017-0020-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Autism spectrum disorder is a developmental condition of early childhood onset, which impacts socio-communicative functioning and is principally genetic in etiology. Currently, more than 50 genomic loci are deemed to be associated with susceptibility to autism spectrum disorder, showing de novo and inherited unbalanced copy number variants and smaller insertions and deletions (indels), more complex structural variants, as well as single-nucleotide variants deemed of pathological significance. However, the phenotypes associated with many of these genes are variable, and penetrance is largely unelaborated in clinical descriptions. This case report describes a family harboring two copy number variant microdeletions, which affect regions of NRXN1 and MBD5—each well-established in association with risk of autism spectrum disorder and other neurodevelopmental disorders. Although each copy number variant would likely be categorized as pathologically significant, both genomic alterations are transmitted in this family from an unaffected father to the proband, and shared by an unaffected sibling. This family case illustrates the importance of recognizing that phenotype can vary among exon overlapping variants of the same gene, and the need to evaluate penetrance of such variants in order to properly inform on risks.
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Affiliation(s)
- Marc Woodbury-Smith
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON, Canada.,Program in Genetics and Genome Biology, The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Rob Nicolson
- Department of Psychiatry, University of Western Ontario, London, ON, Canada
| | - Mehdi Zarrei
- Program in Genetics and Genome Biology, The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Ryan K C Yuen
- Program in Genetics and Genome Biology, The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Susan Walker
- Program in Genetics and Genome Biology, The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Jennifer Howe
- Program in Genetics and Genome Biology, The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Mohammed Uddin
- Program in Genetics and Genome Biology, The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Ny Hoang
- Autism Research Unit, The Hospital for Sick Children, Toronto, ON, Canada
| | - Janet A Buchanan
- Program in Genetics and Genome Biology, The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Christina Chrysler
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON, Canada
| | - Ann Thompson
- Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON, Canada
| | - Peter Szatmari
- Centre for Addiction and Mental Health, The Hospital for Sick Children & University of Toronto, Toronto, ON, Canada
| | - Stephen W Scherer
- Program in Genetics and Genome Biology, The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada.,McLaughlin Centre and Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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183
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van Leeuwen J, Pons C, Mellor JC, Yamaguchi TN, Friesen H, Koschwanez J, Ušaj MM, Pechlaner M, Takar M, Ušaj M, VanderSluis B, Andrusiak K, Bansal P, Baryshnikova A, Boone CE, Cao J, Cote A, Gebbia M, Horecka G, Horecka I, Kuzmin E, Legro N, Liang W, van Lieshout N, McNee M, San Luis BJ, Shaeri F, Shuteriqi E, Sun S, Yang L, Youn JY, Yuen M, Costanzo M, Gingras AC, Aloy P, Oostenbrink C, Murray A, Graham TR, Myers CL, Andrews BJ, Roth FP, Boone C. Exploring genetic suppression interactions on a global scale. Science 2017; 354:354/6312/aag0839. [PMID: 27811238 DOI: 10.1126/science.aag0839] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Accepted: 10/04/2016] [Indexed: 12/21/2022]
Abstract
Genetic suppression occurs when the phenotypic defects caused by a mutation in a particular gene are rescued by a mutation in a second gene. To explore the principles of genetic suppression, we examined both literature-curated and unbiased experimental data, involving systematic genetic mapping and whole-genome sequencing, to generate a large-scale suppression network among yeast genes. Most suppression pairs identified novel relationships among functionally related genes, providing new insights into the functional wiring diagram of the cell. In addition to suppressor mutations, we identified frequent secondary mutations,in a subset of genes, that likely cause a delay in the onset of stationary phase, which appears to promote their enrichment within a propagating population. These findings allow us to formulate and quantify general mechanisms of genetic suppression.
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Affiliation(s)
- Jolanda van Leeuwen
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Carles Pons
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, 200 Union Street, Minneapolis, MN 55455, USA.,Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute for Science and Technology, Barcelona, Catalonia, Spain
| | - Joseph C Mellor
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada
| | - Takafumi N Yamaguchi
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada.,Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Helena Friesen
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - John Koschwanez
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - Mojca Mattiazzi Ušaj
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Maria Pechlaner
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Mehmet Takar
- Department of Biological Sciences, Vanderbilt University, 1161 21st Avenue South, Nashville, TN 37232, USA
| | - Matej Ušaj
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Benjamin VanderSluis
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, 200 Union Street, Minneapolis, MN 55455, USA
| | - Kerry Andrusiak
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada.,Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Pritpal Bansal
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada
| | - Anastasia Baryshnikova
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Claire E Boone
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Jessica Cao
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Atina Cote
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada
| | - Marinella Gebbia
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada
| | - Gene Horecka
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Ira Horecka
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Elena Kuzmin
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada.,Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Nicole Legro
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Wendy Liang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Natascha van Lieshout
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada.,Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Margaret McNee
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Bryan-Joseph San Luis
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Fatemeh Shaeri
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada
| | - Ermira Shuteriqi
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Song Sun
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Lu Yang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Ji-Young Youn
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada
| | - Michael Yuen
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Michael Costanzo
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada.,Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Patrick Aloy
- Institute for Research in Biomedicine (IRB Barcelona), the Barcelona Institute for Science and Technology, Barcelona, Catalonia, Spain.,Institució Catalana de Recerca i Estudis Avançats, Barcelona, Catalonia, Spain
| | - Chris Oostenbrink
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria
| | - Andrew Murray
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA
| | - Todd R Graham
- Department of Biological Sciences, Vanderbilt University, 1161 21st Avenue South, Nashville, TN 37232, USA
| | - Chad L Myers
- Department of Computer Science and Engineering, University of Minnesota-Twin Cities, 200 Union Street, Minneapolis, MN 55455, USA. .,Canadian Institute for Advanced Research, 180 Dundas Street West, Toronto, Ontario M5G 1Z8, Canada
| | - Brenda J Andrews
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada. .,Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Frederick P Roth
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada. .,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada.,Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada.,Canadian Institute for Advanced Research, 180 Dundas Street West, Toronto, Ontario M5G 1Z8, Canada.,Department of Computer Science, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Charles Boone
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada. .,Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada.,Canadian Institute for Advanced Research, 180 Dundas Street West, Toronto, Ontario M5G 1Z8, Canada
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184
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Boudellioua I, Mahamad Razali RB, Kulmanov M, Hashish Y, Bajic VB, Goncalves-Serra E, Schoenmakers N, Gkoutos GV, Schofield PN, Hoehndorf R. Semantic prioritization of novel causative genomic variants. PLoS Comput Biol 2017; 13:e1005500. [PMID: 28414800 PMCID: PMC5411092 DOI: 10.1371/journal.pcbi.1005500] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 05/01/2017] [Accepted: 04/04/2017] [Indexed: 12/14/2022] Open
Abstract
Discriminating the causative disease variant(s) for individuals with inherited or de novo mutations presents one of the main challenges faced by the clinical genetics community today. Computational approaches for variant prioritization include machine learning methods utilizing a large number of features, including molecular information, interaction networks, or phenotypes. Here, we demonstrate the PhenomeNET Variant Predictor (PVP) system that exploits semantic technologies and automated reasoning over genotype-phenotype relations to filter and prioritize variants in whole exome and whole genome sequencing datasets. We demonstrate the performance of PVP in identifying causative variants on a large number of synthetic whole exome and whole genome sequences, covering a wide range of diseases and syndromes. In a retrospective study, we further illustrate the application of PVP for the interpretation of whole exome sequencing data in patients suffering from congenital hypothyroidism. We find that PVP accurately identifies causative variants in whole exome and whole genome sequencing datasets and provides a powerful resource for the discovery of causal variants. We address the problem of how to distinguish which of the many thousands of DNA sequence variants carried by an individual with a rare disease is responsible for the disease phenotypes. This can help clinicians arrive at a diagnosis, but also can be instrumental in improving our understanding of the pathobiology of the disease. Many methods are currently available to help with the problem of determining causative variant, using information about evolutionary conservation and prediction of the functional consequences of the sequence variant. We have developed a novel algorithm (PVP) which augments existing strategies by using the similarity of the patients phenotype to known phenotype-genotype data in human and model organism databases to further rank potential candidate genes. In a retrospective study, we apply PVP to the interpretation of whole exome sequencing data in patients suffering from congenital hypothyroidism, and find that PVP accurately identifies causative variants in whole exome and whole genome sequencing datasets and provides a powerful resource for the discovery of causal variants.
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Affiliation(s)
- Imane Boudellioua
- King Abdullah University of Science and Technology, Computer, Electrical & Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, Thuwal, Saudi Arabia
| | - Rozaimi B. Mahamad Razali
- King Abdullah University of Science and Technology, Computer, Electrical & Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, Thuwal, Saudi Arabia
| | - Maxat Kulmanov
- King Abdullah University of Science and Technology, Computer, Electrical & Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, Thuwal, Saudi Arabia
| | - Yasmeen Hashish
- King Abdullah University of Science and Technology, Computer, Electrical & Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, Thuwal, Saudi Arabia
| | - Vladimir B. Bajic
- King Abdullah University of Science and Technology, Computer, Electrical & Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, Thuwal, Saudi Arabia
| | - Eva Goncalves-Serra
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Nadia Schoenmakers
- University of Cambridge Metabolic Research Laboratories, Wellcome Trust—Medical Research Council, Institute of Metabolic Science, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Georgios V. Gkoutos
- College of Medical and Dental Sciences, Institute of Cancer and Genomic Sciences, Centre for Computational Biology, University of Birmingham, Birmingham, United Kingdom
- Institute of Translational Medicine, University Hospitals Birmingham, NHS Foundation Trust, Birmingham, United Kingdom
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
- * E-mail: (GVG); (PNS); (RH)
| | - Paul N. Schofield
- Department of Physiology, Development & Neuroscience, University of Cambridge, Cambridge, United Kingdom
- * E-mail: (GVG); (PNS); (RH)
| | - Robert Hoehndorf
- King Abdullah University of Science and Technology, Computer, Electrical & Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, Thuwal, Saudi Arabia
- * E-mail: (GVG); (PNS); (RH)
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185
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Louvain de Souza T, de Souza Campos Fernandes RC, Azevedo da Silva J, Gomes Alves Júnior V, Gomes Coelho A, Souza Faria AC, Moreira Salomão Simão NM, Souto Filho JT, Deswarte C, Boisson-Dupuis S, Torgerson D, Casanova JL, Bustamante J, Medina-Acosta E. Microbial Disease Spectrum Linked to a Novel IL-12Rβ1 N-Terminal Signal Peptide Stop-Gain Homozygous Mutation with Paradoxical Receptor Cell-Surface Expression. Front Microbiol 2017; 8:616. [PMID: 28450854 PMCID: PMC5389975 DOI: 10.3389/fmicb.2017.00616] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 03/27/2017] [Indexed: 01/07/2023] Open
Abstract
Patients with Mendelian Susceptibility to Mycobacterial Diseases (MSMD) exhibit variable vulnerability to infections by mycobacteria and other intramacrophagic bacteria (e.g., Salmonella and Klebsiella) and fungi (e.g., Histoplasma, Candida, Paracoccidioides, Coccidioides, and Cryptococcus). The hallmark of MSMD is the inherited impaired production of interferon gamma (IFN-γ) or the lack of response to it. Mutations in the interleukin (IL)-12 receptor subunit beta 1 (IL12RB1) gene accounts for 38% of cases of MSMD. Most IL12RB1 pathogenic allele mutations, including ten known stop-gain variants, cause IL-12Rβ1 complete deficiency (immunodeficiency-30, IMD30) by knocking out receptor cell-surface expression. IL12RB1 loss-of-function genotypes impair both IL-12 and IL-23 responses. Here, we assess the health effects of a rare, novel IL12RB1 stop-gain homozygous genotype with paradoxical IL-12Rβ1 cell-surface expression. We appraise four MSMD children from three unrelated Brazilian kindreds by clinical consultation, medical records, and genetic and immunologic studies. The clinical spectrum narrowed down to Bacillus Calmette-Guerin (BCG) vaccine-related suppurative adenitis in all patients with one death, and recrudescence in two, histoplasmosis, and recurrence in one patient, extraintestinal salmonellosis in one child, and cutaneous vasculitis in another. In three patients, we established the homozygous Trp7Ter predicted loss-of-function inherited genotype and inferred it from the heterozygote parents of the fourth case. The Trp7Ter mutation maps to the predicted IL-12Rβ1 N-terminal signal peptide sequence. BCG- or phytohemagglutinin-blasts from the three patients have reduced cell-surface expression of IL-12Rβ1 with impaired production of IFN-γ and IL-17A. Screening of 227 unrelated healthy subjects from the same geographic region revealed one heterozygous genotype (allele frequency 0.0022) vs. one in over 841,883 public genome/exomes. We also show that the carriers bear European ancestry-informative alleles and share the extended CACCAGTCCGG IL12RB1 haplotype that occurs worldwide with a frequency of 8.4%. We conclude that the novel IL12RB1 N-terminal signal peptide stop-gain loss-of-function homozygous genotype confers IL-12Rβ1 deficiency with varying severity and early-onset age through diminished cell-surface expression of an impaired IL-12Rβ1 polypeptide. We firmly recommend attending to warning signs of IMD30 in children who are HIV-1 negative with a history of adverse effects to the BCG vaccine and presenting with recurrent Histoplasma spp. and extraintestinal Salmonella spp. infections.
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Affiliation(s)
- Thais Louvain de Souza
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Universidade Estadual do Norte FluminenseCampos dos Goytacazes, Brazil.,Faculdade de Medicina de CamposCampos dos Goytacazes, Brazil
| | - Regina C de Souza Campos Fernandes
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Universidade Estadual do Norte FluminenseCampos dos Goytacazes, Brazil.,Faculdade de Medicina de CamposCampos dos Goytacazes, Brazil
| | - Juliana Azevedo da Silva
- Laboratório de Biologia do Reconhecer, Universidade Estadual do Norte FluminenseCampos dos Goytacazes, Brazil
| | - Vladimir Gomes Alves Júnior
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Universidade Estadual do Norte FluminenseCampos dos Goytacazes, Brazil.,Faculdade de Medicina de CamposCampos dos Goytacazes, Brazil
| | | | | | | | | | - Caroline Deswarte
- Laboratory of Human Genetics of Infectious Diseases, Institut National de la Santé et de la Recherche MédicaleParis, France.,Laboratory of Human Genetics of Infectious Diseases: Mendelian Predisposition, Imagine Institute, Paris Descartes UniversityParis, France
| | - Stéphanie Boisson-Dupuis
- Laboratory of Human Genetics of Infectious Diseases, Institut National de la Santé et de la Recherche MédicaleParis, France.,Laboratory of Human Genetics of Infectious Diseases: Mendelian Predisposition, Imagine Institute, Paris Descartes UniversityParis, France.,St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller UniversityNew York, NY, USA
| | - Dara Torgerson
- Department of Medicine, University of California San FranciscoSan Francisco, CA, USA
| | - Jean-Laurent Casanova
- Laboratory of Human Genetics of Infectious Diseases, Institut National de la Santé et de la Recherche MédicaleParis, France.,Laboratory of Human Genetics of Infectious Diseases: Mendelian Predisposition, Imagine Institute, Paris Descartes UniversityParis, France.,St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller UniversityNew York, NY, USA.,Pediatric Hematology-Immunology Unit, Necker Hospital for Sick Children, Assistance Publique Hôpitaux de ParisParis, France.,Howard Hughes Medical Institute, The Rockefeller UniversityNew York, NY, USA
| | - Jacinta Bustamante
- Laboratory of Human Genetics of Infectious Diseases, Institut National de la Santé et de la Recherche MédicaleParis, France.,Laboratory of Human Genetics of Infectious Diseases: Mendelian Predisposition, Imagine Institute, Paris Descartes UniversityParis, France.,St. Giles Laboratory of Human Genetics of Infectious Diseases, The Rockefeller UniversityNew York, NY, USA.,Study Center of Primary Immunodeficiencies, Assistance Publique Hôpitaux de Paris, Necker Hospital for Sick ChildrenParis, France
| | - Enrique Medina-Acosta
- Núcleo de Diagnóstico e Investigação Molecular, Laboratório de Biotecnologia, Universidade Estadual do Norte FluminenseCampos dos Goytacazes, Brazil
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186
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Chan Y, Tung M, Garruss AS, Zaranek SW, Chan YK, Lunshof JE, Zaranek AW, Ball MP, Chou MF, Lim ET, Church GM. An unbiased index to quantify participant's phenotypic contribution to an open-access cohort. Sci Rep 2017; 7:46148. [PMID: 28387241 PMCID: PMC5384003 DOI: 10.1038/srep46148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 03/10/2017] [Indexed: 01/03/2023] Open
Abstract
The Personal Genome Project (PGP) is an effort to enroll many participants to create an open-access repository of genome, health and trait data for research. However, PGP participants are not enrolled for studying any specific traits and participants choose the phenotypes to disclose. To measure the extent and willingness and to encourage and guide participants to contribute phenotypes, we developed an algorithm to score and rank the phenotypes and participants of the PGP. The scoring algorithm calculates the participation index (P-index) for every participant, where 0 indicates no reported phenotypes and 100 indicate complete phenotype reporting. We calculated the P-index for all 5,015 participants in the PGP and they ranged from 0 to 96.7. We found that participants mainly have either high scores (P-index > 90, 29.5%) or low scores (P-index < 10, 57.8%). While, there are significantly more males than female participants (1,793 versus 1,271), females tend to have on average higher P-indexes (P = 0.015). We also reported the P-indexes of participants based on demographics and states like Missouri and Massachusetts have better P-indexes than states like Utah and Minnesota. The P-index can therefore be used as an unbiased way to measure and rank participant's phenotypic contribution towards the PGP.
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Affiliation(s)
- Yingleong Chan
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA
| | - Michael Tung
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Alexander S. Garruss
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Program in Bioinformatics and Integrative Genomics, Division of Medical Sciences, Graduate School of Arts and Sciences, Harvard University, Cambridge, MA 02138, USA
| | | | - Ying Kai Chan
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Jeantine E. Lunshof
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA
- Department of Genetics, University Medical Centre Groningen, University of Groningen, 9700 RB Groningen, The Netherlands
| | | | | | - Michael F. Chou
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Elaine T. Lim
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA 02115, USA
| | - George M. Church
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
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187
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188
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Carlston CM, O'Donnell-Luria AH, Underhill HR, Cummings BB, Weisburd B, Minikel EV, Birnbaum DP, Tvrdik T, MacArthur DG, Mao R. Pathogenic ASXL1 somatic variants in reference databases complicate germline variant interpretation for Bohring-Opitz Syndrome. Hum Mutat 2017; 38:517-523. [PMID: 28229513 DOI: 10.1002/humu.23203] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 01/31/2017] [Accepted: 02/18/2017] [Indexed: 01/09/2023]
Abstract
The clinical interpretation of genetic variants has come to rely heavily on reference population databases such as the Exome Aggregation Consortium (ExAC) database. Pathogenic variants in genes associated with severe, pediatric-onset, highly penetrant, autosomal dominant conditions are assumed to be absent or rare in these databases. Exome sequencing of a 6-year-old female patient with seizures, developmental delay, dysmorphic features, and failure to thrive identified an ASXL1 variant previously reported as causative of Bohring-Opitz syndrome (BOS). Surprisingly, the variant was observed seven times in the ExAC database, presumably in individuals without BOS. Although the BOS phenotype fit, the presence of the variant in reference population databases introduced ambiguity in result interpretation. Review of the literature revealed that acquired somatic mosaicism of ASXL1 variants (including pathogenic variants) during hematopoietic clonal expansion can occur with aging in healthy individuals. We examined all ASXL1 truncating variants in the ExAC database and determined most are likely somatic. Failure to consider somatic mosaicism may lead to the inaccurate assumption that conditions like BOS have reduced penetrance, or the misclassification of potentially pathogenic variants.
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Affiliation(s)
- Colleen M Carlston
- Department of Pathology, University of Utah, Salt Lake City, Utah.,ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, Utah
| | - Anne H O'Donnell-Luria
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts.,Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts.,Division of Genetics and Genomics, Boston Children's Hospital, Boston, Massachusetts
| | - Hunter R Underhill
- Department of Pediatrics, Division of Medical Genetics, University of Utah, Salt Lake City, Utah.,Department of Radiology, University of Utah, Salt Lake City, Utah
| | - Beryl B Cummings
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts.,Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts.,Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, Massachusetts
| | - Ben Weisburd
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts.,Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts
| | - Eric V Minikel
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts.,Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts.,Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, Massachusetts
| | - Daniel P Birnbaum
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts.,Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts
| | | | - Tatiana Tvrdik
- ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, Utah
| | - Daniel G MacArthur
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts.,Program in Medical and Population Genetics, Broad Institute, Cambridge, Massachusetts
| | - Rong Mao
- Department of Pathology, University of Utah, Salt Lake City, Utah.,ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, Utah
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189
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Jansen ME, Lister KJ, van Kranen HJ, Cornel MC. Policy Making in Newborn Screening Needs a Structured and Transparent Approach. Front Public Health 2017; 5:53. [PMID: 28377917 PMCID: PMC5359248 DOI: 10.3389/fpubh.2017.00053] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 03/01/2017] [Indexed: 01/21/2023] Open
Abstract
PURPOSE Newborn bloodspot screening (NBS) programs have expanded significantly in the past years and are expected to expand further with the emergence of genetic technologies. Historically, NBS expansion has often occurred following ad hoc consideration of conditions, instead of a structured and transparent approach. In this review, we explore issues pertinent to NBS policy making, through the lens of the policy cycle: (a) agenda setting, (b) policy advice, (c) policy decision, (d) implementation, and (e) evaluation. METHODS A literature search was conducted to gather information on the elements specific to NBS and its policy making process. RESULTS The review highlighted two approaches to nominate a condition: a structured approach through horizon scanning; and an ad hoc process. For assessment of a condition, there was unanimous support for a robust process based on criteria. While the need to assess harms and benefits was a repeated theme in the articles, there is no agreed-upon threshold for benefit in decision-making. Furthermore, the literature was consistent in its recommendation for an overarching, independent, multidisciplinary group providing recommendations to government. An implementation plan focusing on the different levels on which NBS operates and the information needed on each level is essential for successful implementation. Continuously monitoring, and improving a program is vital, particularly following the implementation of screening for a new condition. An advisory committee could advise on implementation, development, review, modification, and cessation of (parts of) NBS. CONCLUSION The results highlight that there are a wave of issues facing NBS programs that policy makers must take into account when developing policy processes. What conditions to screen, and the technologies used in NBS, are both up for debate.
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Affiliation(s)
- Marleen E Jansen
- Section Community Genetics, Department of Clinical Genetics, Amsterdam Public Health Research Institute, Amsterdam, Netherlands; Institute for Public Health Genomics, School for Oncology and Developmental Biology (GROW), Faculty of Health, Medicine, and Life Sciences, Maastricht University, Maastricht, Netherlands
| | - Karla J Lister
- Screening Policy Section, Office of Population Health Genomics, Department of Health, Government of Western Australia , Perth, WA , Australia
| | - Henk J van Kranen
- Institute for Public Health Genomics, School for Oncology and Developmental Biology (GROW), Faculty of Health, Medicine, and Life Sciences, Maastricht University, Maastricht, Netherlands; Center for Nutrition, Prevention and Health Services, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Martina C Cornel
- Section Community Genetics, Department of Clinical Genetics, Amsterdam Public Health Research Institute , Amsterdam , Netherlands
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190
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Tarailo-Graovac M, Wasserman WW, Van Karnebeek CDM. Impact of next-generation sequencing on diagnosis and management of neurometabolic disorders: current advances and future perspectives. Expert Rev Mol Diagn 2017; 17:307-309. [PMID: 28277145 DOI: 10.1080/14737159.2017.1293527] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Maja Tarailo-Graovac
- a Institute of Physiology and Biochemistry, Faculty of Biology , The University of Belgrade , Belgrade , Serbia.,b BC Children's Hospital Research Institute, Centre for Molecular Medicine and Therapeutics, and Department of Medical Genetics , University of British Columbia , Vancouver , Canada
| | - Wyeth W Wasserman
- b BC Children's Hospital Research Institute, Centre for Molecular Medicine and Therapeutics, and Department of Medical Genetics , University of British Columbia , Vancouver , Canada
| | - Clara D M Van Karnebeek
- c BC Children's Hospital Research Institute, Centre for Molecular Medicine and Therapeutics, Department of Pediatrics , University of British Columbia , Vancouver , Canada.,d Department of Pediatrics , Emma Children's Hospital, Academic Medical Centre , Amsterdam , The Netherlands
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191
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Hamazaki T, El Rouby N, Fredette NC, Santostefano KE, Terada N. Concise Review: Induced Pluripotent Stem Cell Research in the Era of Precision Medicine. Stem Cells 2017; 35:545-550. [PMID: 28100040 DOI: 10.1002/stem.2570] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 12/08/2016] [Indexed: 02/06/2023]
Abstract
Recent advances in DNA sequencing technologies are revealing how human genetic variations associate with differential health risks, disease susceptibilities, and drug responses. Such information is now expected to help evaluate individual health risks, design personalized health plans and treat patients with precision. It is still challenging, however, to understand how such genetic variations cause the phenotypic alterations in pathobiologies and treatment response. Human induced pluripotent stem cell (iPSC) technologies are emerging as a promising strategy to fill the knowledge gaps between genetic association studies and underlying molecular mechanisms. Breakthroughs in genome editing technologies and continuous improvement in iPSC differentiation techniques are particularly making this research direction more realistic and practical. Pioneering studies have shown that iPSCs derived from a variety of monogenic diseases can faithfully recapitulate disease phenotypes in vitro when differentiated into disease-relevant cell types. It has been shown possible to partially recapitulate disease phenotypes, even with late onset and polygenic diseases. More recently, iPSCs have been shown to validate effects of disease and treatment-related single nucleotide polymorphisms identified through genome wide association analysis. In this review, we will discuss how iPSC research will further contribute to human health in the coming era of precision medicine. Stem Cells 2017;35:545-550.
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Affiliation(s)
- Takashi Hamazaki
- Department of Pediatrics, Osaka City University Graduate School of Medicine, Osaka, Japan
| | - Nihal El Rouby
- Department of Pharmacotherapy and Translational Research, College of Pharmacy, and Center for Pharmacogenomics, Gainesville, Florida, USA
| | - Natalie C Fredette
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, and Center for Cellular Reprogramming, University of Florida, Gainesville, Florida, USA
| | - Katherine E Santostefano
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, and Center for Cellular Reprogramming, University of Florida, Gainesville, Florida, USA
| | - Naohiro Terada
- Department of Pathology, Immunology, and Laboratory Medicine, College of Medicine, and Center for Cellular Reprogramming, University of Florida, Gainesville, Florida, USA
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192
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Ferrari R, Lovering RC, Hardy J, Lewis PA, Manzoni C. Weighted Protein Interaction Network Analysis of Frontotemporal Dementia. J Proteome Res 2017; 16:999-1013. [PMID: 28004582 PMCID: PMC6152613 DOI: 10.1021/acs.jproteome.6b00934] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
![]()
The genetic analysis
of complex disorders has undoubtedly led to
the identification of a wealth of associations between genes and specific
traits. However, moving from genetics to biochemistry one gene at
a time has, to date, rather proved inefficient and under-powered to
comprehensively explain the molecular basis of phenotypes. Here we
present a novel approach, weighted protein–protein interaction
network analysis (W-PPI-NA), to highlight key functional players within
relevant biological processes associated with a given trait. This
is exemplified in the current study by applying W-PPI-NA to frontotemporal
dementia (FTD): We first built the state of the art FTD protein network
(FTD-PN) and then analyzed both its topological and functional features.
The FTD-PN resulted from the sum of the individual interactomes built
around FTD-spectrum genes, leading to a total of 4198 nodes. Twenty
nine of 4198 nodes, called inter-interactome hubs (IIHs), represented
those interactors able to bridge over 60% of the individual interactomes.
Functional annotation analysis not only reiterated and reinforced
previous findings from single genes and gene-coexpression analyses
but also indicated a number of novel potential disease related mechanisms,
including DNA damage response, gene expression
regulation, and cell waste disposal and
potential biomarkers or therapeutic targets including EP300. These
processes and targets likely represent the functional core impacted
in FTD, reflecting the underlying genetic architecture contributing
to disease. The approach presented in this study can be applied to
other complex traits for which risk-causative genes are known as it
provides a promising tool for setting the foundations for collating
genomics and wet laboratory data in a bidirectional manner. This is
and will be critical to accelerate molecular target prioritization
and drug discovery.
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Affiliation(s)
- Raffaele Ferrari
- Department of Molecular Neuroscience, UCL Institute of Neurology , Russell Square House, 9-12 Russell Square House, London WC1B 5EH, United Kingdom
| | - Ruth C Lovering
- Centre for Cardiovascular Genetics, Institute of Cardiovascular Science, University College London , London WC1E 6JF, United Kingdom
| | - John Hardy
- Department of Molecular Neuroscience, UCL Institute of Neurology , Russell Square House, 9-12 Russell Square House, London WC1B 5EH, United Kingdom
| | - Patrick A Lewis
- Department of Molecular Neuroscience, UCL Institute of Neurology , Russell Square House, 9-12 Russell Square House, London WC1B 5EH, United Kingdom.,School of Pharmacy, University of Reading , Whiteknights, Reading RG6 6AP, United Kingdom
| | - Claudia Manzoni
- Department of Molecular Neuroscience, UCL Institute of Neurology , Russell Square House, 9-12 Russell Square House, London WC1B 5EH, United Kingdom.,School of Pharmacy, University of Reading , Whiteknights, Reading RG6 6AP, United Kingdom
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193
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Abstract
Whole-genome and exome sequencing in human populations has revealed the tolerance of each gene for loss-of-function variation. By understanding this tolerance, it has become increasingly possible to identify genes that would make safe therapeutic targets and to identify rare genetic risk factors and phenotypes at the scale of individual genomes. To date, the vast majority of surveyed loss-of-function variants are in protein-coding regions of the genome mainly due to the focus on these regions by exome-based sequencing projects and their relative ease of interpretability. As whole-genome sequencing becomes more prevalent, new strategies will be required to uncover impactful variation in non-coding regions of the genome where the architecture of genome function is more complex. In this review, we investigate recent studies of loss-of-function variation and emerging approaches for interpreting whole-genome sequencing data to identify rare and impactful non-coding loss-of-function variants.
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Affiliation(s)
- Zachary Zappala
- Department of Genetics, Stanford University, California, USA
| | - Stephen B. Montgomery
- Department of Genetics, Stanford University, California, USA
- Department of Pathology, Stanford University, California, USA
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194
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Exome sequencing of Pakistani consanguineous families identifies 30 novel candidate genes for recessive intellectual disability. Mol Psychiatry 2017; 22:1604-1614. [PMID: 27457812 PMCID: PMC5658665 DOI: 10.1038/mp.2016.109] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 05/18/2016] [Accepted: 06/01/2016] [Indexed: 12/13/2022]
Abstract
Intellectual disability (ID) is a clinically and genetically heterogeneous disorder, affecting 1-3% of the general population. Although research into the genetic causes of ID has recently gained momentum, identification of pathogenic mutations that cause autosomal recessive ID (ARID) has lagged behind, predominantly due to non-availability of sizeable families. Here we present the results of exome sequencing in 121 large consanguineous Pakistani ID families. In 60 families, we identified homozygous or compound heterozygous DNA variants in a single gene, 30 affecting reported ID genes and 30 affecting novel candidate ID genes. Potential pathogenicity of these alleles was supported by co-segregation with the phenotype, low frequency in control populations and the application of stringent bioinformatics analyses. In another eight families segregation of multiple pathogenic variants was observed, affecting 19 genes that were either known or are novel candidates for ID. Transcriptome profiles of normal human brain tissues showed that the novel candidate ID genes formed a network significantly enriched for transcriptional co-expression (P<0.0001) in the frontal cortex during fetal development and in the temporal-parietal and sub-cortex during infancy through adulthood. In addition, proteins encoded by 12 novel ID genes directly interact with previously reported ID proteins in six known pathways essential for cognitive function (P<0.0001). These results suggest that disruptions of temporal parietal and sub-cortical neurogenesis during infancy are critical to the pathophysiology of ID. These findings further expand the existing repertoire of genes involved in ARID, and provide new insights into the molecular mechanisms and the transcriptome map of ID.
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195
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de Castro-Miró M, Tonda R, Escudero-Ferruz P, Andrés R, Mayor-Lorenzo A, Castro J, Ciccioli M, Hidalgo DA, Rodríguez-Ezcurra JJ, Farrando J, Pérez-Santonja JJ, Cormand B, Marfany G, Gonzàlez-Duarte R. Novel Candidate Genes and a Wide Spectrum of Structural and Point Mutations Responsible for Inherited Retinal Dystrophies Revealed by Exome Sequencing. PLoS One 2016; 11:e0168966. [PMID: 28005958 PMCID: PMC5179108 DOI: 10.1371/journal.pone.0168966] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 12/09/2016] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND NGS-based genetic diagnosis has completely revolutionized the human genetics field. In this study, we have aimed to identify new genes and mutations by Whole Exome Sequencing (WES) responsible for inherited retinal dystrophies (IRD). METHODS A cohort of 33 pedigrees affected with a variety of retinal disorders was analysed by WES. Initial prioritization analysis included around 300 IRD-associated genes. In non-diagnosed families a search for pathogenic mutations in novel genes was undertaken. RESULTS Genetic diagnosis was attained in 18 families. Moreover, a plausible candidate is proposed for 10 more cases. Two thirds of the mutations were novel, including 4 chromosomal rearrangements, which expand the IRD allelic heterogeneity and highlight the contribution of private mutations. Our results prompted clinical re-evaluation of some patients resulting in assignment to a syndromic instead of non-syndromic IRD. Notably, WES unveiled four new candidates for non-syndromic IRD: SEMA6B, CEP78, CEP250, SCLT1, the two latter previously associated to syndromic disorders. We provide functional data supporting that missense mutations in CEP250 alter cilia formation. CONCLUSION The diagnostic efficiency of WES, and strictly following the ACMG/AMP criteria is 55% in reported causative genes or functionally supported new candidates, plus 30% families in which likely pathogenic or VGUS/VUS variants were identified in plausible candidates. Our results highlight the clinical utility of WES for molecular diagnosis of IRD, provide a wider spectrum of mutations and concomitant genetic variants, and challenge our view on syndromic vs non-syndromic, and causative vs modifier genes.
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Affiliation(s)
- Marta de Castro-Miró
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
- Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Spain
| | - Raul Tonda
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Paula Escudero-Ferruz
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
| | - Rosa Andrés
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
| | | | - Joaquín Castro
- Servicio de Oftalmología, Unidad de Retina, Hospital Universitario Central de Asturias, Oviedo, Spain
| | | | - Daniel A. Hidalgo
- Hospital Interzonal General de Agudos Eva Perón, Buenos Aires, Argentina
| | | | - Jorge Farrando
- Institut Oftalmològic Quirón Barcelona, Barcelona, Spain
| | - Juan J. Pérez-Santonja
- Department of Ophthalmology, Alicante University General Hospital, Alicante Institute for Health and Biomedical Research (ISABIAL-FISABIO Foundation), Alicante, Spain
| | - Bru Cormand
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
- Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Spain
| | - Gemma Marfany
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
- Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Spain
| | - Roser Gonzàlez-Duarte
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
- Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Spain
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196
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Beckmann JS, Lew D. Reconciling evidence-based medicine and precision medicine in the era of big data: challenges and opportunities. Genome Med 2016; 8:134. [PMID: 27993174 PMCID: PMC5165712 DOI: 10.1186/s13073-016-0388-7] [Citation(s) in RCA: 115] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
This era of groundbreaking scientific developments in high-resolution, high-throughput technologies is allowing the cost-effective collection and analysis of huge, disparate datasets on individual health. Proper data mining and translation of the vast datasets into clinically actionable knowledge will require the application of clinical bioinformatics. These developments have triggered multiple national initiatives in precision medicine—a data-driven approach centering on the individual. However, clinical implementation of precision medicine poses numerous challenges. Foremost, precision medicine needs to be contrasted with the powerful and widely used practice of evidence-based medicine, which is informed by meta-analyses or group-centered studies from which mean recommendations are derived. This “one size fits all” approach can provide inadequate solutions for outliers. Such outliers, which are far from an oddity as all of us fall into this category for some traits, can be better managed using precision medicine. Here, we argue that it is necessary and possible to bridge between precision medicine and evidence-based medicine. This will require worldwide and responsible data sharing, as well as regularly updated training programs. We also discuss the challenges and opportunities for achieving clinical utility in precision medicine. We project that, through collection, analyses and sharing of standardized medically relevant data globally, evidence-based precision medicine will shift progressively from therapy to prevention, thus leading eventually to improved, clinician-to-patient communication, citizen-centered healthcare and sustained well-being.
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Affiliation(s)
- Jacques S Beckmann
- Clinical Bioinformatics, SIB Swiss Institute of Bioinformatics, CH-1015, Lausanne, Switzerland.
| | - Daniel Lew
- Clinical Bioinformatics, SIB Swiss Institute of Bioinformatics, CH-1015, Lausanne, Switzerland
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197
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Vihinen M. How to Define Pathogenicity, Health, and Disease? Hum Mutat 2016; 38:129-136. [PMID: 27862583 DOI: 10.1002/humu.23144] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 10/13/2016] [Accepted: 11/03/2016] [Indexed: 11/07/2022]
Abstract
Scientific and clinical communities produce ever increasing amounts of data and details about health and disease. Our ability to understand and utilize this information is limited because of imprecise language and lack of well-defined concepts. This problem involves also the principal concepts of health, disease, and pathogenicity. Here, a systematic model is presented for pathogenicity, as well as for health and disease. It has three components: extent, modulation, and severity, which jointly define the continuum of pathogenicity. The model is population based, and once implemented, it can be used for numerous purposes such as diagnosis, patient stratification, prognosis, finding phenotype-genotype correlations, or explaining adverse drug reactions. The new model has several benefits including health economy by allowing evidence-based personalized/precision medicine.
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Affiliation(s)
- Mauno Vihinen
- Department of Experimental Medical Science, Lund University, BMC B13, Lund, SE-22184, Sweden
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198
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Rodgers GP. First Lecture to New Doctors: 5 Lessons Learned. Am J Med Sci 2016; 352:615-617. [PMID: 27916217 DOI: 10.1016/j.amjms.2016.08.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 08/26/2016] [Indexed: 10/21/2022]
Affiliation(s)
- Griffin P Rodgers
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland.
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199
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Acuna-Hidalgo R, Veltman JA, Hoischen A. New insights into the generation and role of de novo mutations in health and disease. Genome Biol 2016; 17:241. [PMID: 27894357 PMCID: PMC5125044 DOI: 10.1186/s13059-016-1110-1] [Citation(s) in RCA: 266] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Aside from inheriting half of the genome of each of our parents, we are born with a small number of novel mutations that occurred during gametogenesis and postzygotically. Recent genome and exome sequencing studies of parent-offspring trios have provided the first insights into the number and distribution of these de novo mutations in health and disease, pointing to risk factors that increase their number in the offspring. De novo mutations have been shown to be a major cause of severe early-onset genetic disorders such as intellectual disability, autism spectrum disorder, and other developmental diseases. In fact, the occurrence of novel mutations in each generation explains why these reproductively lethal disorders continue to occur in our population. Recent studies have also shown that de novo mutations are predominantly of paternal origin and that their number increases with advanced paternal age. Here, we review the recent literature on de novo mutations, covering their detection, biological characterization, and medical impact.
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Affiliation(s)
- Rocio Acuna-Hidalgo
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
| | - Joris A Veltman
- Department of Human Genetics, Donders Institute of Neuroscience, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands.
- Department of Clinical Genetics, GROW - School for Oncology and Developmental Biology, Maastricht University Medical Centre, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands.
| | - Alexander Hoischen
- Department of Human Genetics, Donders Institute of Neuroscience, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands
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200
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Abstract
Studies of human genetic disorders have traditionally followed a reductionist paradigm. Traits are defined as Mendelian or complex based on family pedigree and population data, whereas alleles are deemed rare, common, benign, or deleterious based on their population frequencies. The availability of exome and genome data, as well as gene and allele discovery for various conditions, is beginning to challenge classic definitions of genetic causality. Here, I discuss recent advances in our understanding of the overlap between rare and complex diseases and the context-dependent effect of both rare and common alleles that underscores the need for revising the traditional categorizations of genetic traits.
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Affiliation(s)
- Nicholas Katsanis
- Center for Human Disease Modeling, Duke University Medical Center, Durham, NC, 27701, USA.
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