February 23, 2023

Health 2030 Genome Center – Clinical Genomic Analysis Center (CGAC) of the PHRT Swiss Multi-Omics Center

Platform, SMOC

Short Summary

The Health 2030 Genome Center (GC) is a national genomics Competence Center and serves as the Clinical Genomic Analysis Center (CGAC) of the PHRT Swiss Multi-Omics Center. Established to propel genomic medicine in Switzerland, the Center actively supports large-scale human genomics research projects and facilitates genomics applications in hospitals and clinics.

Goals

The overarching goal of the GC, operating as CGAC, is to promote personalized health and genomic medicine. By actively supporting large-scale genomics research initiatives and facilitating genomics applications in healthcare settings, the GC aims to significantly shape genomics practices in Switzerland.

Significance

The importance of the GC as national genomics competence center is underscored by its ISO 15189–accredited sequencing and data analysis services. Positioned strategically, this accreditation enables the GC to provide crucial support to national genomics initiatives, universities, hospitals, clinics, and other healthcare providers. The GC’s dedicated efforts to advance genomics in healthcare and research establish it as a central hub for transformative initiatives. Strategic Areas: Over the past 5 years, the GC has demonstrated preparedness in three strategically important areas: 1. State-of-the-Art Infrastructure: The GC established a clinically accredited, state-of-the-art infrastructure for large-scale nucleic acid sequencing, data analytics, and data governance. This platform is ready to support the clinical community’s diverse needs. 2. Integration of multi-omic data: Actively participating in the PHRT Swiss Multi-Omic Center (SMOC), the GC promotes national and multi-disciplinary collaboration, allowing better integration of molecular analyses and more precise modelling of diseases. 3. Readiness for public health needs: The GC has demonstrated readiness to quickly respond to public health needs, such as the FOPH-supported SARS-CoV-2 genomic surveillance program, and actively contributes to national genomics initiatives. The GC has successfully established a unique infrastructure in Switzerland. With its multipronged competence, accredited and non-accredited services, and services in development, the GC is uniquely positioned to serve as the regional and national hub for medical genomics. Moreover, it aims to actively participate in pan-European initiatives focusing on genomic data generation, governance, and sharing. In summary, the GC is a national genomics competence center dedicated to advancing personalized health and genomic medicine. Through strategic expertise and ISO 15189–accredited services, the GC significantly contributes to the progress of genomics in Switzerland.

Background

Recognizing the gap in Switzerland’s strategy for harnessing genomics resources in health management, the GC develops sequencing and analytic pipelines for clinical-grade DNA and RNA exploration. It initiates projects such as the Swiss Federated Genomics Network (SFGN) and Genome of Switzerland (GoS) to pave the way for implementing genomic medicine. In its pilot phase the GoS aims to sequence 1,000 clinical-grade genomes before scaling up to 15,000 genomes to create a national reference dataset and enable Swiss participation in the European ‘1+ Million Genomes’ Initiative.

Publications

A multi-omics digital research object for the genetics of sleep regulation. Jan M, Gobet N, Diessler S, Franken P, Xenarios I. Sci Data. 2019 Oct 31;6(1):258. doi: 10.1038/s41597-019-0171-x.
An anti-influenza combined therapy assessed by single cell RNA-sequencing. Medaglia C, Kolpakov I, Zwygart AC, Zhu Y, Constant S, Huang S, Cagno V, Dermitzakis ET, Stellacci F, Xenarios I, Tapparel C. Commun Biol. 2022 Oct 10;5(1):1075.
“Continuous population-level monitoring of SARS-CoV-2 seroprevalence in a large European metropolitan region.
Emmenegger M, De Cecco E, Lamparter D, Jacquat RPB, Riou J, Menges D, Ballouz T, Ebner D, Schneider MM, Morales IC, Doğançay B, Guo J, Wiedmer A, Domange J, Imeri M, Moos R, Zografou C, Batkitar L, Madrigal L, Schneider D, Trevisan C, Gonzalez-Guerra A, Carrella A, Dubach IL, Xu CK, Meisl G, Kosmoliaptsis V, Malinauskas T, Burgess-Brown N, Owens R, Hatch S, Mongkolsapaya J, Screaton GR, Schubert K, Huck JD, Liu F, Pojer F, Lau K, Hacker D, Probst-Müller E, Cervia C, Nilsson J, Boyman O, Saleh L, Spanaus K, von Eckardstein A, Schaer DJ, Ban N, Tsai CJ, Marino J, Schertler GFX, Ebert N, Thiel V, Gottschalk J, Frey BM, Reimann RR, Hornemann S, Ring AM, Knowles TPJ, Puhan MA, Althaus CL, Xenarios I, Stuart DI, Aguzzi A. iScience. 2023 Feb 17;26(2):105928.”
External Quality Assessment of SARS-CoV-2 Sequencing: an ESGMD-SSM Pilot Trial across 15 European Laboratories. Wegner F, Roloff T, Huber M, Cordey S, Ramette A, Gerth Y, Bertelli C, Stange M, Seth-Smith HMB, Mari A, Leuzinger K, Cerutti L, Harshman K, Xenarios I, Le Mercier P, Bittel P, Neuenschwander S, Opota O, Fuchs J, Panning M, Michel C, Hallin M, Demuyser T, De Mendonca R, Savelkoul P, Dingemans J, van der Veer B, Boers SA, Claas ECJ, Coolen JPM, Melchers WJG, Gunell M, Kallonen T, Vuorinen T, Hakanen AJ, Bernhoff E, Hetland MAK, Golan Berman H, Adar S, Moran-Gilad J, Wolf DG, Leib SL, Nolte O, Kaiser L, Schmutz S, Kufner V, Zaheri M, Trkola A, Aamot HV, Hirsch HH, Greub G, Egli A. J Clin Microbiol. 2022 Jan 19;60(1):e0169821.
HENA, heterogeneous network-based data set for Alzheimer’s disease. Sügis E, Dauvillier J, Leontjeva A, Adler P, Hindie V, Moncion T, Collura V, Daudin R, Loe-Mie Y, Herault Y, Lambert JC, Hermjakob H, Pupko T, Rain JC, Xenarios I, Vilo J, Simonneau M, Peterson H. Sci Data. 2019 Aug 14;6(1):151. doi: 10.1038/s41597-019-0152-0. PMID: 31413325
“Integrated multi-omics reveals anaplerotic rewiring in methylmalonyl-CoA mutase deficiency
Forny, Patrick; Bonilla, Ximena; Lamparter, David; Shao, Wenguang; Plessl, Tanja; Frei, Caroline; Bingisser, Anna; Goetze, Sandra; van Drogen, Audrey; Harshman, Keith; Pedrioli, Patrick G A; Howald, Cédric; Poms, Martin; Traversi, Florian; Cherkaoui, Sarah; Morscher, Raphael J; Simmons, Luke; Forny, Merima; Xenarios, Ioannis; Aebersold, Ruedi; Zamboni, Nicola; Raetsch, Gunnar; Dermitzakis, Emmanouil; Wollscheid, Bernd; Baumgartner, Matthias R; Froese, D Sean In press in Nature Metabolism”
Integrated proteogenomic deep sequencing and analytics accurately identify non-canonical peptides in tumor immunopeptidomes. Chong C, Müller M, Pak H, Harnett D, Huber F, Grun D, Leleu M, Auger A, Arnaud M, Stevenson BJ, Michaux J, Bilic I, Hirsekorn A, Calviello L, Simó-Riudalbas L, Planet E, Lubiński J, Bryśkiewicz M, Wiznerowicz M, Xenarios I, Zhang L, Trono D, Harari A, Ohler U, Coukos G, Bassani-Sternberg M. Nat Commun. 2020 Mar 10;11(1):1293. doi: 10.1038/s41467-020-14968-9
Prevalence of post-COVID Condition 12 Weeks after Omicron Infection Compared to Negative Controls and Association with Vaccination Status. Nehme M, Vetter P, Chappuis F, Kaiser L, Guessous I; CoviCare Study team. Clin Infect Dis. 2022 Dec 15:ciac947.
Quantification of the spread of SARS-CoV-2 variant B.1.1.7 in Switzerland. Chen C, Nadeau SA, Topolsky I, Manceau M, Huisman JS, Jablonski KP, Fuhrmann L, Dreifuss D, Jahn K, Beckmann C, Redondo M, Noppen C, Risch L, Risch M, Wohlwend N, Kas S, Bodmer T, Roloff T, Stange M, Egli A, Eckerle I, Kaiser L, Denes R, Feldkamp M, Nissen I, Santacroce N, Burcklen E, Aquino C, de Gouvea AC, Moccia MD, Grüter S, Sykes T, Opitz L, White G, Neff L, Popovic D, Patrignani A, Tracy J, Schlapbach R, Dermitzakis ET, Harshman K, Xenarios I, Pegeot H, Cerutti L, Penet D, Blin A, Elies M, Althaus CL, Beisel C, Beerenwinkel N, Ackermann M, Stadler T. Epidemics. 2021 Aug 9;37:100480. doi: 10.1016/j.epidem.2021.100480. Online ahead of print. PMID: 34488035
Repeat Detector: versatile sizing of expanded tandem repeats and identification of interrupted alleles from targeted DNA sequencing. Taylor AS, Barros D, Gobet N, Schuepbach T, McAllister B, Aeschbach L, Randall EL, Trofimenko E, Heuchan ER, Barszcz P, Ciosi M, Morgan J, Hafford-Tear NJ, Davidson AE, Massey TH, Monckton DG, Jones L, Network RIOTEHD, Xenarios I, Dion V. NAR Genom Bioinform. 2022 Dec 5;4(4)
Towards mouse genetic-specific RNA-sequencing read mapping. Gobet N, Jan M, Franken P, Xenarios I. PLoS Comput Biol. 2022 Sep 26;18(9):e1010552.
XSI-a genotype compression tool for compressive genomics in large biobanks. Wertenbroek R, Rubinacci S, Xenarios I, Thoma Y, Delaneau O. Bioinformatics. 2022 Aug 2;38(15):3778-3784.