Identification of rare disease genes as drivers of common diseases through tissue-specific gene regulatory networks

Authors: Olivier B. Bakker, Annique Claringbould, Harm-Jan Westra, Henry Wiersma, Floranne Boulogne, Urmo Võsa, Carlos G. Urzúa-Traslaviña, Sophie Mulcahy Symmons, Mahmoud M. M. Zidan, Marie C. Sadler, Zoltán Kutalik, Iris H. Jonkers, Lude Franke, Patrick Deelen

Source: Scientific Reports, Vol 14, Iss 1, Pp 1-13 (2024)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://doaj.org/toc/2045-2322

Access URL: https://doaj.org/article/9ce5ca1daf92482e81d7d7d7db513a2a

Co-expression in tissue-specific gene networks links genes in cancer-susceptibility loci to known somatic driver genes

Authors: Carlos G. Urzúa-Traslaviña, Tijs van Lieshout, Floranne Boulogne, Kevin Domanegg, Mahmoud Zidan, Olivier B. Bakker, Annique Claringbould, Jeroen de Ridder, Wilbert Zwart, Harm-Jan Westra, Patrick Deelen, Lude Franke

Source: BMC Medical Genomics, Vol 17, Iss 1, Pp 1-14 (2024)

Subject Terms: Cancer susceptibility genes, Cancer drivers, Tissue-specific, Gene networks, GWAS, recount3, Internal medicine, RC31-1245, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1755-8794

Access URL: https://doaj.org/article/87d4375406f84fe0ab53a48e271de9a9

GRaNIE and GRaNPA: inference and evaluation of enhancer‐mediated gene regulatory networks

Authors: Aryan Kamal, Christian Arnold, Annique Claringbould, Rim Moussa, Nila H Servaas, Maksim Kholmatov, Neha Daga, Daria Nogina, Sophia Mueller‐Dott, Armando Reyes‐Palomares, Giovanni Palla, Olga Sigalova, Daria Bunina, Caroline Pabst, Judith B Zaugg

Source: Molecular Systems Biology, Vol 19, Iss 6, Pp 1-23 (2023)

Subject Terms: enhancers, gene regulatory networks, macrophage biology, multiomics data integration, transcriptional regulation, Biology (General), QH301-705.5, Medicine (General), R5-920

File Description: electronic resource

Relation: https://doaj.org/toc/1744-4292

Access URL: https://doaj.org/article/64677dd99cfa4865b8a94f9c6b6d8885

Anxiety among healthcare workers during the COVID-19 pandemic: a longitudinal study

Authors: Esmee Bosma, Verena Feenstra, Sandra H. van Oostrom, Lifelines Corona Research Initiative, H. Marike Boezen, Jochen O. Mierau, H. Lude Franke, Jackie Dekens, Patrick Deelen, Pauline Lanting, Judith M. Vonk, Ilja Nolte, Anil P.S. Ori, Annique Claringbould, Floranne Boulogne, Marjolein X.L. Dijkema, Henry H. Wiersma, Robert Warmerdam, Soesma A. Jankipersadsing, Irene van Blokland, Geertruida H. de Bock, Judith GM Rosmalen, Cisca Wijmenga

Source: Frontiers in Public Health, Vol 11 (2023)

Subject Terms: healthcare workers, anxiety, mental health, COVID-19 pandemic, longitudinal data, Public aspects of medicine, RA1-1270

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fpubh.2023.1236931/full; https://doaj.org/toc/2296-2565

Access URL: https://doaj.org/article/24480a46884d44199477c59591ea9c95

Limited evidence for blood eQTLs in human sexual dimorphism

Authors: Eleonora Porcu, Annique Claringbould, Antoine Weihs, Kaido Lepik, BIOS Consortium, Tom G. Richardson, Uwe Völker, Federico A. Santoni, Alexander Teumer, Lude Franke, Alexandre Reymond, Zoltán Kutalik

Source: Genome Medicine, Vol 14, Iss 1, Pp 1-13 (2022)

Subject Terms: Medicine, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1756-994X

Access URL: https://doaj.org/article/a3f5c3b678794a75addbb623225d2106

The mediating role of physical activity and sedentary behavior in the association between working from home and musculoskeletal pain during the COVID-19 pandemic

Authors: Bette Loef, Sandra H. van Oostrom, Esmee Bosma, Lifelines Corona Research Initiative, Karin I. Proper, H. Marike Boezen, Jochen O. Mierau, H. Lude Franke, Jackie Dekens, Patrick Deelen, Pauline Lanting, Judith M. Vonk, Ilja Nolte, Anil P.S. Ori, Annique Claringbould, Floranne Boulogne, Marjolein X.L. Dijkema, Henry H. Wiersma, Robert Warmerdam, Soesma A. Jankipersadsing, Irene van Blokland, Geertruida H. de Bock, Judith GM Rosmalen, Cisca Wijmenga

Source: Frontiers in Public Health, Vol 10 (2022)

Subject Terms: COVID-19, home workers, hybrid workers, longitudinal study, mediation, musculoskeletal pain, Public aspects of medicine, RA1-1270

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fpubh.2022.1072030/full; https://doaj.org/toc/2296-2565

Access URL: https://doaj.org/article/4ee4bc4212a54d8eba33c8db025eeff7

Omics-informed CNV calls reduce false-positive rates and improve power for CNV-trait associations

Authors: Maarja Lepamets, Chiara Auwerx, Margit Nõukas, Annique Claringbould, Eleonora Porcu, Mart Kals, Tuuli Jürgenson, Andrew Paul Morris, Urmo Võsa, Murielle Bochud, Silvia Stringhini, Cisca Wijmenga, Lude Franke, Hedi Peterson, Jaak Vilo, Kaido Lepik, Reedik Mägi, Zoltán Kutalik

Source: HGG Advances, Vol 3, Iss 4, Pp 100133- (2022)

Subject Terms: anthropometric traits, copy-number variation, gene expression, methylation, multi-omics, PennCNV, Genetics, QH426-470

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2666247722000495; https://doaj.org/toc/2666-2477

Access URL: https://doaj.org/article/5369874a0d0b42c7aab00d9892063e66

Correction for both common and rare cell types in blood is important to identify genes that correlate with age

Authors: Damiano Pellegrino-Coppola, Annique Claringbould, Maartje Stutvoet, BIOS Consortium, Dorret I. Boomsma, M. Arfan Ikram, P. Eline Slagboom, Harm-Jan Westra, Lude Franke

Source: BMC Genomics, Vol 22, Iss 1, Pp 1-12 (2021)

Subject Terms: Whole blood, Gene expression, Cell counts correction, Aging, Platelet activity, Biotechnology, TP248.13-248.65, Genetics, QH426-470

File Description: electronic resource

Relation: https://doaj.org/toc/1471-2164

Access URL: https://doaj.org/article/a14d99fd12dc480fa0fa492123a10668

Mendelian randomization while jointly modeling cis genetics identifies causal relationships between gene expression and lipids

Authors: Adriaan van der Graaf, Annique Claringbould, Antoine Rimbert, BIOS Consortium, Harm-Jan Westra, Yang Li, Cisca Wijmenga, Serena Sanna

Source: Nature Communications, Vol 11, Iss 1, Pp 1-12 (2020)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/6170c0c58be645728eb55d599c1f7f94

Deconvolution of bulk blood eQTL effects into immune cell subpopulations

Authors: Raúl Aguirre-Gamboa, Niek de Klein, Jennifer di Tommaso, Annique Claringbould, Monique GP van der Wijst, Dylan de Vries, Harm Brugge, Roy Oelen, Urmo Võsa, Maria M. Zorro, Xiaojin Chu, Olivier B. Bakker, Zuzanna Borek, Isis Ricaño-Ponce, Patrick Deelen, Cheng-Jiang Xu, Morris Swertz, Iris Jonkers, Sebo Withoff, Irma Joosten, Serena Sanna, Vinod Kumar, Hans J. P. M. Koenen, Leo A. B. Joosten, Mihai G. Netea, Cisca Wijmenga, BIOS Consortium, Lude Franke, Yang Li

Source: BMC Bioinformatics, Vol 21, Iss 1, Pp 1-23 (2020)

Subject Terms: eQTL, Deconvolution, Cell types, Immune cells, Computer applications to medicine. Medical informatics, R858-859.7, Biology (General), QH301-705.5

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s12859-020-03576-5; https://doaj.org/toc/1471-2105

Access URL: https://doaj.org/article/d968288a4faf422088c9b27830e918ca

Evaluation of commonly used analysis strategies for epigenome- and transcriptome-wide association studies through replication of large-scale population studies

Authors: Jeroen van Rooij, Pooja R. Mandaviya, Annique Claringbould, Janine F. Felix, Jenny van Dongen, Rick Jansen, Lude Franke, BIOS consortium, Peter A. C. ’t Hoen, Bas Heijmans, Joyce B. J. van Meurs

Source: Genome Biology, Vol 20, Iss 1, Pp 1-14 (2019)

Subject Terms: Illumina 450k arrays, DNA methylation, EWAS, RNA sequencing, Differential gene expression, TWAS, Biology (General), QH301-705.5, Genetics, QH426-470

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s13059-019-1878-x; https://doaj.org/toc/1474-760X

Access URL: https://doaj.org/article/24317525c8464e1ba77c895c99e3e27d

Gender differences in the mental health impact of the COVID-19 lockdown: Longitudinal evidence from the Netherlands

Authors: A. Vloo, R.J.M. Alessie, J.O. Mierau, Marike H. Boezen, Jochen O. Mierau, Lude Franke, Jackie Dekens, Patrick Deelen, Pauline Lanting, Judith M. Vonk, Ilja Nolte, Anil P.S. Ori, Annique Claringbould, Floranne Boulogne, Marjolein X.L. Dijkema, Henry H. Wiersma, Robert Warmerdam, Soesma A. Jankipersadsing

Source: SSM: Population Health, Vol 15, Iss , Pp 100878- (2021)

Subject Terms: I10, Public aspects of medicine, RA1-1270, Social sciences (General), H1-99

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S2352827321001531; https://doaj.org/toc/2352-8273

Access URL: https://doaj.org/article/3ed095d67f034557b454065c8330f320

Lifelines COVID-19 cohort: investigating COVID-19 infection and its health and societal impacts in a Dutch population-based cohort

Authors: Judith M Vonk, H Marike Boezen, Sandra Brouwer, Cisca Wijmenga, Ute Bültmann, Jochen Mierau, Johanna C Herkert, Alexandra Zhernakova, Katherine Mc Intyre, Pauline Lanting, Patrick Deelen, Henry H Wiersma, Anil P S Ori, Soesma A Jankipersadsing, Robert Warmerdam, Irene van Blokland, Floranne Boulogne, Marjolein X L Dijkema, Annique Claringbould, Olivier Bakker, Esteban A Lopera Maya, Sijmen A Reijneveld, Elianne Zijlstra, Morris A Swertz, Raun van Ooijen, Viola Angelini, Louise H Dekker, Anna Sijtsma, Sicco A Scherjon, Jackie A M Dekens, Lude Franke

Source: BMJ Open, Vol 11, Iss 3 (2021)

Subject Terms: Medicine

File Description: electronic resource

Relation: https://bmjopen.bmj.com/content/11/3/e044474.full; https://doaj.org/toc/2044-6055

Access URL: https://doaj.org/article/eea6f2f8ba31490abd6efec75d8d475a

Association between socioeconomic status and self-reported, tested and diagnosed COVID-19 status during the first wave in the Northern Netherlands: a general population-based cohort from 49 474 adults

Authors: Jochen Mierau, Pauline Lanting, Patrick Deelen, Robert Warmerdam, Floranne Boulogne, Annique Claringbould, Lude Franke, Yinjie Zhu, Ming-Jie Duan, Hermien H. Dijk, Roel D. Freriks, Louise H. Dekker, Jochen O. Mierau, Marike Boezen, Jackie Dekens, Judith Vonk, Ilja Nolte, Anil Ori, Marjolein Dijkema, Henry Wiersma, Soesma Medema Jankipersadsing

Source: BMJ Open, Vol 11, Iss 3 (2021)

Subject Terms: Medicine

File Description: electronic resource

Relation: https://bmjopen.bmj.com/content/11/3/e048020.full; https://doaj.org/toc/2044-6055

Access URL: https://doaj.org/article/d36c3be833c54a75948bd3937bfb012c

Using symptom-based case predictions to identify host genetic factors that contribute to COVID-19 susceptibility.

Authors: Irene V van Blokland, Pauline Lanting, Anil P S Ori, Judith M Vonk, Robert C A Warmerdam, Johanna C Herkert, Floranne Boulogne, Annique Claringbould, Esteban A Lopera-Maya, Meike Bartels, Jouke-Jan Hottenga, Andrea Ganna, Juha Karjalainen, Lifelines COVID-19 cohort study, COVID-19 Host Genetics Initiative, Caroline Hayward, Chloe Fawns-Ritchie, Archie Campbell, David Porteous, Elizabeth T Cirulli, Kelly M Schiabor Barrett, Stephen Riffle, Alexandre Bolze, Simon White, Francisco Tanudjaja, Xueqing Wang, Jimmy M Ramirez, Yan Wei Lim, James T Lu, Nicole L Washington, Eco J C de Geus, Patrick Deelen, H Marike Boezen, Lude H Franke

Source: PLoS ONE, Vol 16, Iss 8, p e0255402 (2021)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://doaj.org/toc/1932-6203

Access URL: https://doaj.org/article/f56d0cd40e374f90802e5b2a9b90049e

Using symptom-based case predictions to identify host genetic factors that contribute to COVID-19 susceptibility

Authors: Irene V. van Blokland, Pauline Lanting, Anil P. S. Ori, Judith M. Vonk, Robert C. A. Warmerdam, Johanna C. Herkert, Floranne Boulogne, Annique Claringbould, Esteban A. Lopera-Maya, Meike Bartels, Jouke-Jan Hottenga, Andrea Ganna, Juha Karjalainen, Lifelines COVID-19 cohort study, The COVID-19 Host Genetics Initiative, Caroline Hayward, Chloe Fawns-Ritchie, Archie Campbell, David Porteous, Elizabeth T. Cirulli, Kelly M. Schiabor Barrett, Stephen Riffle, Alexandre Bolze, Simon White, Francisco Tanudjaja, Xueqing Wang, Jimmy M. Ramirez, Yan Wei Lim, James T. Lu, Nicole L. Washington, Eco J. C. de Geus, Patrick Deelen, H. Marike Boezen, Lude H. Franke

Source: PLoS ONE, Vol 16, Iss 8 (2021)

Subject Terms: Medicine, Science

File Description: electronic resource

Relation: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8357137/?tool=EBI; https://doaj.org/toc/1932-6203

Access URL: https://doaj.org/article/48e7e653327e48aabd22b8438d85070f

Systematic Prioritization of Candidate Genes in Disease Loci Identifies TRAFD1 as a Master Regulator of IFNγ Signaling in Celiac Disease

Authors: Adriaan van der Graaf, Maria M. Zorro, Annique Claringbould, Urmo Võsa, Raúl Aguirre-Gamboa, Chan Li, Joram Mooiweer, Isis Ricaño-Ponce, Zuzanna Borek, Frits Koning, Yvonne Kooy-Winkelaar, Ludvig M. Sollid, Shuo-Wang Qiao, Vinod Kumar, Yang Li, Lude Franke, Sebo Withoff, Cisca Wijmenga, Serena Sanna, Iris Jonkers, BIOS Consortium

Source: Frontiers in Genetics, Vol 11 (2021)

Subject Terms: celiac disease, gene prioritization, expression quantitative trait locus (eQTL), TRAFD1, trans regulation, Genetics, QH426-470

File Description: electronic resource

Relation: https://www.frontiersin.org/articles/10.3389/fgene.2020.562434/full; https://doaj.org/toc/1664-8021

Access URL: https://doaj.org/article/e122b2ecbc904b5f84b6bf409f7973ed

Genome-wide identification of directed gene networks using large-scale population genomics data

Authors: René Luijk, Koen F. Dekkers, Maarten van Iterson, Wibowo Arindrarto, Annique Claringbould, Paul Hop, Dorret I. Boomsma, Cornelia M. van Duijn, Marleen M. J. van Greevenbroek, Jan H. Veldink, Cisca Wijmenga, Lude Franke, Peter A. C. ’t Hoen, Rick Jansen, Joyce van Meurs, Hailiang Mei, P. Eline Slagboom, Bastiaan T. Heijmans, Erik W. van Zwet, BIOS (Biobank-based Integrative Omics Study) Consortium

Source: Nature Communications, Vol 9, Iss 1, Pp 1-10 (2018)

Subject Terms: Science

File Description: electronic resource

Relation: https://doaj.org/toc/2041-1723

Access URL: https://doaj.org/article/fe4640ea326848b3a9330f5cfa121bef

A SNP panel for identification of DNA and RNA specimens

Authors: Soheil Yousefi, Tooba Abbassi-Daloii, Thirsa Kraaijenbrink, Martijn Vermaat, Hailiang Mei, Peter van ‘t Hof, Maarten van Iterson, Daria V. Zhernakova, Annique Claringbould, Lude Franke, Leen M. ‘t Hart, Roderick C. Slieker, Amber van der Heijden, Peter de Knijff, BIOS consortium, Peter A. C. ’t Hoen

Source: BMC Genomics, Vol 19, Iss 1, Pp 1-12 (2018)

Subject Terms: Genetic variation, Sample tracking, Mix up samples, Biobanking, Forensics, Biotechnology, TP248.13-248.65, Genetics, QH426-470

File Description: electronic resource

Relation: http://link.springer.com/article/10.1186/s12864-018-4482-7; https://doaj.org/toc/1471-2164

Access URL: https://doaj.org/article/0e8138dd70e8467994de1cfcfd00291b