Feasibility of predicting allele specific expression from DNA sequencing using machine learning

Autor: Zhenhua Zhang, Freerk van Dijk, Niek de Klein, Mariëlle E van Gijn, Lude H Franke, Richard J Sinke, Morris A Swertz, K Joeri van der Velde

Publikováno v: Scientific Reports, Vol 11, Iss 1, Pp 1-11 (2021)

Abstract Allele specific expression (ASE) concerns divergent expression quantity of alternative alleles and is measured by RNA sequencing. Multiple studies show that ASE plays a role in hereditary diseases by modulating penetrance or phenotype severi

Externí odkaz: https://doaj.org/article/046bc28e1cc24a58a64d6f222d461d04

Functional analysis helps to define KCNC3 mutational spectrum in Dutch ataxia cases.

Autor: Anna Duarri, Esther A R Nibbeling, Michiel R Fokkens, Michel Meijer, Melissa Boerrigter, Corien C Verschuuren-Bemelmans, Berry P H Kremer, Bart P van de Warrenburg, Dennis Dooijes, Erik Boddeke, Richard J Sinke, Dineke S Verbeek

Publikováno v: PLoS ONE, Vol 10, Iss 3, p e0116599 (2015)

Spinocerebellar ataxia type 13 (SCA13) is an autosomal dominantly inherited neurodegenerative disorder of the cerebellum caused by mutations in the voltage gated potassium channel KCNC3. To identify novel pathogenic SCA13 mutations in KCNC3 and to ga

Externí odkaz: https://doaj.org/article/b2f8101955e14ba6b38e6893d817ef18

CAPICE: a computational method for Consequence-Agnostic Pathogenicity Interpretation of Clinical Exome variations

Autor: Shuang Li, K. Joeri van der Velde, Dick de Ridder, Aalt D. J. van Dijk, Dimitrios Soudis, Leslie R. Zwerwer, Patrick Deelen, Dennis Hendriksen, Bart Charbon, Marielle E. van Gijn, Kristin Abbott, Birgit Sikkema-Raddatz, Cleo C. van Diemen, Wilhelmina S. Kerstjens-Frederikse, Richard J. Sinke, Morris A. Swertz

Publikováno v: Genome Medicine, Vol 12, Iss 1, Pp 1-11 (2020)

Abstract Exome sequencing is now mainstream in clinical practice. However, identification of pathogenic Mendelian variants remains time-consuming, in part, because the limited accuracy of current computational prediction methods requires manual class

Externí odkaz: https://doaj.org/article/aa39ee356dcc409a882f0c4904055b68

Rare functional missense variants in CACNA1H

Autor: Ivana A. Souza, Miaozhen Huang, Fang-Xiong Zhang, Richard J. Sinke, Tjerk J. Lagrand, Dineke S. Verbeek, Johannes H. T. M. Koelman, Marina A. J. Tijssen, Gerald W. Zamponi, Justus L. Groen, Maria A. Gandini, Noam Adir, Esther A. R. Nibbeling

Publikováno v: Molecular Brain, Vol 14, Iss 1, Pp 1-4 (2021)
Molecular Brain
Molecular Brain, 14(1):18. BioMed Central Ltd.
Molecular brain, 14(1):18, 1-4. BMC
Molecular Brain, 14(1). BMC

Writer’s cramp (WC) is a task-specific focal dystonia that occurs selectively in the hand and arm during writing. Previous studies have shown a role for genetics in the pathology of task-specific focal dystonia. However, to date, no causal gene has

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5bf2d2c11f084b2218afe3720e1755f4
https://hdl.handle.net/11370/fb74abf9-393e-49da-a815-5fb0624797da

Dutch genome diagnostic laboratories accelerated and improved variant interpretation and increased accuracy by sharing data

Autor: Bart Charbon, Ivo F.A.C. Fokkema, Ronald H. Lekanne Deprez, Jeroen F.J. Laros, Claudia A. L. Ruivenkamp, Bart de Koning, Richard J. Sinke, Morris A. Swertz, Gert Thijs, Quinten Waisfisz, Nienke Wieskamp, Rolph Pfundt, Marielle E. van Gijn, Johan T. den Dunnen, Isaac J. Nijman, Kristin M. Abbott, R. Moritz, Mariska Slofstra, Jasper J. Saris, Rubayte Rahman, Kasper Joeri van der Velde, Marinus J. Blok, Maartje J Vogel

Publikováno v: Human Mutation, 40, 2230-2238
Fokkema, I F A C, van der Velde, K J, Slofstra, M K, Ruivenkamp, C A L, Vogel, M J, Pfundt, R, Blok, M J, Lekanne Deprez, R H, Waisfisz, Q, Abbott, K M, Sinke, R J, Rahman, R, Nijman, I J, de Koning, B, Thijs, G, Wieskamp, N, Moritz, R J G, Charbon, B, Saris, J J, den Dunnen, J T, Laros, J F J, Swertz, M A & van Gijn, M E 2019, ' Dutch genome diagnostic laboratories accelerated and improved variant interpretation and increased accuracy by sharing data ', Human Mutation, vol. 40, no. 12, pp. 2230-2238 . https://doi.org/10.1002/humu.23896
Human Mutation, 40(12), 2230-2238. Wiley
Human Mutation
Human Mutation, 40(12), 2230-2238. Wiley-Liss Inc.
Human mutation, 40(12), 2230-2238. Wiley-Liss Inc.
Human Mutation, 40(12), 2230. Wiley-Liss Inc.
Human Mutation, 40(12), 2230-2238. WILEY
Human Mutation, 40, 12, pp. 2230-2238

Each year diagnostic laboratories in the Netherlands profile thousands of individuals for heritable disease using next‐generation sequencing (NGS). This requires pathogenicity classification of millions of DNA variants on the standard 5‐tier scal

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::12ed75f037a58c36a8d55cf91aaaa300
https://hdl.handle.net/2066/213593