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PubMed Publications| Keyword search (4,163 papers available) |  |
"Genomics" Keyword-tagged Publications:
| Title | Authors | PubMed ID | |
|---|---|---|---|
| 1 | Integrated metabolomics and metagenomics analysis identifies a unique signature characterizing metabolic syndrome | Wannaiampikul S; Lee B; Chen J; Prentice KJ; Ayansola R; Xu A; Santosa S; Pantopoulos K; Sweeney G; | 41794383 HKAP |
| 2 | Season and city shape urban bioaerosol composition beyond vegetation and socioeconomic gradients | Poirier S; Rondeau-Leclaire J; Faticov M; Roy A; Lajeunesse G; Lucier JF; Tardif S; Kembel SW; Ziter C; Laprise C; Paquette A; Girard C; Laforest-Lapointe I; | 41785576 BIOLOGY |
| 3 | Cross-species evaluation of TANGO2 homologs, including HRG-9 and HRG-10 in em Caenorhabditis elegans, /em challenges a proposed role in heme trafficking | Sandkuhler SE; Youngs KS; Gottipalli O; Owlett LD; Bandora MB; Naaz A; Kim E; Wang L; Wojtovich A; Gupta V; Sacher M; Mackenzie SJ; | 41504601 BIOLOGY |
| 4 | Geography, Ancestry, Age and Sex Shape Somatic Autosomal Mosaic Chromosomal Alterations in Blood | Won Kang JR; Kim YJ; Skead K; Soave D; Evans J; Bruat V; Harwood MP; Morris Q; Matovu E; Mulindwa J; Noyes H; McLeod A; Hazelhurst S; Lombard Z; Ramsay M; Fave MJ; Awadalla P; | 41282824 BIOLOGY |
| 5 | Imaging flow cytometry-based cellular screening elucidates pathophysiology in individuals with Variants of Uncertain Significance | Muffels IJJ; Waterham HR; D' Alessandro G; Zagnoli-Vieira G; Sacher M; Lefeber DJ; Van der Vinne C; Roifman CM; Gassen KLI; Rehmann H; Van Haaften-Visser DY; Nieuwenhuis ESS; Jackson SP; Fuchs SA; Wijk F; van Hasselt P; | 39920830 BIOLOGY |
| 6 | Widespread admixture blurs population structure and confounds Lake Trout (Salvelinus namaycush) conservation even in the genomic era | Bernos TA; Gibelli J; Michaelides S; Won H; Jeon HB; Marin K; Boguski DA; Janjua MY; Gallagher CP; Howland KL; Fraser DJ; | 39730611 BIOLOGY |
| 7 | Evolution of chromosome-arm aberrations in breast cancer through genetic network rewiring | Kuzmin E; Baker TM; Lesluyes T; Monlong J; Abe KT; Coelho PP; Schwartz M; Del Corpo J; Zou D; Morin G; Pacis A; Yang Y; Martinez C; Barber J; Kuasne H; Li R; Bourgey M; Fortier AM; Davison PG; Omeroglu A; Guiot MC; Morris Q; Kleinman CL; Huang S; Gingras AC; Ragoussis J; Bourque G; Van Loo P; Park M; | 38517886 BIOLOGY |
| 8 | Editorial: Computational systems immunovirology | Zarei Ghobadi M; Teymoori-Rad M; Selvaraj G; Wei DQ; | 37475870 CHEMBIOCHEM |
| 9 | Rethinking microbial infallibility in the metagenomics era | O' Malley MA; Walsh DA; | 34160589 BIOLOGY |
| 10 | ChIP-seq protocol for sperm cells and embryos to assess environmental impacts and epigenetic inheritance | Lismer A; Lambrot R; Lafleur C; Dumeaux V; Kimmins S; | 34159325 PERFORM |
| 11 | A Novel Freshwater to Marine Evolutionary Transition Revealed within Methylophilaceae Bacteria from the Arctic Ocean | Ramachandran A; McLatchie S; Walsh DA; | 34154421 BIOLOGY |
| 12 | Identification of a Novel Biosynthetic Gene Cluster in Aspergillus niger Using Comparative Genomics | Evdokias G; Semper C; Mora-Ochomogo M; Di Falco M; Nguyen TTM; Savchenko A; Tsang A; Benoit-Gelber I; | 34064722 BIOLOGY |
| 13 | Core Competencies in Cancer Genomics for Healthcare Professionals: Results From a Systematic Literature Review and a Delphi Process. | Hoxhaj I, Tognetto A, Acampora A, Stojanovic J, Boccia S | 33442861 HKAP |
| 14 | Phylogenomic fingerprinting of tempo and functions of horizontal gene transfer within ochrophytes. | Dorrell RG, Villain A, Perez-Lamarque B, Audren de Kerdrel G, McCallum G, Watson AK, Ait-Mohamed O, Alberti A, Corre E, Frischkorn KR, Pierella Karlusich JJ, Pelletier E, Morlon H, Bowler C, Blanc G | 33419955 BIOLOGY |
| 15 | Genome Sequence Resource of Bacillus velezensis EB14, a native endophytic bacterial strain with biocontrol potential against the poplar stem canker causative pathogen, Sphaerulina musiva. | Naik S, Tsang A, Ramanan US, Dayanandan S | 33263425 BIOLOGY |
| 16 | Functional analysis of low-grade glioma genetic variants predicts key target genes and transcription factors. | Manjunath M; Yan J; Youn Y; Drucker KL; Kollmeyer TM; McKinney AM; Zazubovich V; Zhang Y; Costello JF; Eckel-Passow J; Selvin PR; Jenkins RB; Song JS; | 33130899 PHYSICS |
| 17 | Sediment Metagenomes as Time Capsules of Lake Microbiomes. | Garner RE; Gregory-Eaves I; Walsh DA; | 33148818 BIOLOGY |
| 18 | Size reductions and genomic changes within two generations in wild walleye populations: associated with harvest? | Bowles E, Marin K, Mogensen S, MacLeod P, Fraser DJ | 32684951 CONCORDIA |
| 19 | Plasma levels of one-carbon metabolism nutrients in women with anorexia nervosa | Burdo J; Booij L; Kahan E; Thaler L; Israël M; Agellon LB; Nitschmann E; Wykes L; Steiger H; | 32427359 PSYCHOLOGY |
| 20 | Diversity, evolution, and classification of virophages uncovered through global metagenomics. | Paez-Espino D, Zhou J, Roux S, Nayfach S, Pavlopoulos GA, Schulz F, McMahon KD, Walsh D, Woyke T, Ivanova NN, Eloe-Fadrosh EA, Tringe SG, Kyrpides NC | 31823797 BIOLOGY |
| 21 | Enzymes of early-diverging, zoosporic fungi. | Lange L, Barrett K, Pilgaard B, Gleason F, Tsang A | 31309267 CSFG |
| 22 | Chaco Canyon Dig Unearths Ethical Concerns. | Claw KG, Lippert D, Bardill J, Cordova A, Fox K, Yracheta JM, Bader AC, Bolnick DA, Malhi RS, TallBear K, Garrison NA | 29745246 CONCORDIA |
| 23 | Genetics of mating in members of the Chaetomiaceae as revealed by experimental and genomic characterization of reproduction in Myceliophthora heterothallica. | Hutchinson MI, Powell AJ, Tsang A, O'Toole N, Berka RM, Barry K, Grigoriev IV, Natvig DO | 26608618 CSFG |
| 24 | An Evolutionarily Conserved Transcriptional Activator-Repressor Module Controls Expression of Genes for D-Galacturonic Acid Utilization in Aspergillus niger. | Niu J, Alazi E, Reid ID, Arentshorst M, Punt PJ, Visser J, Tsang A, Ram AF | 28049705 CSFG |
| 25 | Thermostable xylanases from thermophilic fungi and bacteria: Current perspective. | Chadha BS, Kaur B, Basotra N, Tsang A, Pandey A | 30679061 CSFG |
| Title: | Imaging flow cytometry-based cellular screening elucidates pathophysiology in individuals with Variants of Uncertain Significance | ||||
| Authors: | Muffels IJJ, Waterham HR, D', Alessandro G, Zagnoli-Vieira G, Sacher M, Lefeber DJ, Van der Vinne C, Roifman CM, Gassen KLI, Rehmann H, Van Haaften-Visser DY, Nieuwenhuis ESS, Jackson SP, Fuchs SA, Wijk F, van Hasselt P | ||||
| Link: | https://pubmed.ncbi.nlm.nih.gov/39920830/ | ||||
| DOI: | 10.1186/s13073-025-01433-9 | ||||
| Publication: | Genome medicine | ||||
| Keywords: | DNA damage repair defect; Functional genomics; Genetic diseases; High-throughput screening; Imaging flow cytometry; Metabolic disorders; Precision genomic diagnostics; Variant of uncertain significance; | ||||
| PMID: | 39920830 | Category: | Date Added: | 2025-02-08 | |
| Dept Affiliation: |
BIOLOGY
1 Department of Metabolic Diseases, Division Pediatrics, Wilhelmina Children's Hospital University Medical Centre Utrecht, Utrecht University, Utrecht, the Netherlands. i.j.j.muffels-2@umcutrecht.nl. 2 United For Metabolic Diseases (UMD), Amsterdam, the Netherlands. 3 Department of Laboratory Medicine, Laboratory Genetic Metabolic Diseases, Amsterdam UMC - AMC, Amsterdam, the Netherlands. 4 Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK. 5 The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK. 6 Department of Biology, Concordia University, Montreal, QC, Canada. 7 Department of Anatomy and Cell Biology, McGill University, Montreal, QC, Canada. 8 Translational Metabolic Laboratory, Department of Neurology, Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, Nijmegen, the Netherlands. 9 Department of Metabolic Diseases, Division Pediatrics, Wilhelmina Children's Hospital University Medical Centre Utrecht, Utrecht University, Utrecht, the Netherlands. 10 The Hospital for Sick Children and Research Institute, The University of Toronto, Toronto, Canada. 11 Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands. 12 Department of Energy and Biotechnology, Flensburg University of Applied Sciences, Flensburg, Germany. 13 Department of Pediatrics, Center for Lysosomal and Metabolic Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands. 14 Center for Rare Diseases, Erasmus University Medical Center, Rotterdam, the Netherlands. 15 Center for Translational Immunology (CTI), University Medical Center Utrecht (UMC), Utrecht University (UU), Utrecht, The Netherlands. 16 Department of Metabolic Diseases, Division Pediatrics, Wilhelmina Children's Hospital University Medical Centre Utrecht, Utrecht University, Utrecht, the Netherlands. p.vanhasselt@umcutrecht.nl. |
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Description: |
Background: Deciphering variants of uncertain significance (VUS) represents a major diagnostic challenge, partially due to the lack of easy-to-use and versatile cellular readouts that aid the interpretation of pathogenicity and pathophysiology. To address this challenge, we propose a high-throughput screening of cellular functionality through an imaging flow cytometry (IFC)-based platform. Methods: Six assays to evaluate autophagic-, lysosomal-, Golgi- health, mitochondrial function, ER stress, and NF-?ß activity were developed in fibroblasts. Assay sensitivity was verified with compounds (N = 5) and positive control patients (N = 6). Eight healthy controls and 20 individuals with VUS were screened. Results: All molecular compounds and positive controls showed significant changes on their cognate assays, confirming assay sensitivity. Simultaneous screening of positive control patients on all six assays revealed distinct phenotypic profiles. In addition, individuals with VUS(es) in well-known disease genes showed distinct - but similar-phenotypic profiles compared to patients with pathogenic variants in the same gene.. For all individuals with VUSes in Genes of Uncertain Significance (GUS), we found one or more of six assays were significantly altered. Broadening the screening to an untargeted approach led to the identification of two clusters that allowed for the recognition of altered cell cycle dynamics and DNA damage repair defects. Experimental follow-up of the 'DNA damage repair defect cluster' led to the discovery of highly specific defects in top2cc release from double-strand DNA breaks in one of these individuals, harboring a VUS in the RAD54L2 gene. Conclusions: Our high-throughput IFC-based platform simplifies the process of identifying VUS pathogenicity through six assays and allows for the recognition of useful pathophysiological markers that structure follow-up experiments, thereby representing a novel valuable tool for precise functional diagnostics in genomics. |
