Human genetics and genomics : a practical guide PDF
Preview Human genetics and genomics : a practical guide
Human Genetics and Genomics APracticalGuide BaharTaneri EsraAsilmaz TüremDelikurt PembeSavas SeniyeTargen YagmurEsemen Authors AllbookspublishedbyWiley-VCH arecarefullyproduced.Nevertheless, BaharTaneri authors,editors,andpublisherdonot EasternMediterraneanUniversity, warranttheinformationcontainedin DepartmentofBiologicalSciences, thesebooks,includingthisbook,to Famagusta,NorthCyprus befreeoferrors.Readersareadvised and tokeepinmindthatstatements,data, illustrations,proceduraldetailsorother MaastrichtUniversity,Institutefor itemsmayinadvertentlybeinaccurate. PublicHealthGenomics,Department ofGeneticsandCellBiology,Faculty LibraryofCongressCardNo.: ofHealth,Medicine&LifeSciences, appliedfor Maastricht,TheNetherlands BritishLibraryCataloguing-in-Publication EsraAsilmaz Data GastroenterologyandGeneralInternal Acataloguerecordforthisbookis MedicineatHomertonUniversity availablefromtheBritishLibrary. Hospital,London,UnitedKingdom Bibliographicinformationpublishedby TüremDelikurt theDeutscheNationalbibliothek EuropeanBoardofMedicalGenetics TheDeutscheNationalbibliotheklists RegisteredGeneticCounselor thispublicationintheDeutsche Cyprus Nationalbibliografie;detailed bibliographicdataareavailableonthe PembeSavas Internetat<http://dnb.d-nb.de>. EasternMediterraneanUniversity, DepartmentofBiologicalSciences, ©2020Wiley-VCHVerlagGmbH& Famagusta,NorthCyprus Co.KGaA,Boschstr.12,69469 Weinheim,Germany SeniyeTargen BilkentUniversity,MolecularBiology Allrightsreserved(includingthoseof andGeneticsDepartment,Facultyof translationintootherlanguages).No Science,Cankaya,Ankara,Turkey partofthisbookmaybereproducedin anyform–byphotoprinting, YagmurEsemen microfilm,oranyothermeans–nor ImperialCollegeHealthcareNHSTrust, transmittedortranslatedintoa London machinelanguagewithoutwritten UnitedKingdom permissionfromthepublishers. Registerednames,trademarks,etc.used inthisbook,evenwhennotspecifically markedassuch,arenottobe consideredunprotectedbylaw. PrintISBN:978-3-527-33748-4 ePDFISBN:978-3-527-68265-2 ePubISBN:978-3-527-68263-8 CoverDesignGrafik-DesignSchulz Typesetting SPiGlobal,Chennai,India PrintingandBinding Printedonacid-freepaper 10 9 8 7 6 5 4 3 2 1 ForIrmak,Emir,MuharremGüderandCem,RemziyeTaneri-BT ForRüzgarandmyfamily-EA ForthelovingmemoryofmybelovedfatherRetiredMajorDervi¸sDelikurt-TD ForVildanNazandmyfamily-PS FormyfatherTözümTargen,motherBilgeTargenandsisterNe¸seTargen-ST FormymotherNeclaEsemenandmyfamily-YE andforallourstudents. vii Contents AbouttheAuthors xi Introduction xv 1 ExploringOnlineGeneticsSources 1 Background 1 HumanGenomeProject 2 NationalCenterforBiotechnologyInformation(NCBI) 2 UCSCGenomeBrowser 3 TheEncyclopediaofDNAElements(ENCODE) 3 RoadmapEpigenomicProject 5 References 5 ExerciseQuestions 6 AdditionalExerciseQuestions 11 2 ObservationofHumanInheritance 13 Background 13 MendelianGenetics 13 TheTransmissionofHereditaryCharacteristics 16 MendelianDisorders 19 References 20 ExerciseQuestions 21 AdditionalExerciseQuestions 22 3 Reading,Understanding,andConstructingHuman Pedigrees 25 Background 25 BasicPedigreeNomenclature 26 ModesofInheritance 26 AutosomalRecessiveInheritance 28 PedigreesRepresentingAutosomalRecessiveInheritance 28 AutosomalDominantInheritance 29 PedigreesRepresentingAutosomalDominantInheritance 30 X-LinkedRecessiveInheritance 30 PedigreesRepresentingX-LinkedRecessiveInheritance 31 viii Contents X-LinkedDominantInheritance 32 PedigreesRepresentingX-LinkedDominantInheritance 32 Y-LinkedInheritance 34 PedigreesRepresentingY-LinkedInheritance 34 Non-MendelianPatternsofInheritance 35 ConfoundingFactorsinPedigreeGenerationandInterpretation 36 References 36 ExerciseQuestions 38 AdditionalExerciseQuestions 39 4 Cytogenetics 43 Background 43 GenerationofKaryograms/ChromosomeBanding 45 FISH,FluorescentInSituHybridization 47 ComparativeGenomicHybridization(CGH)andArray-BasedCGH Technology 48 ChromosomalAbnormalities 48 NumericalChromosomalAbnormalities 49 StructuralChromosomalAbnormalities 50 References 51 ExerciseQuestions 52 AdditionalExerciseQuestions 54 5 ExploringDNA,RNA,andProteinSequenceDatabasesand GenomeBrowsers 55 Background 55 GeneralBiologicalDatabases 57 RNA-SpecificDatabases 59 Protein-SpecificDatabases 61 RegulatoryDNADatabase 62 GenomeBrowsers 65 References 67 ExerciseQuestions 67 AdditionalExerciseQuestions 68 6 ExploringOnlineBioinformaticsTools 71 Background 71 BLAST 71 ExPASy 72 ClustalOmega 74 Reactome 76 References 77 ExerciseQuestions 77 AdditionalExerciseQuestions 79 Contents ix 7 MultifactorialInheritanceandCommonComplexDiseases 81 Background 81 PolygenicComplexDiseases 82 InvestigatingComplexTraits 82 ObesityasaComplexDisease 83 DiabetesMellitusType2asaComplexDisease 84 CoronaryArteryDiseasesasComplexDiseases 85 References 86 ExerciseQuestions 88 AdditionalExerciseQuestions 88 8 NeurogeneticsandBehavioralGenetics 91 Background 91 GeneticRegulationofNeuralDevelopment 91 StructureandFunctionoftheNervousSystem 92 UnderstandingtheGeneticsofNeurologicalDisease 94 ExamplesofNeurogeneticDisorders 94 Huntington’sDisease 94 Parkinson’sDisease 95 RettSyndrome 95 BehavioralGenetics 96 GeneticsofDepression 97 GeneticsofDrugAddiction 97 GeneticsofSchizophrenia 98 References 99 ExerciseQuestions 100 AdditionalExerciseQuestions 101 9 CancerGenetics 103 Background 103 CellCycleandItsRegulation 104 OncogenesandTumorSuppressorGenes 105 Carcinogens/EnvironmentalFactorsinCancer 107 BreastCancer 108 RoleofMolecularMedicineinBreastCancerTreatment 110 RecentAdvancesinCancerDiagnosisandTreatment 111 References 112 ExerciseQuestions 113 AdditionalExerciseQuestions 114 10 GeneticCounseling 115 Background 115 References 117 ExerciseQuestions 117 AdditionalExerciseQuestions 119 x Contents 11 EvolvingToolsinGenomeEditing:CRISPR-Cas 121 Background 121 MechanismofCRISPR-Cas9System 123 ApplicationsofCRISPR-Cas9System 123 GenerationofAnimalModelsandEngineeringCells 123 SomaticGenomeEditing 124 RepairofGeneticDisorders 124 FunctionalGenomicScreening 124 TreatmentofInfectiousDiseases 125 OtherApplicationsofCRISPR-Cas9System 125 References 126 Acknowledgment 127 ExerciseQuestions 127 AdditionalExerciseQuestions 128 Glossary 129 Index 139 xi AbouttheAuthors Bahar Taneri is a Professor of Molecular Biology and Genetics at Eastern Mediterranean University (EMU), Famagusta, Cyprus. After obtaining her PhDdegreeinBiomedicalSciencesfromTheRock- efellerUniversity,NewYork,USA,in2005,shehas taught several Genetics and Genomics modules at EMU,whereshehasfoundedtheMolecularBiology andGeneticsundergraduateprogram.AtEMU,she has served as the editor-in-chief of the University ResearchNewsletterfortwoyears.ShehasalsobeenchairingtheDepartmentof BiologicalSciencessince2013.ShehasbeenanaffiliatedresearcheroftheInsti- tuteforPublicHealthGenomics,DepartmentofGeneticsandCellBiology,Fac- ultyofHealth,MedicineandLifeSciencesatMaastrichtUniversity,Netherlands, since2011.Shehasauthoredseveralpublicationsinthefieldsofgenomebiology andpersonalizedmedicine.Currently,hermainresearchinterestsincludehuman genomics,epigenomics,andefficienttranslationofpersonalizedgenome-based findingsintohealthcareandmedicine,forpredictionandpreventionofcommon complexdiseases.SheisafoundingmemberoftheMedicalBiotechnologyMas- ter’sprogramatEMU,wheresheteachesmodulesincludingGenomeEditing. Esra Asilmaz is currently a Locum Consultant in Gastroenterology and General Internal Medicine at Homerton University Hospital in London, UK. She obtainedherPhDdegreeinMolecularGeneticsfromThe Rockefeller University, NYC, USA, in 2004. She subse- quently obtained her Bachelor of Medicine, Bachelor of Surgery degree in 2009 from St. George’s University of London, UK. Between 2009 and 2011, she completed an academic foundation program at St. Thomas’ and Guy’s Hospital, London, UK. During this time, she worked at Professor Trembath’s LaboratoryofHumanGeneticsandwasinvolvedintheidentificationofNotch2 mutations in Hadju–Cheney Syndrome, a rare genetic condition. She was an AcademicClinicalFellowatUniversityCollegeHospital,London,UK,between 2011 and 2014 and was a member of Dr. Oben’s laboratory at the Institute of xii AbouttheAuthors LiverandDigestiveHealth.SheobtainedherMRCP(UK)Diplomain2014and Specialist Examination in Gastroenterology in 2016. She obtained her CCT in GastroenterologyandGeneralInternalMedicineinSeptember2019. Turem Delikurt is a registered genetic counselor. She graduated with a BSc in Biology from the University of South Dakota, USA, in 2003. She completed her MSc in Genetic Counseling with merit from the University of Manchester, UK, in 2006. She has been working as a geneticcounselorinCyprussince2006.In2015,shewas registered by the European Board of Medical Genetics. Her main research interest is the exploration of genetic counselingwithinthecontextofculture.Sheisdedicatedtoincreasingawareness aboutgeneticconditionsandgeneticcounseling,inCyprus.Shepennedaweekly columntitled“GeneticsToday”atoneofthemainnewspapersinCyprusfrom 2004until2017.Overtheyears,shehasbeencontinuouslyinvolvedinvarious civilsocietyactivitiesaimedatincreasingthequalityofcareandlifeofpatients andfamiliesatriskoforaffectedbygeneticconditionsinCyprus. Pembe Savas obtained her undergraduate degree in Medical Biochemistry from the University of Leicester, UK, in 2011 and further received an MSc degree in Reproductive Science and Women’s Health at Univer- sity College London, UK, in 2012. She has completed her project on pre-implantation genetic diagnosis of beta-thalassemia at Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus, in 2012, where she gained hands-onlaboratoryexperience.Since2013,PembeSavasisworkingasasenior instructor at the Department of Biological Sciences, Eastern Mediterranean University,Famagusta,Cyprus,wheresheisresponsibleforteachingnumerous modules for the Molecular Biology and Genetics program, including Human Genetics. Her research interests include genetic testing in common complex diseases.Furthermore,since2017shehasbeenactivelyinvolvedintheCyprus Women’sHealthResearchInitiative. Seniye Targen obtained her undergraduate degree in HumanGeneticsfromNewcastleUniversity,UK,in2009 and further specialized in the field of Human Molecular Genetics at Imperial College London, UK, in 2010, where she completed a project on X-linked cataract and Nance–HoranSyndrome.Uponcompletinghergraduate degree,shegainedexperienceinprivatemedicaldiagnos- tic laboratories. She had been employed as a laboratory instructorintheDepartmentofBiologicalSciencesattheEasternMediterranean University, Famagusta, Cyprus, from 2013 to 2015. Currently, she is working toward a PhD degree in Molecular Biology and Genetics Department with particularfocusonbreastcancerbiologyatBilkentUniversity,Ankara,Turkey.
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