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Ferraro, F. (author), Fevga, Christina (author), Bonifati, Vincenzo (author), Mandemakers, Wim (author), Mahfouz, A.M.E.T.A. (author), Reinders, M.J.T. (author)Several studies have analyzed gene expression profiles in the substantia nigra to better understand the pathological mechanisms causing Parkinson’s disease (PD). However, the concordance between the identified gene signatures in these individual studies was generally low. This might have been caused by a change in cell type composition as loss...journal article 2022
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Holstege, H. (author), Hulsman, M.J. (author), Charbonnier, Camille (author), Grenier-Boley, Banjamin (author), Quenez, Olivier (author), Grozeva, Detelina (author), van Rooij, Jeroen G.J. (author), Reinders, M.J.T. (author), van der Lee, S.J. (author)Alzheimer’s disease (AD), the leading cause of dementia, has an estimated<br/>heritability of approximately 70%1. The genetic component of AD has been mainly assessed using genome-wide association studies, which do not capture the risk contributed by rare variants2. Here, we compared the gene-based burden of rare damaging variants in exome...journal article 2022
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van Bree, Elisabeth J. (author), Guimarães, Rita L.F.P. (author), Lundberg, Mischa (author), Blujdea, Elena R. (author), Rosenkrantz, Jimi L. (author), White, Fred T.G. (author), Reinders, M.J.T. (author), Holstege, H. (author), Jacobs, Frank M.J. (author)Genome-wide association studies (GWAS) have been highly informative in discovering disease-associated loci but are not designed to capture all structural variations in the human genome. Using long-read sequencing data, we discovered widespread structural variation within SINE-VNTR-Alu (SVA) elements, a class of great ape-specific transposable...journal article 2022
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Maurits, Marc P. (author), Korsunsky, Ilya (author), Raychaudhuri, Soumya (author), Murphy, Shawn N. (author), Smoller, Jordan W. (author), Weiss, Scott T. (author), Huizinga, Thomas W.J. (author), Reinders, M.J.T. (author), van den Akker, E.B. (author)Objective: To facilitate patient disease subset and risk factor identification by constructing a pipeline which is generalizable, provides easily interpretable results, and allows replication by overcoming electronic health records (EHRs) batch effects. Material and Methods: We used 1872 billing codes in EHRs of 102 880 patients from 12...journal article 2022
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Dekker, J.J. (author), van Dongen, Jacques J.M. (author), Reinders, M.J.T. (author), Khatri, Indu (author)The IMGT database profiles the TR germline alleles for all four TR loci (TRA, TRB, TRG and TRD), however, it does not comprise of the information regarding population specificity and allelic frequencies of these germline alleles. The specificity of allelic variants to different human populations can, however, be a rich source of information...journal article 2022
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Smit, J.M. (author), Krijthe, J.H. (author), Gommers, D.A.M.P.J. (author), Kamps, M. J.A. (author), Cornet, A.J. (author), Arbous, M. S. (author), De Bruin, D. P. (author), Van Bommel, J. (author), Reinders, M.J.T. (author)Background: The COVID-19 pandemic continues to overwhelm intensive care units (ICUs) worldwide, and improved prediction of mortality among COVID-19 patients could assist decision making in the ICU setting. In this work, we report on the development and validation of a dynamic mortality model specifically for critically ill COVID-19 patients...journal article 2022
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Reinders, K.J. (author), Giardina, Giorgia (author), Zurfluh, Florian (author), Ryser, Jurg (author), Hanssen, R.F. (author)In the planning stage of new infrastructure or when designing renovation of existing infrastructure, information about existing slope movements or settlements is essential to make informed design decisions. Interferometric<br/>Synthetic Aperture Radar (InSAR) techniques can be of value to identify these risks in an early stage of a project....journal article 2022
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Bourgonje, Arno R. (author), Hu, Shixian (author), Spekhorst, Lieke M. (author), Zhernakova, Daria V. (author), Vila, Arnau Vich (author), Li, Yanni (author), Charrout, M. (author), Mahfouz, A.M.E.T.A. (author), Reinders, M.J.T. (author)Background and Aims: Protein profiling in patients with inflammatory bowel diseases [IBD] for diagnostic and therapeutic purposes is underexplored. This study analysed the association between phenotype, genotype, and the plasma proteome in IBD. Methods: A total of 92 inflammation-related proteins were quantified in plasma of 1028 patients...journal article 2022
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Zhang, M. (author), Ganz, Andrea B. (author), Rohde, Susan (author), Rozemuller, Annemieke J.M. (author), Bank, Netherlands Brain (author), Reinders, M.J.T. (author), Scheltens, Philip (author), Hulsman, M. (author), Hoozemans, Jeroen J.M. (author), Holstege, H. (author)Introduction: With increasing age, neuropathological substrates associated with Alzheimer's disease (AD) accumulate in brains of cognitively healthy individuals—are they resilient, or resistant to AD-associated neuropathologies?. Methods: In 85 centenarian brains, we correlated NIA (amyloid) stages, Braak (neurofibrillary tangle) stages, and...journal article 2022
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Khatri, I. (author), Diks, Annieck M. (author), van den Akker, E.B. (author), Oosten, Liesbeth E. M. (author), Zwaginga, Jaap Jan (author), Reinders, M.J.T. (author), van Dongen, Jacques J. M. (author), Berkowska, Magdalena A. (author)To mount an adequate immune response against pathogens, stepwise mutation and selection processes are crucial functions of the adaptive immune system. To better characterize a successful vaccination response, we performed longitudinal (days 0, 5, 7, 10, and 14 after Boostrix vaccination) analysis of the single-cell transcriptome as well as the B...journal article 2021
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Bouland, G.A. (author), Mahfouz, A.M.E.T.A. (author), Reinders, M.J.T. (author)Single-cell RNA sequencing data is characterized by a large number of zero counts, yet there is growing evidence that these zeros reflect biological variation rather than technical artifacts. We propose to use binarized expression profiles to identify the effects of biological variation in single-cell RNA sequencing data. Using 16 publicly...journal article 2021
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Reinders, K.J. (author), Hanssen, R.F. (author), van Leijen, F.J. (author), Korff, M. (author)In this work, we investigate if, when, and how satellite InSAR can be used for evaluating surface settlements that occur during shield tunnelling in soft soil areas. We evaluate the applicability of InSAR prior, during, and after tunnel construction. Special emphasis is placed on the influence of the InSAR phase ambiguities in relation to short...journal article 2021
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Tesi, N. (author), van der Lee, S.J. (author), Hulsman, M. (author), Holstege, H. (author), Reinders, M.J.T. (author)Genetic association studies are frequently used to study the genetic basis of numerous human phenotypes. However, the rapid interrogation of how well a certain genomic region associates across traits as well as the interpretation of genetic associations is often complex and requires the integration of multiple sources of annotation, which...journal article 2021
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Tesi, N. (author), van der Lee, S.J. (author), Hulsman, M. (author), Jansen, Iris E. (author), Stringa, N. (author), van Schoor, N.M. (author), Huisman, Martijn (author), Reinders, M.J.T. (author), Holstege, H. (author)Studying the genome of centenarians may give insights into the molecular mechanisms underlying extreme human longevity and the escape of age-related diseases. Here, we set out to construct polygenic risk scores (PRSs) for longevity and to investigate the functions of longevity-associated variants. Using a cohort of centenarians with...journal article 2021
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Reinders, K.J. (author), van Leijen, F.J. (author), Hanssen, R.F. (author), Korff, M. (author)This paper investigates the use of InSAR data during shield tunnel construction when short-term settlements occur within a few days. Additionally, the long-term settlement, which occur over several years, in the vicinity of these tunnels are evaluated with inSAR. The North-South Line in Amsterdam is used as a case study for this research. We...conference paper 2021
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Transcriptomic Signatures Associated With Regional Cortical Thickness Changes in Parkinson’s DiseaseKeo, D.L. (author), Dzyubachyk, Oleh (author), Van Der Grond, Jeroen (author), van Hilten, Jacobus J. (author), Reinders, M.J.T. (author), Mahfouz, A.M.E.T.A. (author)Cortical atrophy is a common manifestation in Parkinson’s disease (PD), particularly in advanced stages of the disease. To elucidate the molecular underpinnings of cortical thickness changes in PD, we performed an integrated analysis of brain-wide healthy transcriptomic data from the Allen Human Brain Atlas and patterns of cortical thickness...journal article 2021
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Ju, Jie (author), Wismans, Leonoor V. (author), Mustafa, Dana A.M. (author), Reinders, M.J.T. (author), van Eijck, Casper H.J. (author), Li, Yunlei (author)A major challenge for treating patients with pancreatic ductal adenocarcinoma (PDAC) is the unpredictability of their prognoses due to high heterogeneity. We present Multi-Omics DEep Learning for Prognosis-correlated subtyping (MODEL-P) to identify PDAC subtypes and to predict prognoses of new patients. MODEL-P was trained on autoencoder...journal article 2021
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Khatri, I. (author), Berkowska, Magdalena A. (author), van den Akker, E.B. (author), Teodosio, Cristina (author), Reinders, M.J.T. (author), van Dongen, Jacques J. M. (author)Immunoglobulin (IG) loci harbor inter-individual allelic variants in many different germline IG variable, diversity and joining genes of the IG heavy (IGH), kappa (IGK) and lambda (IGL) loci, which together form the genetic basis of the highly diverse antigen-specific B-cell receptors. These allelic variants can be shared between or be...journal article 2021
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Genetics Contributes to Concomitant Pathology and Clinical Presentation in Dementia with Lewy Bodiesvan der Lee, S.J. (author), van Steenoven, Inger (author), van de Beek, Marleen (author), Tesi, N. (author), Jansen, Iris E. (author), van Schoor, N.M. (author), Reinders, M.J.T. (author), Huisman, Martijn (author), Scheltens, Philip (author)Background: Dementia with Lewy bodies (DLB) is a complex, progressive neurodegenerative disease with considerable phenotypic, pathological, and genetic heterogeneity. Objective: We tested if genetic variants in part explain the heterogeneity in DLB. Methods: We tested the effects of variants previously associated with DLB (near APOE, GBA, and...journal article 2021
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Reus, Lianne M. (author), Jansen, Iris E. (author), van Rooij, Jeroen (author), van Schoor, Natasja M. (author), Tesi, N. (author), Reinders, M.J.T. (author), Huisman, M.A. (author), van der Lugt, Aad (author), van der Lee, Sven J. (author)Genetic factors play a major role in frontotemporal dementia (FTD). The majority of FTD cannot be genetically explained yet and it is likely that there are still FTD risk loci to be discovered. Common variants have been identified with genome-wide association studies (GWAS), but these studies have not systematically searched for rare variants...journal article 2021