​​Team leader: Zuzana Gerber  
E-mail: gerber​cnrgh.fr

The mission of the Development Lab is to anticipate emerging technologies in genomics and evaluate their potential for research applications. Our goal is to identify innovative strategies and propose novel approaches that will help find answers to research questions that cannot be addressed by current technologies. Some of these evaluations are performed in collaboration with the CRefIX (PFMG2025).

• Third-generation sequencing technologies (long-reads) such as the PromethION24 from Oxford Nanopore (ONT) and the Revio from Pacific Biosciences (PacBio) empower the analysis of complex regions of the human genome, as well as transcriptomic and epigenetic analyses. We leverage these technologies to provide long-read sequencing data for collaborative projects.
• We evaluate new sequencing platforms and innovative approaches that are potentially highly competitive in terms of cost and accuracy, including the AVITI from Element Biosciences and the UG200 from Ultima Genomics.
• Single-Cell approaches provide insight into molecular mechanisms underlying diseases at cellular resolution. For example, we use the Chromium X (10x Genomics) for collaborative projects on neurodegenerative disorders.
• Since the COVID-19 pandemic, we have been developing innovative approaches for epidemiological surveillance and early detection of pathogens in wastewater. 

Publications

2026

• Analysis of low-input and degraded forensic DNA trace samples with NGS using the MiSeq FGx platform. Larnane A, Fund C, Letexier M, Gerber Z, Deleuze JF. Forensic Sci Int Genet. 2027 Jan;86:103569. doi: 10.1016/j.fsigen.2026.103569. Epub 2026 Jun 16. Impact factor : 3.6
• Signaling cascades shape functional subpopulations of cortical astrocytes in male wild-type mice and APP/PS1dE9 Alzheimer's disease model. Poulot-Becq-Giraudon Y, Guillemaud O, Degl'Innocenti E, Letenneur V, Bascarane K, Barbay T, Møller Clausen M, Derbois C, Guillermier M, Juricek L, Riquelme-Perez M, Lakomy T, Benhaim L, Dufour N, Gipchtein P, Petit F, Siron L, Aurégan G, Dechamps N, Gaillard MC, Bemelmans AP, Bos R, Carrillo-de Sauvage MA, Milior G, Rouach N, Brohard S, Muret K, Bonnet E, Escartin C. Nat Commun. 2026 Apr 14;17(1):4194. doi: 10.1038/s41467-026-71826-w. Impact factor : 18.1
• Assessing the integrity of SARS-CoV-2 and F-specific RNA bacteriophage RNA in raw wastewater (ANRS0160). Chaqroun A, Challant J, Jeulin H, Loutreul J, Ansmant T, Labialle S, Gerber Z, Fund C, Aigueperse C, Deleuze JF, Olaso R, Boudaud N, Maréchal V, Gantzer C, Bertrand I. Water Res. 2026 Jan 15;289(Pt B):125002. doi: 10.1016/j.watres.2025.125002. Epub 2025 Nov 18. Impact factor : 12.4

2025

• Interlaboratory evaluation of high molecular weight DNA extraction methods for long-read sequencing and structural variant analysis. Devonshire AS, Morata J, Jubin C, Abreu Pereira RP, Hernandez-Hernandez L, Yener D, Cabannes E, McGinn S, Delepine M, Fund C, Tonda R, Heath S, Dabad M, Gutierrez-Cuesta J, Sanchez Escudero I, Frias-Lopez MC, Cowen S, Whale A, Voss T, Deleuze JF, Gut I, Gut M, Foy CA. BMC Genomics. 2025 Jul 28;26(1):698. doi: 10.1186/s12864-025-11792-7. Impact factor : 3.7
• Characterization of challenging forensic DNA traces using advanced molecular technologies. Larnane A, Lefèvre-Horgues C, Cruaud C, Fund C, Le Floch E, Sandron F, Segurens B, How-Kit A, Deleuze JF. Int J Legal Med. 2025 Jul;139(4):1511-1527. doi: 10.1007/s00414-025-03448-8. Epub 2025 Mar 1. Impact factor : 2.3
• Optimized protocol for direct extraction of SARS-CoV-2 RNA from raw wastewater samples (ANRS 0160). Chaqroun A, El Soufi G, Gerber Z, Loutreul J, Cluzel N, Challant J, Delafoy D, Sandron F, Di Jorio L, Raffestin S, Maréchal V, Gantzer C, Olaso R, Deleuze JF, Rohr O, Boudaud N, Wallet C, Bertrand I. MethodsX. 2025 Apr 18;14:103323. doi: 10.1016/j.mex.2025.103323. eCollection 2025 Jun. Impact factor : 1.9
• Long-Read Whole-Genome Sequencing as a Tool for Variant Detection in Inherited Retinal Dystrophies. Rodilla C, Núñez-Moreno G, Benitez Y, Rodríguez de Alba M, Blanco-Kelly F, López-Alcojor A, Fernández-Caballero L, Perea-Romero I, Del Pozo-Valero M, García-García G, Balanzá M, Villaverde C, Zurita O, Jubin C, Fund C, Delepine M, Leduc A, Deleuze JF, Millán JM, Minguez P, Corton M, Ayuso C. Int J Mol Sci. 2025 Apr 18;26(8):3825. doi: 10.3390/ijms26083825. Impact factor : 4.9
• A detailed analysis of second and third-generation sequencing approaches for accurate length determination of short tandem repeats and homopolymers. Jeanjean SI, Shen Y, Hardy LM, Daunay A, Delépine M, Gerber Z, Alberdi A, Tubacher E, Deleuze JF, How-Kit A. Nucleic Acids Res. 2025 Feb 27;53(5):gkaf131. doi: 10.1093/nar/gkaf131. Impact factor : 13.1

2024

• Definition of a concentration and RNA extraction protocol for optimal whole genome sequencing of SARS-CoV-2 in wastewater (ANRS0160). Chaqroun A, El Soufi G, Gerber Z, Loutreul J, Cluzel N, Delafoy D, Sandron F, Di Jorio L, Raffestin S, Maréchal V, Gantzer C, Olaso R, Deleuze JF, Rohr O, Boudaud N, Wallet C, Bertrand I. Sci Total Environ. 2024 Nov 20;952:175823. doi: 10.1016/j.scitotenv.2024.175823. Epub 2024 Aug 26. PMID: 39197764 Free article. Impact factor : 8.2.
• An elevated level of interleukin-17A in a Senegalese malaria cohort is associated with rs8193038 IL-17A genetic variant. Thiam F, Diop G, Coulonges C, Derbois C, Thiam A, Diouara AAM, Mbaye MN, Diop M, Nguer CM, Dieye Y, Mbengue B, Zagury JF, Deleuze JF, Dieye A. BMC Infect Dis. 2024 Mar 4;24(1):275. doi: 10.1186/s12879-024-09149-8. PMID: 38438955. Impact factor : 3.4.
• Highly efficient and sensitive membrane-based concentration process allows quantification, surveillance, and sequencing of viruses in large volumes of wastewater. El Soufi G, Di Jorio L, Gerber Z, Cluzel N, Van Assche J, Delafoy D, Olaso R, Daviaud C, Loustau T, Schwartz C, Trebouet D, Hernalsteens O, Marechal V, Raffestin S, Rousset D, Van Lint C, Deleuze JF, Boni M; OBEPINE consortium; Rohr O, Villain-Gambier M, Wallet C. Water Res. 2024 Feb 1;249:120959. doi: 10.1016/j.watres.2023.120959. Epub 2023 Dec 3. PMID: 38070350 Free article. Impact factor : 11.5.