153 results on '"de Lange T"'
Search Results
2. A comparative study benchmarking colon polyp detection with CADe software
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Papachrysos, N., additional, Smedsrud, P. H., additional, Anonsen, K., additional, Berstad, T. J., additional, Espeland, H., additional, Petlund, A., additional, Hedenström, P., additional, Halvorsen, P., additional, Varkey, J., additional, Hammer, H., additional, Riegler, M., additional, and de Lange, T., additional
- Published
- 2024
- Full Text
- View/download PDF
3. Health and safety of labor migrants in food industries during Covid-19: Germany, Netherlands and USA
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Gottlieb, N, primary, de Lange, T, additional, Mantu, S, additional, Jungwirth, I, additional, Glassner, M, additional, and Forst, L, additional
- Published
- 2023
- Full Text
- View/download PDF
4. Clinical characteristics of patients with suspected cardiac chest pain and angiographically normal coronary arteries in a secondary care hospital
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de Lange, T. S., Tijssen, R. Y. G, Damman, P., and van Bergen, P. F. M. M.
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- 2017
- Full Text
- View/download PDF
5. Verblijfsrechten voor Surinaamse oud-Nederlanders: een oproep
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Groenendijk, K., den Heijer, M., van Genugten, W., de Groot, G.-R., de Hart, B., de Lange, T., Minderhoud, P., Jessurun d'Oliveira, H.U., Rodrigues, P., Rijpma, J., Schrauwen, A., Slingenberg, L., Spijkerboer, T., Terlouw, A., Zieck, M., and ACIL (FdR)
- Published
- 2022
6. Divided families and devalued citizens: Money matters in mixed-status families in the Netherlands
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de Hart, Betty, De Jong, Judith, De Lange, T, Maas, W, Schrauwen, A, Migration Law, Kooijmans Institute, De Lange, T, Maas, W, and Schrauwen, A
- Abstract
Undocumented immigrants are affected by citizenship boundaries, complicating their everyday lives. Precarious working conditions, social welfare, and security thoroughly impede their opportunities. However, understudied is the family context in which precarious immigrants live. Even though immigration and citizenship laws are directed towards individuals, they often affect the intimate domains of the family. The commonly held belief that criminalizing immigration would protect citizens while punishing immigrants denies the tight links that exists between these groups in practice. This chapter presents ‘spillover effects’ that the weaker legal status of the undocumented partner may have on the stronger legal status of the citizen or permanent resident partner in the European context. From a legal perspective, the effects of restrictions play out along several domains: access and treatment by welfare and social security, housing, and family law. Studying legal anomalies may serve as a lens to grasp the financial consequences of the distinctions between citizens and noncitizens.
- Published
- 2021
7. Cryo-EM structure of human CST bound to DNA polymerase alpha-primase in a recruitment state
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Cai, S.W., primary, Zinder, J.C., additional, Svetlov, V., additional, Bush, M.W., additional, Nudler, E., additional, Walz, T., additional, and de Lange, T., additional
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- 2022
- Full Text
- View/download PDF
8. NEWLY TRAINED ENDOSCOPISTS PERFORM HIGH QUALITY SCREENING COLONOSCOPIES AFTER INTENSIVE TRAINING AND EVEN OUTPERFORM EXPERIENCED GASTROENTEROLOGY CONSULTANTS
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Schult, A.L., additional, Botteri, E., additional, Hoff, G., additional, Holme, Ø., additional, Seip, B., additional, Randel, K.R., additional, Darre-Næss, O., additional, Owen, T., additional, Nilsen, J.A., additional, Nguyen, D.H., additional, Johansen, K., additional, and de Lange, T., additional
- Published
- 2022
- Full Text
- View/download PDF
9. Integrated impact assessment of adaptive management strategies in a Dutch peatland polder
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van Hardeveld, H.A., de Jong, H., Knepfle, M., de Lange, T., Schot, P.P., Spanjers, B., Teurlincx, S., Environmental Sciences, AKWA, and Environmental Sciences
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lcsh:GE1-350 ,Peat ,Cost–benefit analysis ,lcsh:QE1-996.5 ,Stakeholder ,Subsidence ,General Medicine ,lcsh:Geology ,Adaptive management ,Sustainable management ,International ,Sustainability ,Environmental science ,Plan_S-Compliant_OA ,Environmental planning ,lcsh:Environmental sciences ,Groundwater - Abstract
To achieve a more sustainable management of the subsiding Dutch peatlands, adaptations such as progressively higher surface water levels, pressurized field drains and a transition from dairy farming to paludiculture are considered. However, a clear understanding of implementation pathways for adaptive management strategies is lacking. Therefore, we used the RE:PEAT tool to elucidate the short-term and long-term impacts during 2025–2100 of two adaptive management strategies in Polder Zegveld and how to fairly distribute the costs and benefits of these strategies among the stakeholder groups. The strategies resulted in marked differences in soil subsidence and temporal trends in societal costs and benefits that affected stakeholders unequally. The adaptations were shown to reduce soil subsidence and enhance the sustainability of peatland management. We explored several options for a collective implementation of the adaptative management strategies. In addition, we discuss several ideas to further capitalize on the potential of the RE:PEAT tool to support peatland management. Currently, we are developing additional features that enable high spatio-temporal resolution simulations of the integrated dynamics of the surface water system, the shallow groundwater system, rainfall-runoff processes and solute transport. In combination with the PCDitch model, this will also enable detailed ecological assessments. This will pave the way for implementation pathways for adaptive management strategies that will contribute to a more sustainable peatland management.
- Published
- 2020
10. Money Matters in Migration. A Synthetic Approach
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de Lange, T., Maas, W., Schrauwen, A., ACELG (FdR), Lange, T. de, Maas, W., and Schrauwen, A.
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Centre for Migration Law ,Centrum voor Migratierecht - Abstract
This chapter introduces the reader to the book. It first describes the overall purpose of the book that brings together eighteen chapters that use money as a lens to address a wide range of cases from different disciplinary perspectives. Taken together its chapters balance empirical and theoretical work and use multiple methods. While the book does not force an overarching theoretical framework, it aims to facilitate overarching engagement and to encourage new multidisciplinary and interdisciplinary research into the role of money and resources on migration. Secondly, the chapter describes how aims, actors, and instruments are three important elements of analysis that return implicitly or explicitly in the individual chapters. It gives examples of how the lens of money can bring new insights to each of these elements in blurring formal distinctions. Thirdly, the chapter introduces the three parts of the book: migration, participation, and citizenship. It explains the choice for these three parts and how and why the distinct chapters connect under each part.
- Published
- 2021
11. Pushing out the Poor: Unstable Income and Termination of Residence
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Schrauwen, A., de Lange, T., Maas, W., and ACELG (FdR)
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Economics ,Residence ,Demographic economics - Abstract
Access of non-EU nationals to the labour market of EU Member States is based on selection matching skills needs. EU nationals have a right under EU law to reside in other EU Member States on condition that they either are student or economically active, or do have ‘sufficient resources’. This chapter examines whether the differences in framework are also visible on the ground. It looks at the changing practice of monitoring ‘sufficient resources’. During the economic crisis, several Member States increased the threshold for ‘sufficient resources’ and introduced stricter enforcement of the financial conditions. At the same time, the percentage of flexible and temporary labour contracts on the labour market increased, making it harder to fulfil these financial conditions. This chapter analyses how the combination of stricter rules, economic crisis, and flexible contracts may impact on termination of residence of, presumably, less wealthy EU citizens. It argues that the distinction made at EU level between intra-EU mobility and labour migration from outside the EU is not an appropriate starting point to look at the complexities of movement of workers in and to the EU.
- Published
- 2021
12. Money Matters in Migration Policy, Participation, and Citizenship
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de Lange, T., Maas, W., Schrauwen, A., and ACELG (FdR)
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Centre for Migration Law ,Centrum voor Migratierecht - Abstract
Migration, participation, and citizenship, are central political and social concerns, are deeply affected by money. The role of money - tangible, intangible, conceptual, and as a policy tool - is understudied, overlooked, and analytically underdeveloped. For sending and receiving societies, migrants, their families, employers, NGOs, or private institutions, money defines the border, inclusion or exclusion, opportunity structures, and equality or the lack thereof. Through the analytical lens of money, the chapters in this book expose hidden and sometimes contradictory policy objectives, unwanted consequences, and inconsistent regulatory structures. The authors from a range of fields provide multiple perspectives on how money shapes decisions from all actors in migration trajectories, from micro to macro level. Taking an interdisciplinary approach, the book draws on case studies from Europe, the Americas, Asia, and Africa. This comprehensive overview brings to light the deep global impacts money has on migration and citizenship.
- Published
- 2021
13. Arbeid
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Oosterom-Staples, Helen, de Lange, T., Zwaan et al., K., and Public Law & Governance
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kennismigratie ,zelfstandigen ,werknemers ,gvva-plicht ,tewerkstellingsvergunning ,handhaving ,Unieburgers ,derdelanders - Published
- 2020
14. Structural variant evolution after telomere crisis
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Dewhurst, S.M, primary, Yao, X, additional, Rosiene, Joel, additional, Tian, Huasong, additional, Behr, Julie, additional, Bosco, Nazario, additional, Takai, Kaori K., additional, de Lange, T, additional, and Imielinski, M, additional
- Published
- 2020
- Full Text
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15. COLONOSCOPY QUALITY AFTER INTENSIVE TRAINING OF INEXPERIENCED ENDOSCOPISTS IN A NORWEGIAN SCREENING TRIAL FOR COLORECTAL CANCER
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Schult, AL, additional, Randel, KR, additional, Botteri, E, additional, Hoff, G, additional, Bretthauer, M, additional, Ursin, G, additional, Natvig, E, additional, Jørgensen, A, additional, Sandvei, P, additional, Ek Olsen, MK, additional, Frigstad, SO, additional, Darre-Næss, O, additional, Norvard, ER, additional, Kørner, H, additional, Wibe, A, additional, de Lange, T, additional, and Holme, Ø, additional
- Published
- 2020
- Full Text
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16. Key Challenges and Results in the Design of Cubesat Laser Terminals, Optical Heads and Coarse Pointing Assemblies
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Dresscher, M., primary, Human, J. D., additional, Witvoet, G., additional, van der Heiden, N., additional, den Breeje, R., additional, Kuiper, S., additional, Fritz, E. C., additional, Korevaar, C. W., additional, van der Valk, N. C. J., additional, de Lange, T. J., additional, Saathof, R., additional, Doelman, N., additional, Crowcombe, W. E., additional, Duque, C. M., additional, and de Man, H., additional
- Published
- 2019
- Full Text
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17. Intersecting Policies of Innovation and Entrepreneurship Migration in the EU and the Netherlands
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de Lange, T., Carrera, S., den Hertog, L., Panizzon, M., Kostakopoulou, D., and Staats-& Best (FdR)
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Entrepreneurship ,Field (Bourdieu) ,Refugee ,Political science ,Triangulation (psychology) ,Economic system ,Free movement ,Economic migration - Abstract
This chapter addresses the intersection of innovation policy and migration law and regulation on the admission of third country national (TCN) entrepreneurs and how intersection can be pushed forward to benefit both policy fields as well as the policy field of integration. The twain do meet, but doubtfully enough to push for the innovation the EU calls for. The chapter discusses a myriad of international, regional or national trade and migration law instruments to facilitate economic migration with more or less attention to innovation The free movement within an ‘innovation zone’ as proposed by the E15 under GATS is presented as a source of inspiration. The chapter then builds on a Dutch case-study of decisions on the entry of migrant entrepreneurs, where innovation is hardly relevant. The multileveled regulation of economic migration and the multiple public and private actors involved creates an inscrutable legal complexity that calls for improvement. The chapter finally touches on a triangulation of innovation, migration and refugee integration policies, setting the stage for a policy innovation by including refugee entrepreneurship in the quest for innovation.
- Published
- 2019
18. Collective agreements and equal opportunities for women and disadvantaged groups
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Graafland, Johan, Rijken, C., De Lange, T., Research Group: Economics, Department of Economics, and Tilburg Sustainability Center
- Published
- 2018
19. Arbeid
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de Lange, T., Oosterom-Staples, H., Zwaan, K., Terlouw, A., Strik, T., de Hart, B., Grütters, C., Fernhout, R., and Staats-& Best (FdR)
- Published
- 2018
20. Enkele beschouwingen over het Europese arbeidsmigratiebeleid
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de Lange, T., van Melle, A.M., and Staats-& Best (FdR)
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- 2018
21. Parallelle handhaving: match of mismatch?: Het combinatieprincipe opnieuw bezien
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de Moor-van Vugt, A.J.C., Klap, A.P., de Lange, T., Staats-& Best (FdR), Amsterdam Center for Law and Economics (FdR, FEB), and Faculteit der Rechtsgeleerdheid
- Abstract
Dit artikel bespreekt de vraag in hoeverre de naleving van wettelijke regels zowel civielrechtelijk als bestuursrechtelijk kan worden afgedwongen (parallelle handhaving). Wat legitimeert een bestuursrechtelijke handhaving naast of in plaats van de civielrechtelijke handhaving? En in hoeverre staat de mogelijkheid van een civiele vordering in de weg aan bestuursrechtelijke handhaving? De aanleiding voor deze vragen zijn de problemen rond de handhaving van passagiersrechten. De auteurs bespreken ook andere vormen van parallelle handhaving.
- Published
- 2017
22. Britse Amsterdammers na de Brexit: Verslag van een onderzoek naar mogelijke strategische keuzes in het Brexit-proces met als oogpunt het bieden van verblijfszekerheid aan in Nederland verblijvende Britten en het behoud van de mogelijkheid tot tijdelijk verblijf voor Britten in Amsterdam om er te studeren
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Schrauwen, A., de Lange, T., Kraak, J., ACELG (FdR), and Staats-& Best (FdR)
- Abstract
Het verslag vangt aan met een overzicht van de aanbevelingen die uit het onderzoek naar voren komen. Uitgangspunt bij de aanbevelingen is steeds geweest dat de gemeente Amsterdam zich ervoor zal inzetten dat Britten de verblijfsrechten die ze vóór de Brexit hebben zo veel mogelijk behouden na de Brexit. Sommige aanbevelingen betreffen een keuze met betrekking tot het mogelijk resultaat van de EU - VK onderhandelingen over de Brexit. Andere aanbevelingen betreffen vooral keuzes die gemaakt kunnen worden als de onderhandelingen niet tot garanties voor Britse Amsterdammers leiden. Deze tweedeling is ook terug te vinden in de lijst. De aanbevelingen betreffen soms een actie of lobby op Europees niveau (bij de Brexit onderhandelaars, de Europese Commissie of het Europees Parlement), soms op nationaal niveau, en soms op lokaal niveau. De aanbevelingen zijn gerangschikt volgens deze niveaus. Na de lijst volgt een schematisch overzicht van alle aanbevelingen. Het eerste hoofdstuk schetst vervolgens het juridisch kader van de Brexit onderhandelingen tussen de EU en het VK. Uit het juridisch kader volgt dat garanties voor verblijfsrechten van Britten in Amsterdam zowel (1) binnen een akkoord tussen de EU en het VK gezocht moeten worden, als (2) in Europese regels die gelden ten aanzien van niet-EU burgers en (3) nationale regels die gelden ten aanzien van niet-EU burgers. Wat betreft garanties voor Britse studenten aan Amsterdamse universiteiten is dat niet anders. Gezien hun specifieke positie komen de rechten van studenten aan bod in een apart hoofdstuk, namelijk hoofdstuk 4. Het tweede hoofdstuk geeft aan, op basis van bestaande overeenkomsten tussen de EU en derde landen, op welke wijze verblijfsrechten gegarandeerd kunnen worden binnen een akkoord tussen de EU en het VK. Het derde hoofdstuk gaat in op garanties die gevonden kunnen worden in het Europese recht zoals dat geldt ten aanzien van niet-EU burgers. Hoofdstuk 5 geeft ten slotte aan welke acties ondernomen kunnen worden om de verblijfsrechten van Britse Amsterdammers zo veel mogelijk veilig te stellen onder het nationale recht.
- Published
- 2017
23. Van azc naar een baan: De Nederlandse regelgeving over en praktijk van arbeidsmarktintegratie van vluchtelingen
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de Lange, T., Besselsen, E., Rahouti, S., Rijken, C., INTERVICT, Department of Labour Law and Social Policy, and Staats-& Best (FdR)
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arbeidsmarkintegratie ,vluchtelingen - Abstract
Het onderzoeksrapport maakt de vier fases in het traject van azc naar een baan inzichtelijk. In de eerste fase, de asielprocedure, valt de asielzoeker onder de verantwoordelijkheid van het COA in afwachting van een status. Welk werk of andere activiteiten, zoals vrijwilligerswerk, mag een asielzoeker tijdens dat wachten doen en wat niet? Vervolgens breekt de fase aan dat de statushouder nog in een azc woont, maar kan wel beginnen met inburgeren. Juridisch gezien mag de statushouder wel werken, maar praktisch gezien is het vaak nog niet zo ver. Daarna is de statushouder in een gemeente gaan wonen; de gemeente gaat - in het kader van de uitvoering van de Participatiewet - aan de slag met de integratie van de statushouder. Ook de waardering van diploma’s komt dan aan de orde. In de laatste fase wordt vooruitgeblikt. De statushouder woont inmiddels al drie of vijf jaar in Nederland en heeft de verplichting om binnen drie jaar te slagen voor het inburgeringsexamen. Wat is de betekenis van de tijdelijkheid van de verblijfsstatus tot het moment dat na vijf jaar een verblijfsvergunning voor onbepaalde tijd wordt verkregen of de status eventueel wordt ingetrokken als het land van herkomst weer veilig is.
- Published
- 2017
24. Exploring the effect of a lifestyle intervention on cancer risk: 43-year follow-up of the randomized Oslo diet and antismoking study
- Author
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Botteri, E., primary, de Lange, T., additional, Tonstad, S., additional, and Berstad, P., additional
- Published
- 2018
- Full Text
- View/download PDF
25. Increasing clinical relevance in oral radiology: Benefits and challenges when implementing digital assessment
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de Lange, T., primary, Møystad, A., additional, and Torgersen, G. R., additional
- Published
- 2018
- Full Text
- View/download PDF
26. Arbeid
- Author
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Oosterom-Staples, H., de Lange, T., Krop, P., Zwaan, K. (et. al), and Department European and International Public Law
- Published
- 2016
27. De toegang tot de arbeidsmarkt voor asielzoekers, asielstatushouders en uitgeprocedeerden
- Author
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de Lange, T., Department of Labour Law and Social Policy, and Staats-& Best (FdR)
- Abstract
In dit artikel wordt ingegaan op het recht op toegang tot de arbeidsmarkt van asielzoekers die nog in afwachting zijn van een beslissing op hun asielverzoek en op de arbeidsmarktpositie van toegelaten asielzoekers. Ook wordt de vraag besproken of er een weg naar legale arbeid is voor uitgeprocedeerden. De regulering van de toegang tot de arbeidsmarkt van asielzoekers, statushouders en uitgeprocedeerden is geen louter Nederlandse aangelegenheid: bij de bespreking van het recht op toegang tot de arbeidsmarkt van de drie groepen worden de relevante Europese minimumnormen betrokken.
- Published
- 2016
28. Arbeid
- Author
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de Lange, T., Oosterom-Staples, H., Krop, P., Zwaan, K., Terlouw, A., Strik, T., de Hart, B., Grütters, C., Fernhout, R., and Staats-& Best (FdR)
- Published
- 2016
29. 'Hora est!' De nieuwe EU-richtlijn 2016/801 voor onderzoekers en studenten
- Author
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de Lange, T., Overmars, A., and Staats-& Best (FdR)
- Abstract
In mei 2016 werd, nadat de Europese Commissie ruim drie jaar eerder een voorstel daartoe had gedaan, een nieuwe richtlijn gepubliceerd, inhoudende een herziening van de bestaande richtlijnen voor toegang en verblijf van derdelanders met het oog op onderzoek en studie. De nieuwe richtlijn bevat ook bepalingen die zien op andere categorieën: scholierenuitwisseling, bezoldigde en onbezoldigde stages, vrijwilligerswerk en au-pairactiviteiten. In dit overzicht beschrijven Tesseltje de Lange en Arno Overmars de nieuwe voorwaarden en mogelijkheden ten opzichte van de huidige situatie voor derdelander onderzoekers en studenten. Ook wordt een aantal aandachtspunten benoemd waarvoor de nieuwe richtlijn geen oplossing biedt. De Lange en Overmars plaatsen deze beschrijving tegen de achtergrond van een tweetal trends: de trend van Europeanisering van het beleidsterrein in etappes, alsmede de trend van de verschuiving van studie- en onderzoeksmigratie als een vorm van ontwikkelingshulp aan de landen van herkomst naar een vorm van 'ontwikkelingshulp' aan de EU zelf: migratie is noodzakelijk ter verwezenlijking van de innovatie-agenda.
- Published
- 2016
30. Wezenlijk Nederlands Belang. De toelating tot Nederland van ondernemers van buiten de EU
- Author
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de Lange, T. and Staats-& Best (FdR)
- Abstract
Nederland wil een aantrekkelijk vestigingsland zijn voor hooggekwalificeerde kenniswerkers van buiten de EU. Het migratiebeleid biedt die kenniswerkers de mogelijkheid om als zelfstandig ondernemers een bijdrage leveren aan de Nederlandse economie. Toch maken jaarlijks maar een paar honderd buitenlandse ondernemers van die mogelijkheid gebruik en zijn de afwijzingspercentages hoog. De Universiteit van Amsterdam onderzocht hoe de toelating voor arbeid als zelfstandig ondernemer naar Nederland is geregeld, hoe de aanvraag om toelating op grond van het gehanteerde puntenstelsel wordt beoordeeld, wat het resultaat was van die beoordeling en hoe dat resultaat valt te verklaren. Dat veel ondernemers niet in aanmerking komen voor toelating heeft meerdere oorzaken, zowel gelegen aan de kant van de ondernemers als aan de kant van de Nederlands overheid. Met betere informatievoorziening door de overheid, betere voorbereiding door de ondernemers, enkele aanpassingen aan het puntenstelsel en in de uitvoeringspraktijk, zouden meer buitenlandse ondernemers een kans krijgen om een bijdrage te leveren aan de Nederlandse economie. Daarmee dienen zij een wezenlijk Nederlands belang.
- Published
- 2016
31. Langetermijnbetrokkenheid van institutionele beleggers.
- Author
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de Lange, T. H. J.
- Abstract
Copyright of TvOB, Tijdschrift voor Vennootschapsrecht, Rechtspersonenrecht en Ondernemingsbestuur is the property of Uitgeverij Paris and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
- Published
- 2020
32. The Single Permit Directive: A Limited Scope, A Simple Procedure and Limited Good Administration Requirements
- Author
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de Lange, T., Minderhoud, P., Strik, T., and Staats-& Best (FdR)
- Published
- 2015
33. Public-private regulation of labour migration: a challenge to administrative law accountability mechanisms
- Author
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de Lange, T., Panizzon, M., Zürcher, G., Fornalé, E., and Staats-& Best (FdR)
- Published
- 2015
34. The Role of Double-Strand Break Repair Pathways at Functional and Dysfunctional Telomeres
- Author
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Doksani, Y., primary and de Lange, T., additional
- Published
- 2014
- Full Text
- View/download PDF
35. Gezinshereniging en gezinsvorming
- Author
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Hart, B. de, Oosterom-Staples, H., Zwaan, K.M., Terlouw, A.B., Strik, M.H.A., Lange, T. de, Krop, P., Grütters, C.A.F.M., Fernhout, R., Department European and International Public Law, Faculteit der Rechtsgeleerdheid, ACELG (FdR), Zwaan, K.M., Terlouw, A.B., Oosterom-Staples, H., de Lange, T., Krop, P., Strik, M.H.A., de Hart, B., Grütters, C.A.F.M., Fernhout, R., Lange, T. de, Hart, B. de, Grütters, C.A.F.M., Migration Law, and Kooijmans Institute
- Subjects
afgeleid recht ,Unieburgers ,Centre for Migration Law ,Centrum voor Migratierecht ,minderjarige kinderen - Abstract
Item does not contain fulltext
- Published
- 2018
36. Menopausal hormone therapy and colorectal cancer: a linkage between nationwide registries in Norway
- Author
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Nathalie C. Støer, Solveig Sakshaug, Siri Vangen, Thomas de Lange, Sidsel Graff-Iversen, Elisabete Weiderpass, Solveig Hofvind, Giske Ursin, Vincenzo Bagnardi, Edoardo Botteri, Botteri, E, Støer, N, Sakshaug, S, Graff-Iversen, S, Vangen, S, Hofvind, S, de Lange, T, Bagnardi, V, Ursin, G, and Weiderpass, E
- Subjects
0301 basic medicine ,Colorectal cancer ,0302 clinical medicine ,Menopausal hormone therapies ,Risk Factors ,estrogen ,Poisson Distribution ,Registries ,education.field_of_study ,Norway ,Incidence (epidemiology) ,Incidence ,Estrogen Replacement Therapy ,General Medicine ,Middle Aged ,Postmenopause ,Oncology ,030220 oncology & carcinogenesis ,language ,symbols ,Adenocarcinoma ,Female ,Colorectal Neoplasms ,Cohort study ,estrogens ,medicine.medical_specialty ,Population ,menopausal hormone therapy ,colorectal cancer ,Norwegian ,Nationwide registries ,Lower risk ,03 medical and health sciences ,symbols.namesake ,Internal medicine ,medicine ,Humans ,Poisson regression ,education ,Aged ,Gynecology ,business.industry ,VDP::Medical disciplines: 700::Clinical medical disciplines: 750::Oncology: 762 ,Research ,medicine.disease ,language.human_language ,VDP::Medisinske Fag: 700::Klinisk medisinske fag: 750::Onkologi: 762 ,030104 developmental biology ,progestins ,business ,Follow-Up Studies - Abstract
ObjectivesWith the present study, we aimed to investigate the association between menopausal hormone therapy (HT) and risk of colorectal cancer (CRC).SettingCohort study based on the linkage of Norwegian population-based registries.ParticipantsWe selected 466822 Norwegian women, aged 55–79, alive and residing in Norway as of 1 January 2004, and we followed them from 2004 to 2008. Each woman contributed person-years at risk as non-user, current user and/or past HT user.Outcome measuresThe outcome of interest was adenocarcinoma of the colorectal tract, overall, by anatomic site and stage at diagnosis. Incidence rate ratios (RRs) with 95% CIs were estimated by Poisson regression and were used to evaluate the association between HT and CRC incidence.ResultsDuring the median follow-up of 4.8 years, 138 655 (30%) women received HT and 3799 (0.8%) incident CRCs occurred. Current, but not past, use of HT was associated with a lower risk of CRC (RR 0.88; 95% CI 0.80 to 0.98). RRs for localised, regionally advanced and metastatic CRC were 1.13 (95% CI 0.91 to 1.41), 0.81 (95% CI 0.70 to 0.94) and 0.79 (95% CI 0.62 to 1.00), respectively. RRs for current use of oestrogen therapy (ET) were 0.91 (95% CI 0.80 to 1.04) while RR for current use of combined oestrogen–progestin therapy (EPT) was 0.85 (95% CI 0.70 to 1.03), as compared with no use of HT. The same figures for ET and EPT in oral formulations were 0.83 (95% CI 0.68 to 1.03) and 0.86 (95% CI 0.71 to 1.05), respectively.ConclusionsIn our nationwide cohort study, HT use lowered the risk of CRC, specifically the most advanced CRC.
- Published
- 2017
37. Impact of inadequate bowel cleansing in sigmoidoscopy screening.
- Author
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Randel KR, Schult AL, Botteri E, Nawaz M, Nguyen DH, Holme Ø, Bretthauer M, Hoff G, and de Lange T
- Subjects
- Humans, Middle Aged, Female, Male, Aged, Norway, Cross-Sectional Studies, Cathartics administration & dosage, Colonoscopy methods, Logistic Models, Mass Screening methods, Sigmoidoscopy, Colorectal Neoplasms diagnosis, Early Detection of Cancer methods, Adenoma diagnosis
- Abstract
Background and Study Aims: Long-time follow-up of sigmoidoscopy screening trials has shown reduced incidence and mortality of colorectal cancer (CRC), but inadequate bowel cleansing may hamper efficacy. The aim of this study was to assess the impact of bowel cleansing quality in sigmoidoscopy screening., Patients and Methods: Individuals 50 to 74 years old who had a screening sigmoidoscopy in a population-based Norwegian, randomized trial between 2012 and 2019, were included in this cross-sectional study. The bowel cleansing quality was categorised as excellent, good, partly poor, or poor. The effect of bowel cleansing quality on adenoma detection rate (ADR) and referral to colonoscopy was evaluated by fitting multivariable logistic regression models., Results: 35,710 individuals were included. The bowel cleansing at sigmoidoscopy was excellent in 20,934 (58.6%) individuals, good in 6580 (18.4%), partly poor in 7097 (19.9%) and poor in 1099 (3.1%). The corresponding ADRs were 17.0%, 16.6%, 14.5%, and 13.0%. Compared to participants with excellent bowel cleansing, those with poor bowel cleansing had an odds ratio for adenoma detection of 0.66 (95% confidence interval 0.55-0.79). We found substantial differences in the assessment of bowel cleansing quality among endoscopists., Conclusions: Inadequate bowel cleansing reduces the efficacy of sigmoidoscopy screening, by lowering ADR. A validated rating scale and improved bowel preparation are needed to make sigmoidoscopy an appropriate screening method., Trial registration Clinicaltrials.gov (NCT01538550).
- Published
- 2024
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38. Multiple choice as formative assessment in dental education.
- Author
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Haugen HJ and de Lange T
- Subjects
- Humans, Surveys and Questionnaires, Curriculum, Students, Dental psychology, Female, Male, Education, Dental methods, Educational Measurement methods
- Abstract
Introduction: The effectiveness of multiple-choice questions (MCQs) in dental education is pivotal to student performance and knowledge advancement. However, their optimal implementation requires exploration to enhance the benefits., Materials and Methods: An educational tool incorporating MCQs was administered from the 5th to the 10th semester in a dental curriculum. The students filled out a questionnaire after the MCQ, which was linked to the learning management system. Four cohorts of four semesters generated 2300 data points analysed by Spearmen correlation and mixed model regression analysis., Results: Demonstrated a significant correlation between early exam preparation and improved student performance. Independent study hours and lecture attendance emerged as significant predictors, accounting for approximately 10.27% of the variance in student performance on MCQs. While the number of MCQs taken showed an inverse relationship with study hours, the perceived clarity of these questions positively correlated with academic achievement., Conclusion: MCQs have proven effective in enhancing student learning and knowledge within the discipline. Our analysis underscores the important role of independent study and consistent lecture attendance in positively influencing MCQ scores. The study provides valuable insights into using MCQs as a practical tool for dental student learning. Moreover, the clarity of assessment tools, such as MCQs, remains pivotal in influencing student outcomes. This study underscores the multifaceted nature of learning experiences in dental education and the importance of bridging the gap between student expectations and actual performance., (© 2024 The Authors. European Journal of Dental Education published by John Wiley & Sons Ltd.)
- Published
- 2024
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39. POT1 recruits and regulates CST-Polα/primase at human telomeres.
- Author
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Cai SW, Takai H, Zaug AJ, Dilgen TC, Cech TR, Walz T, and de Lange T
- Subjects
- Humans, Cryoelectron Microscopy, DNA Primase metabolism, DNA Primase genetics, Models, Molecular, Phosphorylation, Telomerase metabolism, DNA Polymerase I metabolism, Shelterin Complex metabolism, Telomere metabolism, Telomere-Binding Proteins metabolism
- Abstract
Telomere maintenance requires the extension of the G-rich telomeric repeat strand by telomerase and the fill-in synthesis of the C-rich strand by Polα/primase. At telomeres, Polα/primase is bound to Ctc1/Stn1/Ten1 (CST), a single-stranded DNA-binding complex. Like mutations in telomerase, mutations affecting CST-Polα/primase result in pathological telomere shortening and cause a telomere biology disorder, Coats plus (CP). We determined cryogenic electron microscopy structures of human CST bound to the shelterin heterodimer POT1/TPP1 that reveal how CST is recruited to telomeres by POT1. Our findings suggest that POT1 hinge phosphorylation is required for CST recruitment, and the complex is formed through conserved interactions involving several residues mutated in CP. Our structural and biochemical data suggest that phosphorylated POT1 holds CST-Polα/primase in an inactive, autoinhibited state until telomerase has extended the telomere ends. We propose that dephosphorylation of POT1 releases CST-Polα/primase into an active state that completes telomere replication through fill-in synthesis., Competing Interests: Declaration of interests T.R.C. is a member of the SAB of Storm Therapeutics, Eikon Therapeutics, and SomaLogic, Inc., (Published by Elsevier Inc.)
- Published
- 2024
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40. Replicative senescence is ATM driven, reversible, and accelerated by hyperactivation of ATM at normoxia.
- Author
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Stuart A and de Lange T
- Abstract
Programmed telomere shortening limits tumorigenesis through the induction of replicative senescence. Here we address three long-standing questions concerning senescence. First, we show that the ATM kinase is solely responsible for the induction of replicative senescence. Senescence was delayed by ATM inhibition (ATMi) or overexpression of TRF2, the shelterin subunit dedicated to ATM repression. In contrast, there was no evidence for ATR signaling contributing to replicative senescence even when ATMi was combined with ATR inhibition. Second, we show ATMi can induce apparently normal cell divisions in a subset of senescent cells, indicating that senescence can be reversed. Third, we show that the extended replicative life span at low (physiological) oxygen is due to diminished ATM activity. At low oxygen, cells show a decreased ATM response to dysfunctional telomeres and genome-wide DSBs compared to 20% oxygen. As this effect could be reversed by NAC, the attenuated response of ATM to critically short telomeres and the resulting extended life span at low oxygen is likely due to ROS-induced formation of cysteine disulfide-bridges that crosslink ATM dimers into a form that is not activated by DSBs. These findings show how primary human cells detect shortened telomeres and reveal the molecular mechanism underlying the telomere tumor suppressor pathway.
- Published
- 2024
- Full Text
- View/download PDF
41. Visual explanations for polyp detection: How medical doctors assess intrinsic versus extrinsic explanations.
- Author
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Hicks S, Storås A, Riegler MA, Midoglu C, Hammou M, de Lange T, Parasa S, Halvorsen P, and Strümke I
- Subjects
- Humans, Artificial Intelligence, Neural Networks, Computer, Colonic Polyps diagnosis, Colonoscopy methods, Physicians psychology, Deep Learning
- Abstract
Deep learning has achieved immense success in computer vision and has the potential to help physicians analyze visual content for disease and other abnormalities. However, the current state of deep learning is very much a black box, making medical professionals skeptical about integrating these methods into clinical practice. Several methods have been proposed to shed some light on these black boxes, but there is no consensus on the opinion of medical doctors that will consume these explanations. This paper presents a study asking medical professionals about their opinion of current state-of-the-art explainable artificial intelligence methods when applied to a gastrointestinal disease detection use case. We compare two different categories of explanation methods, intrinsic and extrinsic, and gauge their opinion of the current value of these explanations. The results indicate that intrinsic explanations are preferred and that physicians see value in the explanations. Based on the feedback collected in our study, future explanations of medical deep neural networks can be tailored to the needs and expectations of doctors. Hopefully, this will contribute to solving the issue of black box medical systems and lead to successful implementation of this powerful technology in the clinic., Competing Interests: I have read the journal’s policy and the authors of this manuscript have the following competing interests: Sravanthi Parasa: Consultant Covidien LP; Medical advisory board of Fujifilms Pål Halvorsen: Board member of Augere Medical. This does not alter our adherence to PLOS ONE policies on sharing data and materials., (Copyright: © 2024 Hicks et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)
- Published
- 2024
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42. DNA-PK controls Apollo's access to leading-end telomeres.
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Sonmez C, Toia B, Eickhoff P, Matei AM, El Beyrouthy M, Wallner B, Douglas ME, de Lange T, and Lottersberger F
- Subjects
- Humans, DNA End-Joining Repair, Nuclear Proteins metabolism, Nuclear Proteins genetics, Ku Autoantigen metabolism, Ku Autoantigen genetics, Protein Binding, DNA Breaks, Double-Stranded, Phosphorylation, DNA metabolism, DNA chemistry, DNA genetics, DNA-Activated Protein Kinase metabolism, DNA-Activated Protein Kinase genetics, Telomere metabolism, Telomere genetics, DNA-Binding Proteins metabolism, DNA-Binding Proteins genetics, Endonucleases metabolism, Endonucleases genetics
- Abstract
The complex formed by Ku70/80 and DNA-PKcs (DNA-PK) promotes the synapsis and the joining of double strand breaks (DSBs) during canonical non-homologous end joining (c-NHEJ). In c-NHEJ during V(D)J recombination, DNA-PK promotes the processing of the ends and the opening of the DNA hairpins by recruiting and/or activating the nuclease Artemis/DCLRE1C/SNM1C. Paradoxically, DNA-PK is also required to prevent the fusions of newly replicated leading-end telomeres. Here, we describe the role for DNA-PK in controlling Apollo/DCLRE1B/SNM1B, the nuclease that resects leading-end telomeres. We show that the telomeric function of Apollo requires DNA-PKcs's kinase activity and the binding of Apollo to DNA-PK. Furthermore, AlphaFold-Multimer predicts that Apollo's nuclease domain has extensive additional interactions with DNA-PKcs, and comparison to the cryo-EM structure of Artemis bound to DNA-PK phosphorylated on the ABCDE/Thr2609 cluster suggests that DNA-PK can similarly grant Apollo access to the DNA end. In agreement, the telomeric function of DNA-PK requires the ABCDE/Thr2609 cluster. These data reveal that resection of leading-end telomeres is regulated by DNA-PK through its binding to Apollo and its (auto)phosphorylation-dependent positioning of Apollo at the DNA end, analogous but not identical to DNA-PK dependent regulation of Artemis at hairpins., (© The Author(s) 2024. Published by Oxford University Press on behalf of Nucleic Acids Research.)
- Published
- 2024
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43. Students' perceptions of post-exam feedback in oral radiology-A comparative study from two dental hygienist educational settings.
- Author
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de Lange T, Møystad A, Torgersen G, Ahlqvist J, and Jäghagen EL
- Subjects
- Humans, Feedback, Dental Hygienists, Education, Dental, Students, Educational Measurement methods, Radiology
- Abstract
Introduction: The aim of this study was to investigate how students perceive the benefit of participating in a teacher-organised session providing feedback on exams, termed post-exam feedback, in two dental hygienist programmes., Methods: The study was based on interviews with 22 participants, including 18 students and 4 faculty teachers. The data were approached on the basis of thematic analysis, allowing us to generate insights on how the participants reflected on their participation in the post-exam feedback sessions and how they perceived this arrangement as learners., Results: The findings from the study suggest that motivated students consider post-exam feedback to be beneficial in clearing up uncertainties and deepening their understanding of issues not fully understood during the exam, as well as supporting their further learning. Less motivated students mainly consider post-exam feedback to be relevant for students who do not pass the exams., Conclusions: Organised in a student-centred way and with attentiveness to student learning preferences, the results suggest that post-exam feedback can be valuable for enhancing assessment and supporting student learning related to exams., (© 2023 The Authors. European Journal of Dental Education published by John Wiley & Sons Ltd.)
- Published
- 2024
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- View/download PDF
44. CST-polymerase α-primase solves a second telomere end-replication problem.
- Author
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Takai H, Aria V, Borges P, Yeeles JTP, and de Lange T
- Subjects
- Humans, Telomerase metabolism, DNA Polymerase I metabolism, DNA Primase metabolism, DNA Replication, Telomere genetics, Telomere metabolism, Telomere-Binding Proteins metabolism
- Abstract
Telomerase adds G-rich telomeric repeats to the 3' ends of telomeres
1 , counteracting telomere shortening caused by loss of telomeric 3' overhangs during leading-strand DNA synthesis ('the end-replication problem'2 ). Here we report a second end-replication problem that originates from the incomplete duplication of the C-rich telomeric repeat strand (C-strand) by lagging-strand DNA synthesis. This problem is resolved by fill-in synthesis mediated by polymerase α-primase bound to Ctc1-Stn1-Ten1 (CST-Polα-primase). In vitro, priming for lagging-strand DNA replication does not occur on the 3' overhang and lagging-strand synthesis stops in a zone of approximately 150 nucleotides (nt) more than 26 nt from the end of the template. Consistent with the in vitro data, lagging-end telomeres of cells lacking CST-Polα-primase lost 50-60 nt of telomeric CCCTAA repeats per population doubling. The C-strands of leading-end telomeres shortened by around 100 nt per population doubling, reflecting the generation of 3' overhangs through resection. The measured overall C-strand shortening in the absence of CST-Polα-primase fill-in is consistent with the combined effects of incomplete lagging-strand synthesis and 5' resection at the leading ends. We conclude that canonical DNA replication creates two telomere end-replication problems that require telomerase to maintain the G-rich strand and CST-Polα-primase to maintain the C-strand., (© 2024. The Author(s), under exclusive licence to Springer Nature Limited.)- Published
- 2024
- Full Text
- View/download PDF
45. ATR blocks telomerase from converting DNA breaks into telomeres.
- Author
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Kinzig CG, Zakusilo G, Takai KK, Myler LR, and de Lange T
- Subjects
- Humans, Genetic Techniques, CRISPR-Associated Protein 9, HeLa Cells, Ataxia Telangiectasia Mutated Proteins genetics, Ataxia Telangiectasia Mutated Proteins metabolism, DNA Breaks, Double-Stranded, Telomerase genetics, Telomere genetics, Telomere metabolism
- Abstract
Telomerase, the enzyme that maintains telomeres at natural chromosome ends, should be repressed at double-strand breaks (DSBs), where neotelomere formation can cause terminal truncations. We developed an assay to detect neotelomere formation at Cas9- or I-SceI-induced DSBs in human cells. Telomerase added telomeric repeats to DSBs, leading to interstitial telomeric repeat insertions or the formation of functional neotelomeres accompanied by terminal deletions. The threat that telomerase poses to genome integrity was minimized by ataxia telangiectasia and Rad3-related (ATR) kinase signaling, which inhibited telomerase at resected DSBs. In addition to acting at resected DSBs, telomerase used the extruded strand in the Cas9 enzyme-product complex as a primer for neotelomere formation. We propose that although neotelomere formation is detrimental in normal human cells, it may allow cancer cells to escape from breakage-fusion-bridge cycles.
- Published
- 2024
- Full Text
- View/download PDF
46. Impact of AI-aided colonoscopy in clinical practice: a prospective randomised controlled trial.
- Author
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Schöler J, Alavanja M, de Lange T, Yamamoto S, Hedenström P, and Varkey J
- Subjects
- Humans, Aged, Prospective Studies, Early Detection of Cancer, Colonoscopy, Artificial Intelligence, Adenoma pathology
- Abstract
Objective: Colorectal cancer (CRC) has a significant role in cancer-related mortality. Colonoscopy, combined with adenoma removal, has proven effective in reducing CRC incidence. However, suboptimal colonoscopy quality often leads to missed polyps. The impact of artificial intelligence (AI) on adenoma and polyp detection rate (ADR, PDR) is yet to be established., Design: We conducted a randomised controlled trial at Sahlgrenska University Hospital in Sweden. Patients underwent colonoscopy with or without the assistance of AI (AI-C or conventional colonoscopy (CC)). Examinations were performed with two different AI systems, that is, Fujifilm CADEye and Medtronic GI Genius. The primary outcome was ADR., Results: Among 286 patients, 240 underwent analysis (average age: 66 years). The ADR was 42% for all patients, and no significant difference emerged between AI-C and CC groups (41% vs 43%). The overall PDR was 61%, with a trend towards higher PDR in the AI-C group. Subgroup analysis revealed higher detection rates for sessile serrated lesions (SSL) with AI assistance (AI-C 22%, CC 11%, p=0.004). No difference was noticed in the detection of polyps or adenomas per colonoscopy. Examinations were most often performed by experienced endoscopists, 78% (n=86 AI-C, 100 CC)., Conclusion: Amidst the ongoing AI integration, ADR did not improve with AI. Particularly noteworthy is the enhanced detection rates for SSL by AI assistance, especially since they pose a risk for postcolonoscopy CRC. The integration of AI into standard colonoscopy practice warrants further investigation and the development of improved software might be necessary before enforcing its mandatory implementation., Trial Registration Number: NCT05178095., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2024. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)
- Published
- 2024
- Full Text
- View/download PDF
47. Assessing generalisability of deep learning-based polyp detection and segmentation methods through a computer vision challenge.
- Author
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Ali S, Ghatwary N, Jha D, Isik-Polat E, Polat G, Yang C, Li W, Galdran A, Ballester MG, Thambawita V, Hicks S, Poudel S, Lee SW, Jin Z, Gan T, Yu C, Yan J, Yeo D, Lee H, Tomar NK, Haithami M, Ahmed A, Riegler MA, Daul C, Halvorsen P, Rittscher J, Salem OE, Lamarque D, Cannizzaro R, Realdon S, de Lange T, and East JE
- Subjects
- Humans, Colonoscopy, Computers, Deep Learning, Polyps, Crowdsourcing
- Abstract
Polyps are well-known cancer precursors identified by colonoscopy. However, variability in their size, appearance, and location makes the detection of polyps challenging. Moreover, colonoscopy surveillance and removal of polyps are highly operator-dependent procedures and occur in a highly complex organ topology. There exists a high missed detection rate and incomplete removal of colonic polyps. To assist in clinical procedures and reduce missed rates, automated methods for detecting and segmenting polyps using machine learning have been achieved in past years. However, the major drawback in most of these methods is their ability to generalise to out-of-sample unseen datasets from different centres, populations, modalities, and acquisition systems. To test this hypothesis rigorously, we, together with expert gastroenterologists, curated a multi-centre and multi-population dataset acquired from six different colonoscopy systems and challenged the computational expert teams to develop robust automated detection and segmentation methods in a crowd-sourcing Endoscopic computer vision challenge. This work put forward rigorous generalisability tests and assesses the usability of devised deep learning methods in dynamic and actual clinical colonoscopy procedures. We analyse the results of four top performing teams for the detection task and five top performing teams for the segmentation task. Our analyses demonstrate that the top-ranking teams concentrated mainly on accuracy over the real-time performance required for clinical applicability. We further dissect the devised methods and provide an experiment-based hypothesis that reveals the need for improved generalisability to tackle diversity present in multi-centre datasets and routine clinical procedures., (© 2024. The Author(s).)
- Published
- 2024
- Full Text
- View/download PDF
48. Precarity prevented or reinforced? Migrants' right to change employers in the recast of the EU Single Permit Directive.
- Author
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De Lange T and Falkenhain M
- Abstract
Labor migration policies within the European Union and its Member States typically address two conflictive labor market policy goals. They aim to attract and retain foreign workers in a situation of labor shortage, while at the same time protecting the national workforce from additional labor market competition. The balancing of these two goals is commonly resolved in favor of nationals and with fewer rights for migrant workers. It is precisely this nexus between migrant rights and the protection of the national workforce that is central to the understudied question of whether and under what conditions migrant workers from third countries (i.e. non-EU countries) may change their employer to quit low-quality work or exploitative employment, or for career reasons. Building on scholarly discussions on employer dependency and bureaucratic complexity as general sources of migrant precarity, as well as on international and EU law on the rights of migrant workers, this article presents three policy variations of the right to change employers currently in place in the European context. Thereby we fill a gap in the literature on labor migration, labor market regulation, and migrant workers' rights. To illustrate the mixed ambitions of EU institutions to reduce migrant precarity the article then presents and critically discusses the high-level negotiations over the recast of the EU Single Permit Directive 2011/98 that were centered around the right to change employers., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 De Lange and Falkenhain.)
- Published
- 2024
- Full Text
- View/download PDF
49. CST-Polymeraseα-primase solves a second telomere end-replication problem.
- Author
-
Takai H, Aria V, Borges P, Yeeles JTP, and de Lange T
- Abstract
Telomerase adds G-rich telomeric repeats to the 3' ends of telomeres
1 , counteracting telomere shortening caused by loss of telomeric 3' overhangs during leading-strand DNA synthesis ("the end-replication problem"2 ). We report a second end-replication problem that originates from the incomplete duplication of the C-rich telomeric repeat strand by lagging-strand synthesis. This problem is solved by CST-Polymeraseα(Polα)-primase fill-in synthesis. In vitro, priming for lagging-strand DNA replication does not occur on the 3' overhang and lagging-strand synthesis stops in an ~150-nt zone more than 26 nt from the end of the template. Consistent with the in vitro data, lagging-end telomeres of cells lacking CST-Polα-primase lost ~50-60 nt of CCCTAA repeats per population doubling (PD). The C-strands of leading-end telomeres shortened by ~100 nt/PD, reflecting the generation of 3' overhangs through resection. The measured overall C-strand shortening in absence of CST-Polα-primase fill-in is consistent with the combined effects of incomplete lagging-strand synthesis and 5' resection at the leading-ends. We conclude that canonical DNA replication creates two telomere end-replication problems that require telomerase to maintain the G-strand and CST-Polα-primase to maintain the C-strand., Competing Interests: Conflict of interest The authors declare no conflict of interest.- Published
- 2024
- Full Text
- View/download PDF
50. Most large structural variants in cancer genomes can be detected without long reads.
- Author
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Choo ZN, Behr JM, Deshpande A, Hadi K, Yao X, Tian H, Takai K, Zakusilo G, Rosiene J, Da Cruz Paula A, Weigelt B, Setton J, Riaz N, Powell SN, Busam K, Shoushtari AN, Ariyan C, Reis-Filho J, de Lange T, and Imieliński M
- Subjects
- Humans, Female, Sequence Analysis, DNA methods, Genome, Human genetics, Chromosome Aberrations, High-Throughput Nucleotide Sequencing methods, Genomic Structural Variation genetics, Genomics methods, Breast Neoplasms
- Abstract
Short-read sequencing is the workhorse of cancer genomics yet is thought to miss many structural variants (SVs), particularly large chromosomal alterations. To characterize missing SVs in short-read whole genomes, we analyzed 'loose ends'-local violations of mass balance between adjacent DNA segments. In the landscape of loose ends across 1,330 high-purity cancer whole genomes, most large (>10-kb) clonal SVs were fully resolved by short reads in the 87% of the human genome where copy number could be reliably measured. Some loose ends represent neotelomeres, which we propose as a hallmark of the alternative lengthening of telomeres phenotype. These pan-cancer findings were confirmed by long-molecule profiles of 38 breast cancer and melanoma cases. Our results indicate that aberrant homologous recombination is unlikely to drive the majority of large cancer SVs. Furthermore, analysis of mass balance in short-read whole genome data provides a surprisingly complete picture of cancer chromosomal structure., (© 2023. The Author(s).)
- Published
- 2023
- Full Text
- View/download PDF
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