Neuroepidemiology Slides (4-13) PDF

Module: Neuroepidemiology Slides (4-13) INTRODUCTION TO CLINICAL NEUROGENETICS & NEUROEPIDEMIOLOGY I Brent Fogel, MD, PhD Associate Professor UCLA Department of Neurology [email protected] CME Financial Disclosure Statement I, or an immediate family member including spouse/partner, have at present and...

Module: Neuroepidemiology Slides (4-13) INTRODUCTION TO CLINICAL NEUROGENETICS & NEUROEPIDEMIOLOGY I Brent Fogel, MD, PhD Associate Professor UCLA Department of Neurology [email protected] CME Financial Disclosure Statement I, or an immediate family member including spouse/partner, have at present and/or have had within the last 12 months, or anticipate NO financial interest/arrangement or affiliation with one or more organizations that could be perceived as a real or apparent conflict of interest in context to the design, implementation, presentation, evaluation, etc. of CME activities. – Brent Fogel, MD, PhD Question Based Learning Lecture Modules Neuroepidemiology Molecular Neurogenetics Cytogenetics Question: A teenage girl with Friedreich ataxia visits your office for genetic counseling. Which of the following statements about her disease is correct? A. Transmission is autosomal recessive, carrier frequency is 1/40,000, incidence is 1/85 annually; prevalence is 1.5/100,000 B. Transmission is autosomal dominant, carrier frequency is 1/85, incidence is 1/40,000 annually; prevalence is 1.5/100,000 C. Transmission is autosomal recessive, carrier frequency is 1/85, incidence is 1.5/100,000 annually; prevalence is 1/40,000 D. Transmission is X-linked, carrier frequency is 1/85, incidence is 1/40,000 annually; prevalence is 1/40,000 E. Transmission is autosomal dominant, carrier frequency is 1/85, incidence is 1.5/100,000 annually; prevalence is 1.5/100,000 Introduction Study of the distribution and determinants of neurological disease Goal is to prevent disease Key questions – How many cases of disease in a population? – What are the demographic features of a disease? – What is the natural history of a disease? – What factors determine prognosis? – What are the genetic and/or environmental determinants of a disease? – What are the economic characteristics of a disease? – What are the best treatments for a disease? – How can the disease be prevented? Source: Nelson, Tanner, Van Den Eeden, McGuire eds: Neuroepidemiology, 2004. Notes: Neurology: Introduction to Clinical Neurogenetics & Neuroepidemiology I Brent Fogel © 2009-2018 BeatTheBoards.com 877-225-8384 For exclusive use by : [email protected] Sharing or distribution is a violation of copyright laws. 1 Natural History Source: Modified from: Nelson, Tanner, Van Den Eeden, McGuire eds: Neuroepidemiology, 2004. Demographics Neurological disorders most frequently reported in primary care worldwide (N=102 countries) Demographics Neurological disorders most frequently reported in specialist care worldwide (N=106 countries) Source: World Health Organization, Atlas: country resources for neurological disorders, 2004. Source: World Health Organization, Atlas: country resources for neurological disorders, 2004. Notes: Neurology: Introduction to Clinical Neurogenetics & Neuroepidemiology I Brent Fogel © 2009-2018 BeatTheBoards.com 877-225-8384 2 For exclusive use by : [email protected] Sharing or distribution is a violation of copyright laws. Incidence and Prevalence Source: Hirtz et al. 2007 Neurology. Risk Factors - Examples Source: http://www.stroke.org/site/PageServer?pagename=risk. Notes: Neurology: Introduction to Clinical Neurogenetics & Neuroepidemiology I Brent Fogel © 2009-2018 BeatTheBoards.com 877-225-8384 For exclusive use by : [email protected] Sharing or distribution is a violation of copyright laws. 3 Module: Molecular Neurogenetics Developmental Expression of Genetic Disease Slides (14-20) Question: Genetic factors likely contribute to the risk of developing which of the following neurological diseases? A. Alzheimer disease B. Amyotrophic lateral sclerosis C. Parkinson disease D. Restless legs syndrome E. All of the above Contribution of Genetics to Neurological Disease Common Stroke Autism Migraine Prevalence Restless Legs Epilepsy Multiple Sclerosis Alzheimer Disease Ataxia Parkinson Disease Genetic cause vs. risk Common neurologic diseases occur, in part, due to inherent genetic contributions Source: Pritchard DJ & Korf BR 2003 Medical Genetics at a Glance. Huntington disease Friedreich ataxia Duchenne MD Charcot-Marie-Tooth SCAs Wilson disease All Contribution of genetic factors to disease ALS Rare None Regulation of Gene Expression in the Neuron Source: Adapted from Fogel & Geschwind, Clinical Neurogenetics Neurology in Clinical Practice, 6th ed. Notes: Neurology: Introduction to Clinical Neurogenetics & Neuroepidemiology I Brent Fogel © 2009-2018 BeatTheBoards.com 877-225-8384 4 For exclusive use by : [email protected] Sharing or distribution is a violation of copyright laws. Module: Cytogenetics Slides (21-32) Question: Which of these disorders is the most common genetic cause of intellectual disability? A. Monosomy X B. Trisomy 21 C. Fragile X syndrome D. Spinal muscular atrophy E. Huntington disease Chromosomal Disorders Microscopic syndromes (karyotype) – Monosomy X (Turner syndrome) – Trisomy 21 (Down syndrome) Case Presentation A young boy referred for intellectual disability… Clinical features – Intellectual disability – Upwards-slanting palpebral fissures – Bilateral epicanthal folds – Small nose with flat nasal bridge – Bilateral palmar creases – Open mouth, tendency to protrude tongue Source: http://www2.geneticsolutions.com/?id=1530:1873. Down syndrome Source: http://www.nichd.nih.gov/news/resources/spotlight/images/spotlig ht_012208_large.jpg. Case Presentation Girl age 14 referred for ptosis of the right eye… Clinical features – Short stature – High arched palate – Ovarian failure – Multiple nevi – Webbed neck – No intellectual disability Genetic Inheritance – Chromosomes and Alleles Turner syndrome Source: http://omeweb2.ucdavis.edu/pmd/robbins/gen2/gen240.htm. DNA = deoxyribonucleic acid Source: David Adler, University of Washington. Notes: Neurology: Introduction to Clinical Neurogenetics & Neuroepidemiology I Brent Fogel © 2009-2018 BeatTheBoards.com 877-225-8384 For exclusive use by : [email protected] Sharing or distribution is a violation of copyright laws. 5 Chromosomal Disorders Submicroscopic chromosomal alterations Detection Methods FISH = fluorescent in-situ hybridization (Gold Standard) CGH = comparative genomic hybridization CMA = chromosomal microarray analysis (Most common, molecular karyotype) Chromosomal Disorders - Detection Micro-deletion syndromes (FISH or CGH/CMA) Angelman/Prader-Willi syndrome (15q11.2) Williams syndrome (7q11) Red = marker to Chr 19 Translocation Chrs 11 & 19 Normal Chr 19 Source: Copyright 2001 Nature Publishing Group, Cheung, V.G., et al., Integration of cytogenetic landmarks into the draft sequence of the human genome, Nature 409, 953-958. Source: Fogel & Geschwind, Clinical Neurogenetics Neurology in Clinical Practice, 6th ed. Case Presentation 3 y.o. boy with recent diagnosis of autism… 3q29 microdeletion syndrome Source: Fogel & Geschwind, Clinical Neurogenetics Neurology in Clinical Practice, 6th ed. Notes: Neurology: Introduction to Clinical Neurogenetics & Neuroepidemiology I Brent Fogel © 2009-2018 BeatTheBoards.com 877-225-8384 6 For exclusive use by : [email protected] Sharing or distribution is a violation of copyright laws. Answer Key Question: A teenage girl with Friedreich ataxia visits your office for genetic counseling. Which of the following statements about her disease is correct? A. Transmission is autosomal recessive, carrier frequency is 1/40,000, incidence is 1/85 annually; prevalence is 1.5/100,000 B. Transmission is autosomal dominant, carrier frequency is 1/85, incidence is 1/40,000 annually; prevalence is 1.5/100,000 C. Transmission is autosomal recessive, carrier frequency is 1/85, incidence is 1.5/100,000 annually; prevalence is 1/40,000 D. Transmission is X-linked, carrier frequency is 1/85, incidence is 1/40,000 annually; prevalence is 1/40,000 E. Transmission is autosomal dominant, carrier frequency is 1/85, incidence is 1.5/100,000 annually; prevalence is 1.5/100,000 Answer Explanation Friedreich ataxia is transmitted in an autosomal recessive manner For a recessive disorder, carrier frequency is the proportion of individuals in the population with a single abnormal allele Incidence is the number of new cases per a given time while prevalence is the number of total cases in a population For a disease that is not rapidly fatal, prevalence should always exceed incidence Answer Explanation Genetic factors are thought to influence the susceptibility of individuals to many complex neurological diseases, although the precise extent (and/or individual risk) is currently not clear For some diseases, rare genetic mutations may directly cause the disease in question in certain individuals and families Question: Which of these disorders is the most common genetic cause of intellectual disability? A. Monosomy X B. Trisomy 21 C. Fragile X syndrome D. Spinal muscular atrophy E. Huntington disease Answer Explanation Trisomy 21, or Down syndrome, is the most common chromosomal disorder in humans (monosomy X may be more frequent if include spontaneous abortions), and the most common genetic cause of intellectual disability. The most common cause is maternal non-disjunction during meiosis I of gametogenesis Fragile X syndrome is the most common inherited cause of intellectual disability and the 2nd most common genetic cause after trisomy 21 Spinal muscular atrophy (SMA) is one of the leading genetic causes of infant mortality End of Lecture Question: Genetic factors likely contribute to the risk of developing which of the following neurological diseases? A. Alzheimer disease B. Amyotrophic lateral sclerosis C. Parkinson disease D. Restless legs syndrome E. All of the above Notes: Neurology: Introduction to Clinical Neurogenetics & Neuroepidemiology I Brent Fogel © 2009-2018 BeatTheBoards.com 877-225-8384 For exclusive use by : [email protected] Sharing or distribution is a violation of copyright laws. 7 For exclusive use by : [email protected] Sharing or distribution is a violation of copyright laws. Module: Modes of Inheritance 1 Slides (3-17) INTRODUCTION TO CLINICAL NEUROGENETICS & NEUROEPIDEMIOLOGY II Brent Fogel, MD, PhD Associate Professor UCLA Department of Neurology [email protected] Question: Which of these disorders is the most common genetic cause of inherited intellectual disability? A. Monosomy X B. Trisomy 21 C. Fragile X syndrome D. Spinal muscular atrophy E. Huntington disease Genetic Inheritance – Gregor Mendel Parents pass on discrete heritable factors to children CME Financial Disclosure Statement I, or an immediate family member including spouse/partner, have at present and/or have had within the last 12 months, or anticipate NO financial interest/arrangement or affiliation with one or more organizations that could be perceived as a real or apparent conflict of interest in context to the design, implementation, presentation, evaluation, etc. of CME activities. – Brent Fogel, MD, PhD Question Based Learning Lecture Modules Modes of Inheritance 1 Modes of Inheritance 2 Mitochondrial Disorders Source: http://history.nih.gov/exhibits/nirenberg/popup_htm/01_mendel.htm. Case Presentation 28 y.o. woman with chief complaint of muscle weakness Weakness affects distal muscles of hands and feet On examination there is mild facial muscle weakness Ophthalmological examination shows early cataract development EKG with mild conduction block Mother with similar symptoms Brother born hypotonic and died of respiratory failure Notes: Neurology: Introduction to Clinical Neurogenetics & Neuroepidemiology II Brent Fogel © 2009-2018 BeatTheBoards.com 877-225-8384 For exclusive use by : [email protected] Sharing or distribution is a violation of copyright laws. 1 Christmas Tree Cataract Case Presentation cont’d Met d Autosomal Dominant Disorders Examples Charcot-Marie-Tooth (Types 1A, 2, etc.) Huntington disease Myotonic dystrophy (DM1, DM2) Neurofibromatosis 1 & 2 Spinocerebellar ataxias (SCAs) Tuberous sclerosis Case Presentation 24 y.o. woman complains of an inability to walk Onset age 12 with progressive gait disturbance Profound limb and gait ataxia, dysarthria Weakness distally in the legs Severe vibration and joint position sensory loss Absent patellar reflexes Upgoing toes Scoliosis as a child Parents are asymptomatic MRI shows normal cerebellum but cervical cord atrophy Myotonic dystrophy (DM1, DMPK gene) Source: http://neuromuscular.wustl.edu/pics/people/patients/ DM1cataractvsm.jpg. Question: A patient with severe peripheral neuropathy tells you his mother, sister, and maternal grandfather have similar symptoms. What is the most likely mode of inheritance in this family? A. X-linked recessive B. Autosomal dominant C. Uniparental disomy D. Autosomal recessive E. Mitochondrial Patterns of Single-Gene Inheritance Autosomal Dominant Key Points Mutation of one allele “Heterozygous” 50% risk of transmission Equal males and females Affects multiple generations (vertical) Male to male transmission Usually gain of function – Haploinsufficiency – Dominant negative uphatypes Penetrance / expressivity often u doyousee of disease personal disease in someone w defect Source: Fogel & Geschwind, Clinical Neurogenetics Neurology in Clinical Practice, 6th ed. Friedreich ataxia Source: Fogel & Perlman, 2007. Patterns of Single-Gene Inheritance Autosomal Recessive Key Points – Mutation of both alleles – “Homozygous” – “Compound Heterozygous” – 25% risk of transmission – Equal males and females – Single generation affected (horizontal) – Consanguinity common (but not required) – Usually loss of function – Pseudodominance Notes: Neurology: Introduction to Clinical Neurogenetics & Neuroepidemiology II Brent Fogel © 2009-2018 BeatTheBoards.com 877-225-8384 2 For exclusive use by : [email protected] Sharing or distribution is a violation of copyright laws. Patterns of Single-Gene Inheritance cont’d Source: Fogel & Geschwind, Clinical Neurogenetics Neurology in Clinical Practice, 6th ed. Lossof An usually A r Autosomal Recessive Disorders Examples Friedreich ataxia Most inborn errors of metabolism (e.g., maple syrup urine disease, Niemann-Pick type C, phenylketonuria, Tay-Sachs, etc.) Wilson disease et Module: Modes of Inheritance 2 Slides (18-28) Question: You see a 4 y.o. girl with a new diagnosis of autism. Her development was normal until age two followed by a loss of acquired speech and hand skills and the development of seizures. She is cognitively impaired, socially withdrawn, and has difficulty walking. During the examination she exhibits stereotypical hand movements. You diagnose her with Rett syndrome. Question cont’d: Why is the classic form of Rett syndrome seen almost exclusively in girls? A. The disorder is X-linked recessive and therefore the mutation is only expressed in females B. The disorder is inherited through mitochondria C. The disorder is X-linked dominant and the mutation is generally fatal to hemizygous males D. The Y chromosome protects males from the causative mutation E. The disorder has incomplete penetrance in males Case Presentation 10 y.o. boy seen for progressive neurological decline Developed nystagmus and head titubation at 1 month of age Hypotonic at birth but now with spasticity, legs > arms Ataxia of trunk and limbs Dystonic posturing, athetosis Intellectual disability Speech very slow Never walked Mother was “clumsy” as a child but “grew out so of it” Very long chain fatty acids normal (rules out what common disorder?) adreno new d ystrophy co diffusewhite disease matter leabodystrophy X Irnk ed Pelizaeus-Merzbacher disease (PLP1 duplication or missense mutations) Source: http://emedicine.medscape.com/article/1153103-media. Notes: Neurology: Introduction to Clinical Neurogenetics & Neuroepidemiology II Brent Fogel © 2009-2018 BeatTheBoards.com 877-225-8384 For exclusive use by : [email protected] Sharing or distribution is a violation of copyright laws. 3 Patterns of Single-Gene Inheritance X-linked, Recessive Key Points – Mother: 50% risk of transmission – Father: 100% of daughters are carriers – Typically only males affected (recessive) – Multiple generations affected 8 Case Presentation cont’d q or d spitypes FMR1-related disorders Source: Adapted from Hagerman RJ et al. 2009 Jan;123(1):378-90. Source: Fogel & Geschwind, Clinical Neurogenetics Neurology in Clinical Practice, 6th ed. Patterns of Single-Gene Inheritance X-linked, Dominant Key Points – Mother: 50% risk of transmission – Father: 100% of daughters are carriers – Multiple generations affected – X-linked dominant Females are affected Males either die or have more severe disease Case Presentation 12 y.o. boys with developmental delay, intellectual disability, autism, attentiondeficit/hyperactivity disorder (ADHD), dysmorphic features Sister with ADHD Mother with primary ovarian insufficiency in her 30s Maternal Grandmother with ataxia and intention tremor Maternal Great-Grandfather with ataxia, tremor, dementia, parkinsonism, polyneuropathy Source: Fogel & Geschwind, Clinical Neurogenetics Neurology in Clinical Practice, 6th ed. Notes: Neurology: Introduction to Clinical Neurogenetics & Neuroepidemiology II Brent Fogel © 2009-2018 BeatTheBoards.com 877-225-8384 4 For exclusive use by : [email protected] Sharing or distribution is a violation of copyright laws. X-Linked Disease in Women – Lyonization Random inactivation of one X chromosome per cell Met Met X-linked recessive disorders Examples Duchenne muscular dystrophy Menkes disease (kinky hair disease) Spinal bulbar muscular atrophy (Kennedy disease) Pelizaeus-Merzbacher disease and hereditary spastic paraplegia type 2 X-linked adrenoleukodystrophy and adrenomyeloneuropathy X-linked dominant disorders Examples Aicardi syndrome Incontinentia pigmenti Rett syndrome Fragile X syndrome and Fragile X-associated tremor/ataxia syndrome (FXTAS) Module: Mitochondrial Disorders Slides (29-38) Case Presentation 8 y.o. girl with generalized seizures Onset of myoclonus at age 3 Development otherwise normal Progressively worsening symptoms Ataxia Diffuse muscle weakness Severe intellectual decline Hearing loss Mother and grandmother with various neurological complaints Gomori trichrome stain of muscle biopsy as shown MERRF Myoclonic epilepsy with ragged red fibers Source: http://www.neuropathologyweb.org/chapter10/images10/10rrfs.jpg. Patterns of Single-Gene Inheritance Mitochondrial Key Points – Exclusively female transmission – Both males and females have disease – Variable expressivity due to heteroplasmy Question: You are evaluating a family with a 10 y.o. child with pigmentary retinopathy, progressive external ophthalmoplegia, and cerebellar ataxia. Genetic testing reveals a large deletion in her mitochondrial DNA. What is the most likely cause for differences in age of onset and severity in patients with the identical mutation? A. The extent of disease in the patient’s mother B. Changes in the proportion of affected mitochondria C. Whether or not the patient’s father was affected D. Elevated levels of lactic acid in the blood E. The sex of the patient Source: Fogel & Geschwind, Clinical Neurogenetics Neurology in Clinical Practice, 6th ed. Notes: Neurology: Introduction to Clinical Neurogenetics & Neuroepidemiology II Brent Fogel © 2009-2018 BeatTheBoards.com 877-225-8384 For exclusive use by : [email protected] Sharing or distribution is a violation of copyright laws. 5 Heteroplasmy % abnormal mitochondria per cell Can vary over lifetime and by tissue LearnMitochondrial Disorders Examples Kearn-Sayre syndrome Leber’s hereditary optic neuropathy (LHON) Mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS) Myoclonic epilepsy with ragged-red fibers (MERRF) Mitochondrial Disorders Autosomal Genes Mitochondria only contain 37 genes All other proteins are from the nuclear genome so most disorders that disrupt mitochondrial function do not show maternal inheritance Answer Key Question: Which of these disorders is the most common genetic cause of inherited intellectual disability? A. Monosomy X B. Trisomy 21 C. Fragile X syndrome D. Spinal muscular atrophy E. Huntington disease Answer Explanation Trisomy 21, or Down syndrome, is the most common chromosomal disorder in humans (monosomy X may be more frequent if include spontaneous abortions), and the most common genetic cause of intellectual disability. The most common cause is maternal non-disjunction during meiosis I of gametogenesis Fragile X syndrome is the most common inherited cause of intellectual disability and the 2nd most common genetic cause after trisomy 21 Spinal muscular atrophy (SMA) is one of the leading genetic causes of infant mortality Question: A patient with severe peripheral neuropathy tells you his mother, sister, and maternal grandfather have similar symptoms. What is the most likely mode of inheritance in this family? A. X-linked recessive B. Autosomal dominant C. Uniparental disomy D. Autosomal recessive E. Mitochondrial Answer Explanation Disease present in multiple successive generations that does not exhibit a sex preference for either transmission or expression are hallmark features of autosomal dominant inheritance Source: http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/E/Endosym biosis.html. Notes: Neurology: Introduction to Clinical Neurogenetics & Neuroepidemiology II Brent Fogel © 2009-2018 BeatTheBoards.com 877-225-8384 6 For exclusive use by : [email protected] Sharing or distribution is a violation of copyright laws. Question: You see a 4 y.o. girl with a new diagnosis of autism. Her development was normal until age two followed by a loss of acquired speech and hand skills and the development of seizures. She is cognitively impaired, socially withdrawn, and has difficulty walking. During the examination she exhibits stereotypical hand movements. You diagnose her with Rett syndrome. Why is the classic form of Rett syndrome seen almost exclusively in girls? A. The disorder is X-linked recessive and therefore the mutation is only expressed in females B. The disorder is inherited through mitochondria C. The disorder is X-linked dominant and the mutation is generally fatal to hemizygous males D. The Y chromosome protects males from the causative mutation E. The disorder has incomplete penetrance in males Question: You are evaluating a family with a 10 y.o. child with pigmentary retinopathy, progressive external ophthalmoplegia, and cerebellar ataxia. Genetic testing reveals a large deletion in her mitochondrial DNA. What is the most likely cause for differences in age of onset and severity in patients with the identical mutation? A. The extent of disease in the patient’s mother B. Changes in the proportion of affected mitochondria C. Whether or not the patient’s father was affected D. Elevated levels of lactic acid in the blood E. The sex of the patient Answer Explanation The proportion of affected versus normal mitochondria, or heteroplasmy, in critical tissues directly relates to the expression of the disease phenotype End of Lecture Answer Explanation Rett syndrome is caused by mutation of the methyl-CpG-binding protein-2 (MECP2) gene. The disease is X-linked dominant and is typically fatal to hemizygous males (or causes a severe neonatal encephalopathy) although milder mutations have recently been found in boys with intellectual disability Notes: Neurology: Introduction to Clinical Neurogenetics & Neuroepidemiology II Brent Fogel © 2009-2018 BeatTheBoards.com 877-225-8384 For exclusive use by : [email protected] Sharing or distribution is a violation of copyright laws. 7 For exclusive use by : [email protected] Sharing or distribution is a violation of copyright laws. Module: Mechanisms of Mutation Slides (4-13) ADVANCED TOPICS IN CLINICAL NEUROGENETICS I Brent Fogel, MD, PhD Associate Professor UCLA Department of Neurology [email protected] Question: Which of the following types of mutations can be causes for Angelman syndrome? A. Imprinting defects B. Point mutations C. Copy number variation D. Uniparental disomy E. All of the above Types of Genetic Mutations – Coding Mutations CME Financial Disclosure Statement I, or an immediate family member including spouse/partner, have at present and/or have had within the last 12 months, or anticipate NO financial interest/arrangement or affiliation with one or more organizations that could be perceived as a real or apparent conflict of interest in context to the design, implementation, presentation, evaluation, etc. of CME activities. – Brent Fogel, MD, PhD Question Based Learning Lecture Modules Mechanisms of Mutation Repeat Expansion Disorders Channelopathies Coding mutations estimated to cause up to 85% of Neurological Disease (but likely an overestimate) Source: Fogel & Geschwind, Clinical Neurogenetics Neurology in Clinical Practice, 6th ed. Notes: Neurology: Advanced Topics in Clinical Neurogenetics I Brent Fogel © 2009-2018 BeatTheBoards.com 877-225-8384 For exclusive use by : [email protected] Sharing or distribution is a violation of copyright laws. 1 Types of Genetic Mutations – Splice Site Mutations Genetic Diversity: Exon Shuffling, Alternative Splicing Types of Genetic Mutations – Imprinting Angelman syndrome – Developmental delay – Intellectual disability – Impaired speech – Ataxia – Epilepsy – Characteristic demeanor/ behaviors – Often due to maternal 15q11-q13 deletion Prader-Willi syndrome – Intellectual disability & learning disorders – Short stature – Poor motor skills – Weight gain and morbid obesity – Underdeveloped genitalia – Behavioral problems – Often due to paternal 15q11-q13 deletion Source: Fogel & Geschwind, Clinical Neurogenetics Neurology in Clinical Practice, 6th ed. Source: Fogel & Geschwind, Clinical Neurogenetics Neurology in Clinical Practice, 6th ed. Source: http://www.ncbi.nlm.nih.gov/bookshelf/ br.fcgi?book=hmg&part=A1049. Notes: Neurology: Advanced Topics in Clinical Neurogenetics I Brent Fogel © 2009-2018 BeatTheBoards.com 877-225-8384 2 For exclusive use by : [email protected] Sharing or distribution is a violation of copyright laws. Types of Genetic Mutations – Uniparental Disomy Case Presentation 40 y.o. man presents for involuntary movements noticed by his wife Has recently had trouble with balance Examination shows chorea of the hands Wife reports new behavior changes (irritability, anger, depression) Has become more forgetful and is easily confused Father committed suicide in his late 40’s Paternal grandfather was institutionalized Source: Fogel & Geschwind, Clinical Neurogenetics Neurology in Clinical Practice, 6th ed. Module: Repeat Expansion Disorders Slides (14-21) Question: You are managing the care of a family with spinocerebellar ataxia type 3 (SCA3). An affected man in the family comes to you for genetic counseling. Which of the following is correct regarding inheritance of this disease? A. Autosomal dominant, 50% of children will be affected, with a risk of more severe disease B. Autosomal dominant, 25% of children will be affected, no risk of more severe disease C. Autosomal dominant, 100% of male children will be affected with risk of more severe disease D. Autosomal dominant, 50% of children will be affected, no risk of more severe disease E. Autosomal dominant, 100% of children will be affected, with risk of more severe disease Huntington disease (HTT gene) Source: http://medgen.genetics.utah.edu/photographs/diseases/high/cns10 1.jpg. Types of Genetic Mutations – Repeat Expansion Disorders Key features – Location (exonic, intronic, untranslated region [UTR]) – Most autosomal dominant – Most are triplet repeat expansion – Most common repeat is CAG (polyglutamine) – Diseases often show anticipation Notes: Neurology: Advanced Topics in Clinical Neurogenetics I Brent Fogel © 2009-2018 BeatTheBoards.com 877-225-8384 For exclusive use by : [email protected] Sharing or distribution is a violation of copyright laws. 3 Types of Genetic Mutations – Repeat Expansion Disorders cont’d Types of Genetic Mutations – Repeat Expansion Disorders Diseases caused by CAG repeats are likely due to toxic cellular effects and/or altered gene expression/ protein function in cellular or metabolic pathways Source: Modified from Schöls et al, Lancet Neurol, 2004. Module: Channelopathies Slides (22-29) Source: Adapted from: Bird T & Tapscott S, Clinical Neurogenetics Neurology in Clinical Practice, 5th ed 781-806. Repeats are unstable and tend to increase through paternal lineage Question: In a patient with epilepsy due to an ion channel mutation, which is the least likely cause of their symptoms? A. Ion channels fixed in an active conformation B. Alterations in ion channel kinetics C. Reduced numbers of an ion channel on the cell membrane D. Polyglutamine aggregates affecting calcium channel function E. Increased neuronal excitability Introduction Mutation leads to dysfunction of an ion channel Causes familial epilepsies as well as other neurological diseases Anticipation: Disease severity is worse as number of repeats increase Source: Filla et al. 1999, J Neurol. Source: Kullman, 2010 Annu. Rev. Neurosci. Notes: Neurology: Advanced Topics in Clinical Neurogenetics I Brent Fogel © 2009-2018 BeatTheBoards.com 877-225-8384 4 For exclusive use by : [email protected] Sharing or distribution is a violation of copyright laws. Case Presentation A young girl age 8 presents with a history of unremitting myoclonic seizures starting at age 6 months. By age 2 years developmental delays were noticed as well as ataxia. EEG performed early are normal but repeat EEGs show polyspike and wave discharges Dravet Syndrome (SCN1A) Source: http://www.dravet.org.uk/. Epilepsy Disease most commonly due to – Mutation alters current dynamics or ligandbinding – Mutation “locks” channel in an open/active state – Haploinsufficiency Result: increased excitability or decreased inhibition in neurons/inter-neurons leading to seizure initiation and subsequent spread Excitatory channels – Sodium, nicotinic acetylcholine, and calcium channels Inhibitory channels – Potassium and chloride channels CACNA1A (CAV2.1) Voltage-gated Ca++ channel  Mutations cause - Idiopathic generalized epilepsy - Spinocerebellar ataxia type 6 - Familial hemiplegic migraine - Episodic ataxia type 2 Answer Key Question: Which of the following types of mutations can be causes for Angelman syndrome? A. Imprinting defects B. Point mutations C. Copy number variation D. Uniparental disomy E. All of the above Answer Explanation Angelman syndrome is a neurodevelopmental syndrome primarily caused (~80%) by mutations on chromosome 15q11-q13 resulting a loss of the maternal-specific DNA methylation pattern. These mutations include deletions, uniparental disomy, and imprinting defects. Point mutations in the UBE3A gene cause another 10% of all cases Question: You are managing the care of a family with spinocerebellar ataxia type 3 (SCA3). An affected man in the family comes to you for genetic counseling. Which of the following is correct regarding inheritance of this disease? A. Autosomal dominant, 50% of children will be affected, with a risk of more severe disease B. Autosomal dominant, 25% of children will be affected, no risk of more severe disease C. Autosomal dominant, 100% of male children will be affected with risk of more severe disease D. Autosomal dominant, 50% of children will be affected, no risk of more severe disease E. Autosomal dominant, 100% of children will be affected, with risk of more severe disease Source: Fogel and Jen, 2010. Notes: Neurology: Advanced Topics in Clinical Neurogenetics I Brent Fogel © 2009-2018 BeatTheBoards.com 877-225-8384 For exclusive use by : [email protected] Sharing or distribution is a violation of copyright laws. 5 Answer Explanation SCA3 is caused by CAG nucleotide repeat expansion in the ATXN3 gene and is transmitted in an autosomal dominant manner. 50% of the patient’s children will be affected on average. Because repeat expansions are unstable and can expand each generation (and increased numbers of repeats correlate with worsening disease severity) there is a risk of the children having more severe disease than the parent. This is termed anticipation and, for most repeat expansions, is more common if the mutant allele is transmitted paternally Question: In a patient with epilepsy due to an ion channel mutation, which is the least likely cause of their symptoms? A. Ion channels fixed in an active conformation B. Alterations in ion channel kinetics C. Reduced numbers of an ion channel on the cell membrane D. Polyglutamine aggregates affecting calcium channel function E. Increased neuronal excitability Answer Explanation Polyglutamine repeat expansions have not been reported to cause epilepsy due to disruption of an ion channel. Expansions in the calcium channel encoded by the CACNA1A gene (CAV2.1) are associated with spinocerebellar ataxia type 6 (SCA6) but are not associated with a known epilepsy syndrome. Missense mutations in the CACNA1A gene, however, can cause a form of epilepsy End of Lecture Notes: Neurology: Advanced Topics in Clinical Neurogenetics I Brent Fogel © 2009-2018 BeatTheBoards.com 877-225-8384 6 For exclusive use by : [email protected] Sharing or distribution is a violation of copyright laws. Module: Copy Number Variation Slides (3-9) ADVANCED TOPICS IN CLINICAL NEUROGENETICS II Brent Fogel, MD, PhD Associate Professor UCLA Department of Neurology [email protected] Case Presentation 22 y.o. man with chief complaint of weakness Onset age 9 with gait problems Slowly progressive symptoms Distal muscle weakness (esp. feet) Mild multimodal sensory loss Absent patellar reflexes Pes cavus, atrophy of intrinsic muscles hands/feet Father, paternal aunt and grandmother affected Nerve conduction study (NCS) shows demyelinating neuropathy CME Financial Disclosure Statement I, or an immediate family member including spouse/partner, have at present and/or have had within the last 12 months, or anticipate NO financial interest/arrangement or affiliation with one or more organizations that could be perceived as a real or apparent conflict of interest in context to the design, implementation, presentation, evaluation, etc. of CME activities. – Brent Fogel, MD, PhD Question Based Learning Lecture Modules Copy Number Variation Clinical Evaluation Diagnostic Evaluation Next-Generation Sequencing in Diagnostic Testing Charcot-Marie-Tooth disease type 1A (PMP22 duplication) Source: Gallardo et al. Brain 2006 129(2):426-437. Definition Small structural changes (copy number variations [CNVs]) in the genome have recently been identified as an important cause of human genetic variability CNVs: empirically defined as gains or losses of DNA greater than 1,000 bases in size (1 kb) Such changes are common! CNVs occur between 100 and 10,000 times more frequently per generation than point mutations. Represents 4%-13% of human genome CNVs likely result in more significant changes between individuals than all other forms of mutation Changes can be silent or affect gene function, regulation, or expression to cause disease (e.g., uncover a masked recessive allele) Notes: Neurology: Advanced Topics in Clinical Neurogenetics II Brent Fogel © 2009-2018 BeatTheBoards.com 877-225-8384 For exclusive use by : [email protected] Sharing or distribution is a violation of copyright laws. 1 Mechanism Source: Eichler, E. E. (2008) Nature Education 1(3). Notes: Neurology: Advanced Topics in Clinical Neurogenetics II Brent Fogel © 2009-2018 BeatTheBoards.com 877-225-8384 2 For exclusive use by : [email protected] Sharing or distribution is a violation of copyright laws. Examples Source: Fogel & Geschwind, Clinical Neurogenetics Neurology in Clinical Practice, 6th ed. Testing Classic methodology is comparative genomic hybridization Newer tests typically use single nucleotide polymorphism array for increased precision Molecular karyotyping Will detect large deletions/duplications Identifies specific single gene disorders associated with known CNVs Recommended 1st tier for sporadic Intellectual Disability and Autism Spectrum Disorder (identifies ~ 15%-20% of cases) Testing cont’d Source: Fogel & Geschwind, Clinical Neurogenetics Neurology in Clinical Practice, 6th ed. Notes: Neurology: Advanced Topics in Clinical Neurogenetics II Brent Fogel © 2009-2018 BeatTheBoards.com 877-225-8384 For exclusive use by : [email protected] Sharing or distribution is a violation of copyright laws. 3 Module: Clinical Evaluation Slides (10-17) Question: Which of the following, if present, is most suggestive of a genetic cause for a patient’s neurological disease? A. Young age of onset B. An associated medical condition C. A family member with similar symptoms D. Having been adopted as a child E. Involuntary movements Potential Clues to a Genetic Disease Positive family history Similarity to a known genetic syndrome Chronic, progressive clinical course Consanguinity Increased frequency in a specific ethnic group Source: Lynch and Farmer, eds: Neurogenetics, 2006. Why Is There No Family History? You didn’t ask Information unavailable – Adoption – Loss of contact – Non-cooperation – Paternity issues Anticipation/incomplete penetrance/ mosaicism Recessive, X-linked, or mitochondrial Maybe it really isn’t genetic! Diagnostic Reservoirs for Neurogenetic Disease Cerebral palsy Intellectual Disability Epilepsy Movement disorders Ataxias Dementias Multiple sclerosis Peripheral neuropathy Source: Lynch and Farmer, eds: Neurogenetics, 2006. Simple Rules for Clinical Evaluation & Testing Establish the clinical phenotype. All patients need a thorough history, physical examination, and family history. Develop a differential diagnosis Rule out non-genetic etiologies first unless the genetic condition is treatable Order gene tests for phenotypes not symptoms. They are not screening tests When possible, use disease biomarkers prior to genetic testing Iscreening Avoid Sanger-based gene “panels”. They are costly and waste resources. (Exome sequencing or panels using next-generation sequencing technology are more appropriate for heterogeneous phenotypes) Remember that patients need genetic counseling both before and after testing. When you diagnose a patient with a genetic disease you are often diagnosing their whole family For challenging cases, utilize neurogenetic/genetic specialists Module: Diagnostic Evaluation Slides (18-25) Question: You examine a child referred for intellectual disability, anxiety, and attention problems. Height is less than the 5th percentile. He has epicanthal folds, small widely spaced teeth, and strabismus. There is a history of an umbilical hernia, early onset of puberty, and a heart murmur. You clinically diagnose the patient with Williams syndrome. What is the correct confirmatory test? A. DNA sequencing for a missense mutation in the elastin gene (ELN) B. Florescent in-situ hybridization (FISH) for a contiguous gene deletion C. Polymerase chain reaction (PCR) testing for a CAG repeat expansion D. Chromosomal microarray analysis for duplication of the ELN, LIMK1, and GTF2I genes E. None. There is no associated molecular genetic etiology for this disorder Notes: Neurology: Advanced Topics in Clinical Neurogenetics II Brent Fogel © 2009-2018 BeatTheBoards.com 877-225-8384 4 For exclusive use by : [email protected] Sharing or distribution is a violation of copyright laws. Commercial Genetic Testing Number of genetic tests available per year Module: Next-Generation Sequencing in Diagnostic Testing Slides (26-36) Source: Adapted from Fogel & Geschwind, Clinical Neurogenetics Neurology in Clinical Practice, 6th ed. Types of Common Commercial Single-Gene Tests Full gene sequencing (Traditional Sanger method) – Most complete test but also most expensive – Can potentially discover novel coding mutations – REMEMBER: Not every sequence change causes disease! Targeted mutation analysis (Traditional Sanger method) – In general, detects only pre-defined mutations (useful in families) – REMEMBER: Negative test rules out only specific mutations! Copy number variation testing – Cannot identify sequence changes or other types of mutations Repeat expansion testing – Cannot identify sequence changes or other types of mutations Types of Common Commercial Multi-Gene Tests Genetic Panels - combine multiple types of testing for many different genes – Full gene sequencing – Targeted mutation analysis – Deletion/Duplication (CNV) testing – Repeat expansion testing Next-Generation Sequencing – greatly expands testing capacity – NGS panel testing – higher capacity and more flexibility – Exome sequencing (all 20,000+ genes in the genome) – Genome sequencing (includes non-coding regions & CNVs) Question: You are evaluating a patient with adult-onset spinocerebellar ataxia. Clinical evaluation has identified no cause to explain her condition. Her father had a balance disorder later in life. How might you best proceed with genetic testing in this patient? A. Genetic testing is not indicated because management will not change regardless of the molecular diagnosis B. Initial genetic testing should include the largest number of genes known to cause ataxic disorders C. Genetic testing should only focus on the most common disorders and/or genes relevant to the patient, genomic testing is not indicated D. Genetic testing should focus initially on the most common disorders and/or genes relevant to the patient, genomic testing could be considered if negative E. This phenotype is caused by mutation a single gene Exome Sequencing: An Unbiased Tool for Diagnosis Source: http://www.genome.gov/dmd/index.cfm?node=Photos/Graphics. Notes: Neurology: Advanced Topics in Clinical Neurogenetics II Brent Fogel © 2009-2018 BeatTheBoards.com 877-225-8384 For exclusive use by : [email protected] Sharing or distribution is a violation of copyright laws. 5 Next-Generation DNA Sequencing - Technology Source: Modified from Shendure & Ji, Nature Biotechnology (2008). Types of Commercial Next-Generation Sequencing Whole Exome (sometimes called a “Clinical Exome”) – Most complete test, covers all ~20,000 genes in the genome – Most expensive overall (~$5-10K) but least expensive per gene Next-Generation Panels (sometimes called “Exome Panels” or a “Clinical Exome”) – Less expensive per gene than traditional Sanger panels – Typically includes only a few to hundreds of genes depending on the test (some “Clinical Exome” panels are up to ~5,000 genes) – Some laboratories may offer reflex to whole exome if negative REMEMBER! – Different laboratories may analyze and/or report results differently – Exome sequencing can’t detect repeat expansions or all CNVs – Not every sequence change causes disease Advanced Clinical Genetic Testing Exome Sequencing is an unbiased form of genomic testing that assesses all 20,000 genes in the human genome simultaneously (cheap and efficient) Exome Sequencing improves diagnosis of clinically heterogeneous neurogenetic phenotypes (broad application) Exome Sequencing can lead to diagnoses that directly affect and improve patient management (clinically meaningful) Exome Sequencing reduces time to diagnosis sparing patients an extensive diagnostic odyssey (and sparing payers the subsequent costs) Advanced Clinical Genetic Testing Results can theoretically be re-examined as new genes or mutations are discovered (clinically dynamic) but may also return unintended results (e.g., breast cancer 1 (BRCA1) mutations) (unique ethical considerations) Exome Sequencing should compliment, not replace, a systematic patient evaluation (including high yield genetic testing if appropriate) Because results are not typically “positive” or “negative” physicians must receive education and training in the proper use and interpretation of exome sequencing (diseasespecific interpretation) Glossary of Genetic Terms Source: Adapted from Fogel & Geschwind, Clinical Neurogenetics Neurology in Clinical Practice, 6th ed. Notes: Neurology: Advanced Topics in Clinical Neurogenetics II Brent Fogel © 2009-2018 BeatTheBoards.com 877-225-8384 6 For exclusive use by : [email protected] Sharing or distribution is a violation of copyright laws. Answer Key Question: Which of the following, if present, is most suggestive of a genetic cause for a patient’s neurological disease? A. Young age of onset B. An associated medical condition C. A family member with similar symptoms D. Having been adopted as a child E. Involuntary movements Answer Explanation A clearly positive family history of disease is the only unambiguous method of determining a genetic etiology for a patient’s neurological condition in the absence of a previously identified genetic mutation Question: You examine a child referred for intellectual disability, anxiety, and attention problems. Height is less than the 5th percentile. He has epicanthal folds, small widely spaced teeth, and strabismus. There is a history of an umbilical hernia, early onset of puberty, and a heart murmur. You clinically diagnose the patient with Williams syndrome. What is the correct confirmatory test? A. DNA sequencing for a missense mutation in the elastin gene (ELN) B. Florescent in-situ hybridization (FISH) for a contiguous gene deletion C. Polymerase chain reaction (PCR) testing for a CAG repeat expansion D. Chromosomal microarray analysis for duplication of the ELN, LIMK1, and GTF2I genes E. None. There is no associated molecular genetic etiology for this disorder Answer Explanation Williams syndrome is caused by contiguous deletion of a region on chromosome 7 which includes the ELN, LIMK1, and GTF2I genes. Chromosomal microarray or comparative genomic hybridization could also be performed to detect this. Pathologic duplication of this region has been reported but has a distinctly different phenotype Question: You are evaluating a patient with adult-onset spinocerebellar ataxia. Clinical evaluation has identified no cause to explain her condition. Her father had a balance disorder later in life. How might you best proceed with genetic testing in this patient? A. Genetic testing is not indicated because management will not change regardless of the molecular diagnosis B. Initial genetic testing should include the largest number of genes known to cause ataxic disorders C. Genetic testing should only focus on the most common disorders and/or genes relevant to the patient, genomic testing is not indicated D. Genetic testing should focus initially on the most common disorders and/or genes relevant to the patient, genomic testing could be considered if negative E. This phenotype is caused by mutation a single gene Answer Explanation Spinocerebellar ataxia is a genetically heterogeneous neurological condition that can arise from mutation of over 600 genes. The majority of familial cases (~50%) are represented by a small number of genes while the remaining cases comprise rare disorders each of which cause