{"id":4823,"date":"2021-11-18T00:00:00","date_gmt":"2021-11-18T00:00:00","guid":{"rendered":"https:\/\/www.proefschriftmaken.nl\/portfolio\/zeinab-fadaie\/"},"modified":"2026-03-18T08:36:54","modified_gmt":"2026-03-18T08:36:54","slug":"zeinab-fadaie","status":"publish","type":"us_portfolio","link":"https:\/\/www.proefschriftmaken.nl\/en\/portfolio\/zeinab-fadaie\/","title":{"rendered":"Zeinab Fadaie"},"content":{"rendered":"","protected":false},"excerpt":{"rendered":"","protected":false},"author":7,"featured_media":4825,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"footnotes":""},"us_portfolio_category":[45],"class_list":["post-4823","us_portfolio","type-us_portfolio","status-publish","has-post-thumbnail","hentry","us_portfolio_category-new-template"],"acf":{"naam_van_het_proefschift":"Inherited retinal diseases","samenvatting":"versterken of verzwakken. Gebruik makend van deze voorspellingen konden we kandidaat varianten\nbeter selecteren.\n\nHoofdstuk 3.2 beschrijft de identificatie van een RNA splice site variant (c.7N8H2PG>A) die aanwezig\nis buiten de consensus splice site sequentie in TULPN. De variant werd door WES ge\u00efdentificeerd bij\neen broer en zus met vroegoptredende retinitis pigmentosa bij wie eerder een andere pathogene\nmissense variant in TULPN werd gevonden. De c.7N8H2PG>A variant heeft geen significant effect op de\nsplice donor site van exon 7. Echter de balans wordt verstoord tussen de versterker en verzwakker\nmotieven in deze positie en leidt tot een splice defect. Dit hoofdstuk belicht de belangrijke rol van\ngeconserveerde motieven in de splicing processen.\n\nDe nadruk in hoofdstuk 3.3 ligt op het effect van varianten in cis op de resulterende eiwitfunctie. We\nbeschreven twee niet-verwante families met vitelliforme macula-dystrofie met ziekte aanvang op\nvolwassen leeftijd die een complex allel in IMPG2 dragen (c.[3023-NST>AIPO2PG>A]) na analyse van\nWES-gegevens. De c.PO2PG>A variant is niet alleen een mogelijke pathogene missense mutatie op\nzichzelf, maar fungeert ook als een modificerend element voor c.3023-NST>A door het splice defect\nals gevolg van deze variant te versterken. In beide families ontwikkelden individuen die dit complexe\nallel op een heterozygote manier droegen niet altijd een macula dystrofie, wat het belang onderstreept\nvan andere genetische en omgevingsfactoren die bijdragen aan deze ziekte.\n\nHoofdstuk 3.4 werpt licht op de pathogene rol van een \u2018branchpoint\u2019 variant (c.592-2NA>T) in BBSN\nin vier niet-verwante families met niet-syndromale retinitis pigmentosa die c.NNS9T>G droegen, de\nmeest voorkomende variant in BBSN, in de andere allel. De branchpoint-variant werd ge\u00efdentificeerd\ndoor middel van WGS-analyse en het complexe splice defect werd gevonden met behulp van in vitro\nmidigene splice-assays. In dit hoofdstuk wordt de eerste pathogene branchpoint variant beschreven die\nin IRDs wordt gerapporteerd.\n\nHoofdstuk 4 beschrijft een uitgebreide studie waarin 100 individuen met verschillende IRDs werden\nbestudeerd m.b.v. WGS. De index pati\u00ebnten waren eerder gescreend via WES of gen-specifieke\nsequencing en waren genetisch nog niet opgelost. De WGS-analyse werd uitgevoerd met speciale\naandacht voor de niet-coderende varianten en de mogelijk causale varianten werden onderzocht m.b.v. 7\nin vitro functionele assays om de pathogeniciteit te bewijzen. We bieden een moleculaire diagnose voor\n27% van de vooraf gescreende gevallen en suggereren een verdere verbetering van\nsequentietechnologie\u00ebn en interpretatie van varianten om de diagnostische opbrengst voor IRDs te\nverhogen.\n\nHoofdstuk 5 illustreert de implementatie van een nieuwe strategie voor de identificatie van het\ngenetisch defect in IRDs met een sterke correlatie tussen genotype en fenotype. In een familie met\nchoroideremie toonde eerdere RNA-analyse van een pati\u00ebnt het overslaan van CHM exon 12, maar\nhet onderliggende DNA-defect bleef 18 jaar lang ongrijpbaar. Met behulp van optische genoom mapping\nen WGS waarin lange DNA-moleculen werden geanalyseerd, werd een omgekeerde duplicatie in CHM\nge\u00efdentificeerd. We hebben een model verstrekt dat de oorsprong van de SV aantoont door middel\nvan \u2018fork stalling and a template switching\/microhomology-mediated break-induced replication\nmechanism\u2019. Daarnaast speculeerden we over het mechanisme van het splice defect en stelden we de\nvorming voor van een secundaire RNA-structuur die de splicing van exon 12 verstoorde. Dit hoofdstuk\nbenadrukt de grote mogelijkheden van optische genoom mapping en lange moleculen WGS om de\nverborgen SVs in onopgeloste gevallen te ontrafelen evenals de ondergewaardeerde rol van\nveranderingen van de secundaire structuur van RNA als ziektemechanisme.\n\nTen slotte geeft Hoofdstuk 6 een algemene bespreking van de belangrijkste bevindingen in dit\nproefschrift en hun implicaties voor een verbeterde diagnose van IRDs. De toepassing van verschillende\nsequentietechnologie\u00ebn en hun voor en nadelen worden uitgelegd. Het belang van branchpoint\nvarianten, complexe allelen en varianten die de secundaire RNA-structuur be\u00efnvloeden, werd\nbesproken. Bovendien werd de behoefte aan nauwkeurige splicing voorspellingsprogramma\u2019s verklaard\ndoor verschillende voorspellingsalgoritmen te vergelijken en hun belang in in vitro functionele\nsplicingtesten te benadrukken. Ten slotte werden mogelijke redenen voor het missen van pathogene\nvarianten in de bestudeerde cohort besproken en werd gepostuleerd dat de toepassing van lange DNA-\nmoleculen sequencing een belangrijke techniek kan zijn voor de toekomst van IRDs en andere\ngenetische aandoeningen. Daarnaast kunnen de verschillende cellulaire systemen voor in vitro\nfunctionele analyse lichtschijnen op gemiste oorzaken van IRDs in de toekomst.\n\nSimpele\n\nWe krijgen ons erfelijk materiaal van onze ouders. Dit erfelijk materiaal is het DNA. We krijgen van\nelke ouder \u00e9\u00e9n kopie van het DNA. Maar wat is DNA? DNA is het boek van het leven. Het heeft\nverschillende hoofdstukken die genen worden genoemd. Het alfabet van dit boek bestaat uit slechts\nvier letters, namelijk A, T, G en C. Elk gen bevat instructies voor het maken van een eiwit. Eiwitten\nzijn de bouwstenen van ons lichaam; het zijn de eiwitten die ons eten verteren, die onze botten\nstevigheid geven, die onze spieren doen bewegen, die onze ogen laten zien etc. Om een eiwit te maken\nworden de instructies uit het gen eerst gekopieerd in RNA. De RNA kopie\u00ebn worden gebruikt om\neiwitten te maken.\nHet RNA is een kopie van een gen en bevat dus dezelfde informatie als het gen. Maar niet alle informatie\nis nodig om een eiwit te maken. Sommige pagina\u2019s bevatten belangrijke instructies om het eiwit te\nmaken. Deze pagina\u2019s worden exonen genoemd. De andere pagina's, die tussen de exonen in liggen,\nzijn niet belangrijk en worden intronen genoemd. De niet-belangrijke pagina's (intronen) moeten\nworden verwijderd voordat de RNA kopie gebruikt kan worden om een eiwit te maken.\nEr zijn verschillende technologie\u00ebn die het complete levensboek (DNA) kunnen lezen of alleen de\nbelangrijke pagina's ervan (exonen). Met behulp van deze technologie\u00ebn kunnen we verschillen tussen\npersonen of afwijkingen ontdekken. Sommige afwijkingen zijn niet schadelijk: de instructies kunnen\nnog steeds gebruikt worden om een functioneel eiwit te maken. Maar andere afwijkingen zijn schadelijk.\nDeze afwijkingen worden mutaties genoemd. Als deze fouten (mutaties) voorkomen in een van de\nhoofdstukken, kloppen de instructies voor het maken van een eiwit niet meer. In dit geval worden er\nniet-werkende eiwitten gemaakt of zelfs helemaal geen eiwitten. De schadelijke fouten (mutaties)\nkunnen voorkomen in de hoofdstukken (genen) die blindheid kunnen veroorzaken. In mijn\npromotieproject gebruikten we verschillende technologie\u00ebn en probeerden we deze schadelijke fouten\nte vinden in oog-gerelateerde genen. Bovendien wilden we begrijpen hoe de instructies voor het maken\nvan eiwitten door de fouten wordt veranderd.\nDeze schadelijke fouten kunnen voorkomen op de belangrijke pagina's (exonen). Maar ze kunnen ook\nvoorkomen op de niet-belangrijke pagina's (intronen) die verwijderd moeten worden. Mijn\npromotieproject richt zich op de fouten in de niet-belangrijke pagina's. Het is niet altijd gemakkelijk\nom te interpreteren hoe de instructies voor het maken van eiwitten zullen veranderen door de fouten\nin de niet-belangrijke pagina's. Er kan bijvoorbeeld een schadelijke fout in het midden van een niet-\nbelangrijke pagina staan die ervoor zorgt dat er een extra stap wordt toegevoegd aan de\nbouwinstructies voor een eiwit. Op deze manier bevat de kopie (RNA) te veel informatie. De\neiwitfabriek leest ook de extra informatie en resulteert in misvormde eiwitten of helemaal geen\neiwitten. Het gevolg is dat dat specifieke eiwit zijn werk niet kan doen. We hebben verschillende\nvoorbeelden van deze fouten gevonden, zoals is te lezen in hoofdstuk 3.1 en hoofdstuk 4 van mijn\nproefschrift.\nSoms bevinden de schadelijke fouten zich op de overgang van een belangrijke pagina (exon) naar een\nniet-belangrijke pagina (intron). De gevolgen van deze schadelijke fouten zijn verschillend. Soms\nverwijderen ze (een deel van) een belangrijke pagina. Hierdoor kan er geen gezond eiwit worden\ngemaakt. Andere keren blijft een deel van de niet-belangrijke pagina op de belangrijke pagina staan en\nwordt niet verwijderd. Dat leidt uiteindelijk ook tot verkeerde instructies en een niet-functioneel eiwit.\nIn mijn proefschrift vonden we verschillende van deze schadelijke fouten, zoals is te lezen in\nHoofdstuk 3 en Hoofdstuk 4.\nDe schadelijke fouten bestaan niet altijd uit slechts \u00e9\u00e9n letter. Ze kunnen ook groter zijn. In dat geval\nzijn er meerdere pagina's of hoofdstukken gekopieerd of verwijderd. Verder kan de volgorde van de\npagina\u2019s of de hoofdstukken veranderd zijn. Deze fouten leiden er eveneens toe dat de instructies voor\nhet maken van eiwitten niet meer kloppen en daardoor worden er geen functionele eiwitten meer\n\nSimpele\n\ngemaakt. In Hoofdstuk 4 en Hoofdstuk 5 van mijn proefschrift hebben we enkele van deze grote\nschadelijke fouten beschreven.\n\nTijdens mijn promotieonderzoek hebben we veel schadelijke kleine en grote fouten ontdekt die de\ninstructies voor het maken van eiwitten be\u00efnvloeden. Alleen als we weten hoe de instructies zijn\nveranderd, kunnen we een manier vinden om de fouten te herstellen, zodat er weer een functioneel\neiwit gemaakt kan worden. Mijn onderzoek is een eerste stap in dit proces en maakt het op termijn\nmogelijk om pati\u00ebnten met een erfelijke vorm van slechtziendheid te kunnen helpen.\n\n\u0647\u062f\ufe8e\ufeb3 \u0646\ufe8e\ufe91\u0632 \ufeea\ufe91 \ufbfd\ufeb3\u0631\ufe8e\ufed3 \ufeea\ufebb\ufefc\ufea7\n\n\ufeea\ufea8\ufeb4\ufee7 \ufb8f\ufbfe \u0631\u062f\ufe8e\ufee3 \ufe8e\ufbfe \u0631\ufeaa\ufb58 \ufeae\ufeeb \u0632\u0627 \ufe8e\ufee3 \u0648 \u062f\ufeee\ufeb7 \ufbfd\ufee3 \u0647\ufeaa\ufbff\ufee3\ufe8e\ufee7 DNA \ufbfd\ufe9b\u0631\u0627 \u0647\u062f\ufe8e\ufee3 \ufee6\ufbfe\u0627 . \ufee2\ufbfe\ufeae\ufe91 \ufbfd\ufee3 \u062b\u0631\u0627 \ufeea\ufe91 \u062f\ufeee\ufea7 \u0646\u0627\u0631\ufeaa\ufb58 \u0648 \u0646\u0627\u0631\u062f\ufe8e\ufee3 \u0632\u0627 \u0627\u0631 \u062f\ufeee\ufea7 \ufbfd\ufe98\ufe9b\u0627\u0631\u0648 \u062f\u0627\ufeee\ufee3 \ufe8e\ufee3\n\u0647\ufeaa\ufbff\ufee3\ufe8e\ufee7 \u0646\u0698 \ufeea\ufb90 \u062f\u0631\u0627\u062f \ufbfd\ufed4\ufee0\ufe98\ufea8\ufee3 \u06cc\ufe8e\ufeeb 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\ufeaa\ufee8\ufe98\ufeb4\ufbff\ufee7 \ufec2\ufe92\ufe97\ufeae\ufee3 \u0646\ufe8e\ufe98\ufeb3\u0627\u062f \u060c \ufe8e\ufe91 \u0646\u0648\ufeb0\ufb94\u0627 \ufee6\ufbff\ufe91 \u0631\u062f \u060c\ufeae\ufb95\ufbfe\u062f \u062a\ufe8e\ufea4\ufed4\ufebb \u0648 \ufeaa\ufee7\ufeee\ufeb7 \ufbfd\ufee3 \u0647\ufeaa\ufbff\ufee3\ufe8e\ufee7\n. \u062f\ufeee\ufeb7 \ufeea\ufe98\ufea7\ufe8e\ufeb3 \ufee2\ufedf\ufe8e\ufeb3 \ufee6\ufbff\ufe8c\ufe97\u0648\ufeae\ufb58 \ufb8f\ufbfe \ufe8e\ufeec\ufe98\ufee7\u0627 \u0631\u062f \ufe8e\ufe97 \ufeaa\ufee7\ufeee\ufeb7 \u0627\ufeaa\ufe9f \ufeea\ufe98\ufeb4\ufeeb \u0632\u0627 \u062c\u0631\ufe8e\ufea7 \ufeea\ufe91 \u0646\ufe8e\ufeb3\u0631 \u0645\ufe8e\ufbff\ufb58 \u0644\ufe8e\ufeb3\u0631\u0627 \u0632\u0627 \ufede\ufe92\ufed7 \ufeaa\ufbfe\ufe8e\ufe91\n\n. \ufe8e\ufe91 \ufeaa\ufee7\u0627\ufeee\ufea8\ufe91 \u0627\u0631 ( \ufe8e\ufeeb \u0646\u0648\ufeb0\ufb94\u0627 ) \u0646\u0622 \ufee2\ufeec\ufee3 \u062a\ufe8e\ufea4\ufed4\ufebb \ufe8e\ufeec\ufee8\ufe97 \ufe8e\ufbfe \ufede\ufee3\ufe8e\ufb90 \u0631\ufeee\ufec3 \u0627\u0631 \ufeea\ufe91 ( DNA ) \ufbfd\ufb94\ufeaa\ufee7\u0632 \u0628\ufe8e\ufe98\ufb90 \u0641\u0648\ufeae\ufea3 \ufeaa\ufee7\u0627\ufeee\ufe97 \ufbfd\ufee3 \ufeea\ufb90 \u062f\u0631\u0627\u062f \u062f\ufeee\ufe9f\u0648 \u06cc\u0631\u0648\ufe8e\ufee8\ufed3 \ufee6\ufbfe\ufeaa\ufee8\ufb7c\n\ufeaa\ufbff\ufedf\ufeee\ufe97 \ufeea\ufee7\ufe8e\ufea7\u0631\ufe8e\ufb90 \u0648 \ufeaa\ufee8\ufe98\ufeb4\ufbff\ufee7 \u0631\u0648\u0622 \u0646\ufe8e \u0632 \ufbfe \u062a\ufe8e\ufeeb\ufe8e\ufe92\ufe98\ufeb7\u0627 \u0632\u0627 \ufbfd\ufea7\ufeae\ufe91 . \ufe96\ufed3\ufe8e\ufbfe \u0627\u0631 \u0628\ufe8e\ufe98\ufb90 \ufee6\ufbfe\u0627 \u0631\u062f \u062f\ufeee\ufe9f\ufeee\ufee3 \u062a\ufe8e\ufeeb\ufe8e\ufe92\ufe98\ufeb7\u0627 \u0646\u0627\ufeee\ufe97 \ufbfd\ufee3 \ufe8e\ufeeb \u06cc\u0631\u0648\ufe8e\ufee8\ufed3 \ufee6\ufbfe\u0627 \u0632\u0627 \u0647\u062f\ufe8e\ufed4\ufe98\ufeb3\u0627\n\u0631\ufe8e\ufbff\ufeb4\ufe91 \u062a\ufe8e\ufeeb\ufe8e\ufe92\ufe98\ufeb7\u0627 \u0632\u0627 \ufbfd\ufea7\ufeae\ufe91 \u060c \u0644\ufe8e\ufea3 \ufee6\ufbfe\u0627 . \ufe8e\ufe91 \u062f\u0632\ufe8e\ufeb4\ufe91 \ufbfd\ufee4\ufedf\ufe8e\ufeb3 \u0648 \u0628\ufeee\ufea7 \ufee6\ufbff\ufe8c\ufe97\u0648\ufeae\ufb58 \u0646\u0622 \u0648 \u0632\u0627 \ufeaa\ufee7\u0627\ufeee\ufea8\ufe91 \u0627\u0631 \u0646\ufe8e\ufe98\ufeb3\u0627\u062f \ufeaa\ufee7\u0627\ufeee\ufe97 \ufbfd\ufee3 \u0646\ufe8e\ufee8\ufb7d\ufee4\ufeeb \u0644\ufeee\ufee0\ufeb3 \u0631\u062f \ufee6\ufbff\ufe8c\ufe97\u0648\ufeae\ufb58\n\ufee6\ufb91\ufee4\ufee3 \ufee6\ufbff\ufe8c\ufe97\u0648\ufeae\ufb58 \ufeea\ufee7\ufe8e\ufea7\u0631\ufe8e\ufb90 \u060c \ufeaa\ufe98\ufed4\ufbff\ufe91 \u0642\ufe8e\ufed4\ufe97\u0627 \ufe8e\ufeeb \ufede\ufebc\ufed3 \u0632\u0627 \ufbfd\ufb91\ufbfe \u0631\u062f ( \ufe8e\ufeeb \ufeb6\ufeec\ufe9f ) \u062a\ufe8e\ufeeb\ufe8e\ufe92\ufe98\ufeb7\u0627 \ufee6\ufbfe\u0627 \ufeae\ufb94\u0627 . \ufeaa\ufee7\ufeee\ufeb7 \ufbfd\ufee3 \u0647\ufeaa\ufbff\ufee3\ufe8e\ufee7 \ufeb6\ufeec\ufe9f \ufeea\ufb90 \ufeaa\ufee8\ufe98\ufeb4\ufeeb \u0631\u0648\u0622 \u0646\ufe8e \u0632 \ufbfe\n\ufee2\ufedf\ufe8e\ufeb3\ufe8e\ufee7 \ufee6\ufbff\ufe8c\ufe97\u0648\ufeae\ufb58 \u0648 \ufe8e\ufbfe \ufe96\ufeb7\u0627\u062f \ufee2\ufbff\ufeeb\u0627\ufeee\ufea8\ufee7 \ufee6\ufbff\ufe8c\ufe97\u0648\ufeae\ufb58 \ufb7b\ufbff\ufeeb \ufe8e\ufbfe \ufe96\ufedf\ufe8e\ufea3 \ufee6\ufbfe\u0627 \u0631\u062f . \ufeaa\ufee7\u0627\ufeee\ufea8\ufe91 \u0627\u0631 \u0646\u0622 \ufeaa\ufee7\u0627\ufeee\ufe98\ufee7 \u064b\ufefc\ufebb\u0627 \ufe8e\ufbfe \ufeaa\ufee8\ufb90 \ufeae\ufbff\ufe92\ufecc\ufe97 \ufeee\ufeb3 \u0627\u0631 \ufee6\ufbff\ufe8c\ufe97\u0648\ufeae\ufb58 \u0646\ufe8e\ufe98\ufeb3\u0627\u062f \ufe96\ufeb3\u0627\n\ufbfd\ufbfe\ufe8e\ufee8\ufbff\ufe91\ufe8e\ufee7 \ufeea\ufe91 \ufeae\ufea0\ufee8\ufee3 \ufeaa\ufee7\u0627\ufeee\ufe97 \ufbfd\ufee3 \ufeea\ufb90 \ufeaa\ufee8\ufeeb\u062f \u062e\u0631 \ufee2\ufeb8\ufb7c \ufeea\ufe91 \u0637\ufeee\ufe91\ufeae\ufee3 \u06cc ( \ufe8e\ufeeb \u0646\u0698 \ufe8e\ufeeb ) \ufede\ufebc\ufed3 \u0631\u062f \ufe96\ufeb3\u0627 \ufee6\ufb91\ufee4\ufee3 ( \ufe8e\ufeeb \ufeb6\ufeec\ufe9f ) \u062a\ufe8e\ufeeb\ufe8e\ufe92\ufe98\ufeb7\u0627 . \ufeaa\ufeb7 \ufeaa\ufeeb\u0627\ufeee\ufea7 \ufeaa\ufbff\ufedf\ufeee\ufe97\n\u06cc\ufe8e\ufeeb \u0646\u0698 \u0631\u062f \u0627\u0631 ( \ufe8e\ufeeb \ufeb6\ufeec\ufe9f ) \u062a\ufe8e\ufeeb\ufe8e\ufe92\ufe98\ufeb7\u0627 \ufee6\ufbfe\u0627 \ufee2\ufbfe\u062f\ufeae\ufb90 \ufbfd\ufecc\ufeb3 \u0648 \ufee2\ufbfe\u062f\ufeae\ufb90 \u0647\u062f\ufe8e\ufed4\ufe98\ufeb3\u0627 \ufbfd\ufed4\ufee0\ufe98\ufea8\ufee3 \u06cc\ufe8e\ufeeb \u06cc\u0631\u0648\u0622 \ufee6\ufed3 \u0632\u0627 \ufe8e\ufee3 \u060c\ufee6\ufee3 \u06cc\u0627\ufeae\ufe98\ufb90\u062f \u0647\u0698\u0648\ufeae\ufb58 \u0631\u062f . \u062f\ufeee\ufeb7\n\u06a9\u0631\u062f \u0648 \ufbfd\ufee8\ufbff\ufe91 \ufeb6\ufbff\ufb58 \u062a\ufe8e\ufeeb\ufe8e\ufe92\ufe98\ufeb7\u0627 \ufee6\ufbfe\u0627 \u0633\ufe8e\ufeb3\u0627 \ufe8e\ufeeb \u0627\u0631 \ufeae\ufe91 \ufee6\ufbff\ufe8c\ufe97\u0648\ufeae\ufb58 \ufeea\ufe98\ufed3\ufe8e\ufbfe \ufeae\ufbff\ufbff\ufed0\ufe97 \u0646\ufe8e\ufe98\ufeb3\u0627\u062f \ufee2\ufbfe\u062f\ufeae\ufb90 \u0634\ufefc\ufe97 \ufe8e\ufee3 \u060c\ufee6\ufbfe\u0627 \ufeae\ufe91 \u0647\u0648\ufefc\ufecb . \ufee2\ufbff\ufee8\ufb90 \u0627\ufeaa\ufbff\ufb58 \ufee2\ufeb8\ufb7c \ufeea\ufe91 \u0637\ufeee\ufe91\ufeae\ufee3\n. \ufee2\ufbff\ufee8\ufb90\n\ufeea\ufb90 ( \u060c \ufe8e\ufeeb \u0646\u0648\ufeae\ufe98\ufee8\ufbfe\u0627 ) \ufec2\ufe92\ufe97\ufeae\ufee3\ufeae\ufbff\ufecf \u062a\ufe8e\ufea4\ufed4\ufebb \u0631\u062f \u062f\u0631\u0627\u062f \u0646\ufe8e\ufb91\ufee3\u0627 \ufee6\ufbff\ufee8\ufb7d\ufee4\ufeeb . \ufeaa\ufe98\ufed4\ufbff\ufe91 \u0642\ufe8e\ufed4\ufe97\u0627 ( \ufe8e\ufeeb \u0646\u0648\ufeb0\ufb94\u0627 ) \ufee2\ufeec\ufee3 \u062a\ufe8e\ufea4\ufed4\ufebb \u0631\u062f \u062a\ufe8e\ufeeb\ufe8e\ufe92\ufe98\ufeb7\u0627 \ufee6\ufbfe\u0627 \ufe96\ufeb3\u0627 \ufee6\ufb91\ufee4\ufee3\n\u0646\ufe8e\ufe98\ufeb3\u0627\u062f \u06a9\u0631\u062f \u0648 \ufeae\ufbff\ufeb4\ufed4\ufe97 . \ufe96\ufeb3\u0627 \ufeb0\ufb90\ufeae\ufee4\ufe98\ufee3 \ufec2\ufe92\ufe97\ufeae\ufee3 \ufeae\ufbff\ufecf \u062a\ufe8e\ufea4\ufed4\ufebb \u0631\u062f \u062a\ufe8e\ufeeb\ufe8e\ufe92\ufe98\ufeb7\u0627 \u06cc\u0648\u0631 \ufee6\ufee3 \u06cc\u0627\ufeae\ufe98\ufb90\u062f \u06cc \u0647\u0698\u0648\ufeae\ufb58 . \ufeaa\ufe98\ufed4\ufbff\ufe91 \u0642\ufe8e\ufed4\ufe97\u0627 \ufeb0\ufbff\ufee7 \u060c\ufeaa\ufee7\ufeee\ufeb7 \u0641\ufeac\ufea3 \ufeaa\ufbfe\ufe8e\ufe91\n\u0647\ufe8e\ufe92\ufe98\ufeb7\u0627 \ufb8f\ufbfe \ufe96\ufeb3\u0627 \ufee6\ufb91\ufee4\ufee3 \u060c\u0644\ufe8e\ufe9c\ufee3 \u0646\u0627\ufeee\ufee8\ufecb \ufeea\ufe91 . \ufe96\ufeb4\ufbff\ufee7 \u0646\ufe8e\ufeb3\u0622 \ufeea\ufeb8\ufbff\ufee4\ufeeb \ufec2\ufe92\ufe97\ufeae\ufee3 \ufeae\ufbff\ufecf \u062a\ufe8e\ufea4\ufed4\ufebb \u0631\u062f \u062a\ufe8e\ufeeb\ufe8e\ufe92\ufe98\ufeb7\u0627 \u062f\u0627\ufeaa\ufea7\u0631 \ufede\ufbff\ufedf\u062f \ufeea\ufe91 \ufee6\ufbff\ufe8c\ufe97\u0648\ufeae\ufb58 \ufeea\ufe98\ufed3\ufe8e\ufbfe \ufeae\ufbff\ufbff\ufed0\ufe97\n\ufeea\ufe91 . \ufeaa\ufee8\ufb90 \ufeea\ufed3\ufe8e\ufebf\u0627 \ufee6\ufbff\ufe8c\ufe97\u0648\ufeae\ufb58 \u0646\ufe8e\ufe98\ufeb3\u0627\u062f \u0627\u0631 \ufeea\ufe91 \ufbfd\ufed3\ufe8e\ufebf\u0627 \ufe96\ufeb3\u0631\u062f\ufe8e\ufee7 \u062a\ufe8e\ufecb\ufefc\ufec3\u0627 \ufeaa\ufee7\u0627\ufeee\ufe97 \ufbfd\ufee3 \ufeea\ufb90 \ufeaa\ufeb7\ufe8e\ufe91 \ufeea\ufe98\ufeb7\u0627\u062f \u062f\ufeee\ufe9f\u0648 ( \u0646\u0648\ufeae\ufe98\ufee8\ufbfe\u0627 ) \ufec2\ufe92\ufe97\ufeae\ufee3 \ufeae\ufbff\ufecf \ufeea\ufea4\ufed4\ufebb \ufec2\ufeb3\u0648 \u0631\u062f\n\u0646\ufe8e\ufe98\ufeb3\u0627\u062f \ufee6\ufbfe\u0627 \ufeb0\ufbff\ufee7 \ufee6\ufbff\ufe8c\ufe97\u0648\ufeae\ufb58 \ufeaa\ufbff\ufedf\ufeee\ufe97 \ufeea\ufee7\ufe8e\ufea7\u0631\ufe8e\ufb90 . \u062f\ufeee\ufeb7 \ufbfd\ufee4\ufee7 \u0627\ufeaa\ufe9f \u0648 \ufeaa\ufee7\ufe8e\ufee3 \ufbfd\ufee3 \ufbfd\ufed7\ufe8e\ufe91 \u0646\ufe8e\ufeb3\u0631 \u0645\ufe8e\ufbff\ufb58 \u0631\u062f \ufec2\ufe92\ufe97\ufeae\ufee3 \ufeae\ufbff\ufecf \ufeea\ufea4\ufed4\ufebb \ufee6\ufbfe\u0627 \u0632\u0627 \ufbfd\ufeb8\ufea8\ufe91 \u060c\ufe90\ufbff\ufe97\ufeae\ufe97 \ufee6\ufbfe\u0627\n\u0644\ufeee\ufee0\ufeb3 \u0631\u062f \u0635\ufe8e\ufea7 \ufee6\ufbff\ufe8c\ufe97\u0648\ufeae\ufb58 \u0646\u0622 \ufeea\ufb90 \ufe96\ufeb3\u0627 \ufee6\ufbfe\u0627 \ufeea\ufea0\ufbff\ufe98\ufee7 . \ufeaa\ufeb3\ufeae\ufbff\ufee4\ufee7 \u0645\ufe8e\ufee4\ufe97\u0627 \u0648 \ufeea\ufe91 \u0647\ufeaa \ufeb7 \ufed2\ufed7\ufeee\ufe98\ufee3 \u0646\ufe8e\ufe98\ufeb3\u0627\u062f \ufec2\ufeb3\u0627\u0648\u0627 \u0631\u062f \u064b\ufefb\ufeee\ufee4\ufecc\ufee3 \ufeea\ufb90 \ufeaa\ufee7\u0627\ufeee\ufea7 \ufbfd\ufee3 \u0627\u0631 \ufee2\ufedf\ufe8e\ufeb3\ufe8e\ufee7\n4 \ufede\ufebc\ufed3 \u0648 \u06f3.\u06f1 \ufede\ufebc\ufed3 \u0631\u062f \u0627\u0631 \ufe8e\ufeeb \u0646\u0622 \u0633\ufe8e\ufeb3\u0627 \ufeae\ufe91 \ufee6\ufbff\ufe8c\ufe97\u0648\ufeae\ufb58 \u0646\ufe8e\ufe98\ufeb3\u0627\u062f \ufeae\ufbff\ufbff\ufed0\ufe97 \ufbfd\ufb95\ufee7\ufeee\ufb95\ufb7c \u0648 \u062a\ufe8e\ufeeb\ufe8e\ufe92\ufe98\ufeb7\u0627 \ufee6\ufbfe\u0627 \u0632\u0627 \ufeea\ufee7\ufeee\ufee4\ufee7 \ufee6\ufbfe\ufeaa\ufee8\ufb7c \ufe8e\ufee3 . \ufeaa\ufeb7 \ufeaa\ufeeb\u0627\ufeee\ufea8\ufee7 \ufeaa\ufbff\ufedf\ufeee\ufe97 \ufe8e\ufeeb\n. \ufee2\ufbfe\u062f\u0627\u062f \u062d\ufeae\ufeb7 \ufeea\ufee3\ufe8e\ufee7 \u0646\ufe8e\ufbfe\ufe8e\ufb58 \ufee6\ufbfe\u0627\n\n\u062a\u0648\ufe8e\ufed4\ufe98\ufee3 \u062a\ufe8e\ufeeb\ufe8e\ufe92\ufe98\ufeb7\u0627 \ufee6\ufbfe\u0627 \ufe90\ufed7\u0627\ufeee\ufecb . \ufeaa\ufee7\u0631\u0627\u062f \u0631\u0627\ufeae\ufed7 ( \u0646\u0648\ufeae\ufe98\ufee8\ufbfe\u0627 ) \ufec2\ufe92\ufe97\ufeae\ufee3\ufeae\ufbff\ufecf \ufeea\ufea4\ufed4\ufebb \u0648 ( \u0646\u0648\ufeb0\ufb94\u0627 ) \ufee2\ufeec\ufee3 \ufeea\ufea4\ufed4\ufebb \u06cc\ufe8e\ufeeb\u0632\ufeae\ufee3 \u0631\u062f \u0631\u0648\u0622 \u0646\ufe8e \u0632 \ufbfe \u062a\ufe8e\ufeeb\ufe8e\ufe92\ufe98\ufeb7\u0627 \u060c \ufbfd\ufeeb\ufe8e\ufb94\n\ufee6\ufbff\ufe8c\ufe97\u0648\ufeae\ufb58 \u0646\ufe8e\ufe98\ufeb3\u0627\u062f \u0632\u0627 \ufbfd\ufeb8\ufea8\ufe91 \ufeea\ufea0\ufbff\ufe98\ufee7 \u0631\u062f . \ufeaa\ufee8\ufee8\ufb90 \ufbfd\ufee3 \u0641\ufeac\ufea3 \u0627\u0631 \u0646\u0622 \u0632\u0627 \ufbfd\ufeb8\ufea8\ufe91 \ufe8e\ufbfe \ufede\ufee3\ufe8e\ufb90 \u0631\ufeee\ufec3 \ufeea\ufe91 \u0627\u0631 \ufee2\ufeec\ufee3 \ufeea\ufea4\ufed4\ufebb \ufb8f\ufbfe \ufe8e\ufeeb \u0646\u0622 \u060c \u062f\u0631\u0627\ufeee\ufee3 \ufbfd\ufea7\ufeae\ufe91 \u0631\u062f . \ufe96\ufeb3\u0627\n\ufbfd\ufee3 \ufbfd\ufed7\ufe8e\ufe91 \ufee2\ufeec\ufee3 \ufeea\ufea4\ufed4\ufebb \ufe8e\ufe91 \ufec2\ufe92\ufe97\ufeae\ufee3 \ufeae\ufbff\ufecf \ufeea\ufea4\ufed4\ufebb \u0632\u0627 \ufbfd\ufeb8\ufea8\ufe91 \u060c\ufeae\ufb95\ufbfe\u062f \ufeca\ufed7\u0627\ufeee\ufee3 \u0631\u062f . \u062f\u0632\ufe8e\ufeb4\ufe91 \ufee2\ufedf\ufe8e\ufeb3 \ufee6\ufbff\ufe8c\ufe97\u0648\ufeae\ufb58 \ufb8f\ufbfe \ufeaa\ufee7\u0627\ufeee\ufe97 \ufbfd\ufee4\ufee7 \ufeea\ufee7\ufe8e\ufea7\u0631\ufe8e\ufb90 \u0648 \u062f\ufeee\ufeb7 \ufbfd\ufee3 \u0641\ufeac\ufea3\n\ufee6\ufbfe\ufeaa\ufee8\ufb7c \u060c\ufee6\ufee3 \ufeea\ufee3\ufe8e\ufee7 \u0646\ufe8e\ufbfe\ufe8e\ufb58 \u0631\u062f . \u062f\ufeee\ufeb7 \ufbfd\ufee3 \ufee2\ufedf\ufe8e\ufeb3\ufe8e\ufee7 \ufee6\ufbff\ufe8c\ufe97\u0648\ufeae\ufb58 \u0648 \u0647\ufe8e\ufe92\ufe98\ufeb7\u0627 \u0646\ufe8e\ufe98\ufeb3\u0627\u062f \ufb8f\ufbfe \ufeea\ufe91 \ufeae\ufea0\ufee8\ufee3 \ufe8e\ufeec\ufe98\ufee7\u0627 \u0631\u062f \ufee6\ufbff\ufee8\ufb7d\ufee4\ufeeb \ufeea\ufb90 \u060c\u062f\ufeee\ufeb7 \ufbfd\ufee4\ufee7 \u0627\ufeaa\ufe9f \u0646\u0622 \u0648 \u0632\u0627 \ufeaa\ufee7\ufe8e\ufee3\n. \ufe96\ufeb3\u0627 \u0647\ufeaa\ufeb7 \u0647\u062f\u0627\u062f \ufea2\ufbff\ufebf\ufeee\ufe97 \u0648 \ufbfd\ufeb3\u0631\ufeae\ufe91 4 \ufede\ufebc\ufed3 3 \u0648 \ufede\ufebc\ufed3 \u0631\u062f \ufe8e\ufeeb \ufee6\ufbff\ufe8c\ufe97\u0648\ufeae\ufb58 \u0646\ufe8e\ufe98\ufeb3\u0627\u062f \ufeae\ufe91 \ufe8e\ufeeb \u0646\u0622 \u062a\u0627\ufeae\ufe9b\u0627 \u0648 \u062a\ufe8e\ufeeb\ufe8e\ufe92\ufe98\ufeb7\u0627 \ufee6\ufbfe\u0627 \u0632\u0627 \u062f\u0631\ufeee\ufee3\n\n\u0648 \ufede\ufebc\ufed3 \ufe8e\ufbfe \ufeea\ufea4\ufed4\ufebb \ufee6\ufbfe\ufeaa\ufee8\ufb7c \ufeae\ufbff\ufe9c\ufb91\ufe97 \ufe8e\ufbfe \u0641\ufeac\ufea3 \ufbfd\ufb94\u0631\ufeb0\ufe91 \ufeea\ufe91 \ufeaa\ufee8\ufee7\u0627\ufeee\ufe97 \ufbfd\ufee3 \ufee6\ufbff\ufee8\ufb7d\ufee4\ufeeb \u062f\u0631\u0627\ufeee\ufee3 \ufee6\ufbfe\u0627 . \ufeaa\ufee8\ufe98\ufeb4\ufbff\ufee7 \u0641\ufeae\ufea3 \ufb8f\ufbfe \ufec2\ufed8\ufed3 \ufeea\ufeb8\ufbff\ufee4\ufeeb \u0631\u0648\u0622 \u0646\ufe8e \u0632 \ufbfe \u062a\ufe8e\ufeeb\ufe8e\ufe92\ufe98\ufeb7\u0627\n\ufeaa\ufbff\ufedf\ufeee\ufe97 \ufeea\ufee7\ufe8e\ufea7\u0631\ufe8e\ufb90 . \ufeaa\ufee8\ufe98\ufeb4\ufeeb \u06cc \u0631\u0648\u0622 \u0646\ufe8e \u0632 \ufbfe \u0631\ufe8e\ufbff\ufeb4\ufe91 \u062a\ufe8e\ufeeb\ufe8e\ufe92\ufe98\ufeb7\u0627 \ufeb0\ufbff\ufee7 \ufe8e\ufeeb \ufee6\ufbfe\u0627 . \ufeaa\ufee8\ufeb7\ufe8e\ufe91 \ufe8e\ufeeb \ufede\ufebc\ufed3 \ufee6\ufbff\ufe91 \ufbfd\ufe98\ufea3 \ufe8e\ufbfe \ufede\ufebc\ufed3 \ufb8f\ufbfe \u0631\u062f \u062a\ufe8e\ufea4\ufed4\ufebb \u0646\u062f\ufeae\ufb90 \ufe8e\ufe9f \ufeea\ufe91 \ufe8e\ufe9f \ufe8e\ufbfe\n\nPersian","summary":"effect on the splice donor site of exon 7. However, it disturbs the balance between the enhancer and silencer motifs in this position and thus leads to a splice defect. This chapter highlights the important role of conserved motifs in the splicing processes.\nThe emphasis of Chapter 3.3 is on the effect of variants in cis in the resulting protein function. We described two unrelated families with adult-onset vitelliform macula dystrophy carrying a complex allele in IMPG2 (c.[3023-NST>AIPO2PG>A]) upon analysis of WES data. The c.PO2PG>A variant is not only a putative pathogenic missense mutation by itself but acts as a modifier element for c.3023-NST>A as well by enhancing its splice defect. In both families, individuals carrying this complex allele in a heterozygous manner did not always develop macular dystrophy which highlights the importance of other genetic and environmental factors that contribute to this disease.\n\nChapter 3.4 sheds light on the pathogenic role of a branchpoint variant (c.592-2NA>T) in BBSN in four unrelated families with non-syndromic retinitis pigmentosa, who carried c.NNS9T>G, the most frequent variant in BBSN, in the other allele. The branchpoint variant was identified through WGS analysis and its complex splice defect was revealed using in vitro midigene splice assays. This chapter characterizes the first pathogenic branchpoint variant reported in IRDs.\n\nChapter 4 describes a comprehensive study in which 100 individuals with different IRDs were assessed using WGS-based sequence analysis. The probands were previously screened by WES or targeted sequencing approaches and were genetically unsolved. The WGS analysis was performed with special attention to the non-coding variants and the putative causal variants were investigated by in vitro functional assays to prove the pathogenicity. We provide a molecular diagnosis for 27% of the pre-screened cases and suggest employing improved sequencing technologies and variant interpretation to increase the diagnostics yield for IRDs.\n\nChapter 5 illustrates the implementation of a novel strategy for identification of the genetic defect in IRDs with a strong genotype-phenotype correlation. In a family with choroideremia, previous RNA analysis of an affected proband showed CHM exon 12 skipping, but the underlying DNA defect remained elusive for 18 years. Using optical genome mapping and long-read WGS, an inverted duplication in CHM was identified. We provided a model that demonstrates the origin of the SV through fork stalling and a template switching\/microhomology-mediated break-induced replication mechanism. Additionally, we speculated on the mechanism of the splice defect and proposed an altered RNA secondary structure that disrupted the splicing of exon 12. This chapter emphasizes the great opportunities of optical genome mapping and long-read WGS to unravel the hidden SVs in unsolved cases as well as the underappreciated role of an altered RNA secondary structure as a disease mechanism.\n\nFinally, Chapter 6 provides a general discussion of the main findings in this thesis and their implications towards an improved diagnosis of IRDs. The application of different sequencing technologies and their advantages and disadvantages are explained. The importance of branchpoint variants, complex alleles, and variants which affect the RNA secondary structure were discussed. Additionally, the need of accurate splicing tools was explained by comparing different prediction algorithms and highlighting their importance in in vitro functional splice assays. Finally, potential reasons for missing pathogenic variants in the studied cohort were discussed, and it was postulated that application of long-read sequencing will be an important technology in the future of IRDs and other genetic conditions. Moreover, the different cellular systems for in vitro functional analysis can shed light on the currently missed causes of IRDs in the future.","auteur":"Zeinab Fadaie","auteur_slug":"zeinab-fadaie","publicatiedatum":"18 november 2021","taal":"EN","url_flipbook":"https:\/\/ebook.proefschriftmaken.nl\/ebook\/zeinabfadaie?iframe=true","url_download_pdf":"https:\/\/ebook.proefschriftmaken.nl\/download\/08403c10-fe97-4603-9a6a-c68c73f36ecc\/optimized","url_epub":"","ordernummer":"FTP-202602261505","isbn":"978-94-6423-432-9","doi_nummer":"","naam_universiteit":"Radboud Universiteit","afbeeldingen":4825,"naam_student:":"","binnenwerk":"","universiteit":"Radboud Universiteit","cover":"","afwerking":"","cover_afwerking":"","design":""},"_links":{"self":[{"href":"https:\/\/www.proefschriftmaken.nl\/en\/wp-json\/wp\/v2\/us_portfolio\/4823","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.proefschriftmaken.nl\/en\/wp-json\/wp\/v2\/us_portfolio"}],"about":[{"href":"https:\/\/www.proefschriftmaken.nl\/en\/wp-json\/wp\/v2\/types\/us_portfolio"}],"author":[{"embeddable":true,"href":"https:\/\/www.proefschriftmaken.nl\/en\/wp-json\/wp\/v2\/users\/7"}],"replies":[{"embeddable":true,"href":"https:\/\/www.proefschriftmaken.nl\/en\/wp-json\/wp\/v2\/comments?post=4823"}],"version-history":[{"count":1,"href":"https:\/\/www.proefschriftmaken.nl\/en\/wp-json\/wp\/v2\/us_portfolio\/4823\/revisions"}],"predecessor-version":[{"id":4826,"href":"https:\/\/www.proefschriftmaken.nl\/en\/wp-json\/wp\/v2\/us_portfolio\/4823\/revisions\/4826"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.proefschriftmaken.nl\/en\/wp-json\/wp\/v2\/media\/4825"}],"wp:attachment":[{"href":"https:\/\/www.proefschriftmaken.nl\/en\/wp-json\/wp\/v2\/media?parent=4823"}],"wp:term":[{"taxonomy":"us_portfolio_category","embeddable":true,"href":"https:\/\/www.proefschriftmaken.nl\/en\/wp-json\/wp\/v2\/us_portfolio_category?post=4823"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}