Livrables
Proposed method documented and source-code available on GitHub (Software).
Raw sequences of ChiP-seq and ATAC-seq delivered to ENA and FAANGfastq files and metadata available at FAANG and ENA.
Raw sequences of Hi-C Capture delivered to ENA and FAANGfastq files and metadata available at FAANG and ENA.
Reproducible, scale-able workflows for FAANG data analysisWe will release on GitHub workflows that are 100% reproducible and scale-able from laptop to HPC to cloud, using a workflow language such as Snakemake or NextFlow, integrating best-in-class bioinformatics open-source software
Raw sequences of WGBS and RRBS delivered to ENA and FAANGfastq files and metadata available at FAANG and ENA.
Raw sequences of RNA-seq delivered to ENA and FAANGfastq files and metadata available at FAANG and ENA.
Bio-repository of 3120 samplesA list of 3120 samples corresponding to 10 aliquots * 13 tissues * 4 replicates * 3 developmental stages * 2 species
Production release of the data coordination platform for the validation enrichment and submission of GENESWitCH sample experiment and analysis data to FAANG through the European public archives The preliminary system will already have been heavily tested optimised and utilised from sample and raw data will be submitted steadily from the start of the project This final version will contain the full configuration of the submission process for the requirements of work packages 1 2 4 and 5
Visualisation and API access for improved annotation in chicken and pigProgrammatic access to the underlying data in Ensembl genomes is made available via the Ensembl API, which enables others to build software and services based on public Ensembl data.
Advanced Bioinformatics TrainingsOrganize two trainings of two days each focussing on the genomic prediction models that will be developed within the project.
GENE-SWitCH project data portal presentation platformA customised GENE-SWitCH section of the FAANG data portal (http://data.faang.org/) with pre-filtered tabulated view of GENE-SWitCH generated samples, datasets and analyses. The platform will include innovative presentation displays of GENE-SWitCH analysis tracks, workflows stored in GitHub and the sampling and experimental protocols developed within the project.
Improved chicken annotation, including variant and transcript annotations improvementsA new chicken genome annotation will be released that includes transcript (coding and non-coding) and gene annotation, regulatory regions, location and likely effect of variants, comparative genomics across hundreds of vertebrate species, and tissue- and time-point specific annotations.
WebinarAn interactive webinar will be organized, focussing on the value of genetic information – including richly annotated high-quality genome sequences.
Improved pig annotation, including variant and transcript annotations improvementsA new pig genome annotation will be released that includes transcript (coding and non-coding) and gene annotation, regulatory regions, location and likely effect of variants, comparative genomics across hundreds of vertebrate species, and tissue- and time-point specific annotations.
Project website, social media, newsletters (8 issues) and two brochures will be developed.
Publication on state of the art of SFS-30 projects, the European node of FAANG DCC and FAANG platform developmentsSubmission of a publication that covers the state of the art of the SFS-30 projects and their interaction through the European node of the FAANG Data Coordination Centre. It will cover the developments to the FAANG submission platform and the advances in data presentation methods of the FAANG data portal. It will also report on the breadth, diversity and standardisation of the FAANG SFS-30 datasets and the contribution that these make to the FAANG community.
Project Management GuidelinesReport compiling the guidelines and rules in place for the coordination, reporting and quality control of the project.
Report on coordinated data production, recording and archiving within the European node of FAANG DCCReport on the establishment of the European node of the FAANG Data Coordination Centre through agreement of scope, remit, objectives and priorities between the SFS-30 funded projects. The report will outline the interoperability development work, a basis for sharing of data and analysis methodologies and framework that will lead to cross project comparative analyses.
Outreach, dissemination, and training planD6.1 will be used to implement and evaluate the progress of the activities targeted to relevant stakeholders.
Functional annotations across fine-mapped, selected regions contributing to body-weight in the experimental Virginia chicken linesTwenty loci with known large effect on body weight in the experimental Virginia chicken lines will be fine-mapped, using a large deep intercross mapping population of ~4000 birds, to haplotypes originating from the founder White Plymouth Rock breed.
Empirical validation of improved genomic prediction models in commercial pig populationsResults of the validation of the developed models, and benchmarking against other models, will be described in a scientific publication.
Validation of developed models with simulated or publicly available dataResults of the validation of the developed models and benchmarking against other models will be described in a scientific publication
Integrated analysis of RNA-seq and ATAC-seq dataResults of integrated analyses of two tissues in light of the reference annotation maps (WP3) at these tissues.
Submission of publication on state of the art and usage of ontologiesPublication on state of the art and usage of ontologies within monogastric and wider farm and companion animal communities. WP3 will incorporate findings from the survey of ontology usage and requirements from the monogastric community and reports on the ontological developments and improvements within the project.
Knowledge Exchange Platform recommendations reportMeeting minutes from 4 physical meetings of the Advisory Board will be prepared as a Recommendation Report.
Results of the comparative analysesComparisons within and between species released as data tables and tracks on the FAANG track hub
Final Conference proceedingsProject results will be shared through a final conference.
GENE-SWitCH e-book of abstractsAll project results will be shared through an e-book of abstracts.
Empirical validation of improved genomic prediction models in commercial chicken populationsDemonstrate the potential of using annotation information (ie eQTLs and functional information) to improve accuracy of genomic selection through validation in a commercially relevant population.
Significant associations detected by eQTL analysis in pigsComprehensive map of eQTL in porcine tissues that are central to whole-body energetic homeostasis: small intestine, liver and muscle.
Operational analysis workflows in Embassy CloudFull analysis containerised workflows archived in GitHub and actively processing incoming project data Evidenced by analysis data flowing into FAANG through the European public archives managed by the data coordination platform D32 WP2 will be implementing initial workflows as soon as raw data becomes available By month 24 the operational infrastructure will be in place for analysis results from WP2 WP4 and WP5 to be delivered in the later half of the project
Report on the data management plan for GENE-SWitCH in accordance with the latest FAANG data standards, SOPs and FAANG Data Sharing Principles.
Publications
Auteurs:
Jani de Vos, Richard P.M.A. Crooijmans, Martijn F.L. Derks, Susan L. Kloet, Bert Dibbits , Martien A.M. Groenen, Ole Madsen
Publié dans:
iScience, 2023, ISSN 2589-0042
Éditeur:
Cell Press
Auteurs:
Bart van der Hee; Jerry M. Wells
Publié dans:
Trends in Microbiology, Numéro Aug;29(8): 2021, 2021, Page(s) 700-712, ISSN 0966-842X
Éditeur:
Elsevier BV
DOI:
10.1016/j.tim.2021.02.001
Auteurs:
Emily L. Clark, Alan L. Archibald, Hans D. Daetwyler, Martien A. M. Groenen, Peter W. Harrison, Ross D. Houston, Christa Kühn, Sigbjørn Lien, Daniel J. Macqueen, James M. Reecy, Diego Robledo, Mick Watson, Christopher K. Tuggle, Elisabetta Giuffra
Publié dans:
Genome Biology, Numéro 21/1, 2020, ISSN 1474-760X
Éditeur:
Springer
DOI:
10.1186/s13059-020-02197-8
Auteurs:
Clara Amid, Blaise T F Alako, Vishnukumar Balavenkataraman Kadhirvelu, Tony Burdett, Josephine Burgin, Jun Fan, Peter W Harrison, Sam Holt, Abdulrahman Hussein, Eugene Ivanov, Suran Jayathilaka, Simon Kay, Thomas Keane, Rasko Leinonen, Xin Liu, Josue Martinez-Villacorta, Annalisa Milano, Amir Pakseresht, Nadim Rahman, Jeena Rajan, Kethi Reddy, Edward Richards, Dmitriy Smirnov, Alexey Sokolov, Sen
Publié dans:
Nucleic Acids Research, 2019, ISSN 0305-1048
Éditeur:
Oxford University Press
DOI:
10.1093/nar/gkz1063
Auteurs:
Mollandin, F., Gilbert, H., Croiseau, P., and Rau, A.
Publié dans:
BMC Bioinformatics, 2022, ISSN 1471-2105
Éditeur:
BioMed Central
DOI:
10.1186/s12859-022-04914-5
Auteurs:
C. Hernández-Banqué, T. Jové-Juncà, D. Crespo-Piazuelo, O. González-Rodríguez, Y. Ramayo-Caldas, A. Esteve-Codina, M.J. Mercat, M. Bink, R. Quintanilla1, M. Ballester
Publié dans:
Frontiers in Immunology, 2023, ISSN 1664-3224
Éditeur:
-
DOI:
10.3389/fimmu.2023.1250942
Auteurs:
Daniel Crespo-Piazuelo; Hervé Acloque; Olga González-Rodríguez; Mayrone Mongellaz; Marie-José Mercat; Marco C A M Bink; Abe E Huisman; Yuliaxis Ramayo-Caldas; Juan Pablo Sánchez; Maria Ballester
Publié dans:
GigaScience, Numéro 18, 2023, Page(s) 1-14, ISSN 2047-217X
Éditeur:
Oxford University Press
DOI:
10.1093/gigascience/giad042
Auteurs:
Peter W Harrison, M Ridwan Amode, Olanrewaju Austine-Orimoloye, Andrey G Azov, Matthieu Barba, If Barnes, Arne Becker, Ruth Bennett, Andrew Berry, Jyothish Bhai, Simarpreet Kaur Bhurji, Sanjay Boddu, Paulo R Branco Lins, Lucy Brooks, Shashank Budhanuru Ramaraju, Lahcen I Campbell, Manuel Carbajo Martinez, Mehrnaz Charkhchi, Kapeel Chougule, Alexander Cockburn, Claire Davidson, Nishadi H De Silva,
Publié dans:
Nucleic Acids Research, 2023, ISSN 1362-4962
Éditeur:
Oxford University Press
DOI:
10.1093/nar/gkad1049
Auteurs:
Fiona Cunningham, James E Allen, Jamie Allen, Jorge Alvarez-Jarreta, M Ridwan Amode, Irina M Armean, Olanrewaju Austine-Orimoloye, Andrey G Azov, If Barnes, Ruth Bennett, Andrew Berry, Jyothish Bhai, Alexandra Bignell, Konstantinos Billis, Sanjay Boddu, Lucy Brooks, Mehrnaz Charkhchi, Carla Cummins, Luca Da Rin Fioretto, Claire Davidson, Kamalkumar Dodiya, Sarah Donaldson, Bilal El Houdaigui, Tama
Publié dans:
Nucleic Acids Research, 2022, ISSN 0305-1048
Éditeur:
Oxford University Press
DOI:
10.1093/nar/gkab1049
Auteurs:
Cyril Kurylo; Cervin Guyomar; Sylvain Foissac; Sarah Djebali
Publié dans:
NAR Genomics and Bioinformatics, Numéro 14, 2023, Page(s) Volume 5, Numéro 4,, ISSN 2631-9268
Éditeur:
Oxford
DOI:
10.1093/nargab/lqad089
Auteurs:
Peter W Harrison, Alexey Sokolov, Akshatha Nayak, Jun Fan, Daniel Zerbino, Guy Cochrane, Paul Flicek
Publié dans:
Frontiers in Genetics, Numéro 12 2021/6/17, 2021, Page(s) 873, ISSN 1664-8021
Éditeur:
Frontiers Media
DOI:
10.3389/fgene.2021.639238
Auteurs:
Kevin L Howe, Premanand Achuthan, James Allen, Jamie Allen, Jorge Alvarez-Jarreta, M Ridwan Amode, Irina M Armean, Andrey G Azov, Ruth Bennett, Jyothish Bhai, Konstantinos Billis, Sanjay Boddu, Mehrnaz Charkhchi, Carla Cummins, Luca Da Rin Fioretto, Claire Davidson, Kamalkumar Dodiya, Bilal El Houdaigui, Reham Fatima, Astrid Gall, Carlos Garcia Giron, Tiago Grego, Cristina Guijarro-Clarke, Lea
Publié dans:
Nucleic Acids Research, Numéro 49/D1, 2020, Page(s) D884-D891, ISSN 0305-1048
Éditeur:
Oxford University Press
DOI:
10.1093/nar/gkaa942
Auteurs:
Y. Ramayo-Caldas, D. Crespo-Piazuelo, J. Morata, O. González-Rodríguez, C. Sebastià, A. Castello, A. Dalmau, S. Ramos-Onsins, K.G. Alexiou, J.M. Folch, R. Quintanilla, M. Ballester
Publié dans:
Microbiology Spectrum, 2023, ISSN 2165-0497
Éditeur:
-
DOI:
10.1128/spectrum.05271-22
Auteurs:
Bruno C Perez; Marco C A M Bink; Karen L Svenson; Gary A Churchill; Mario P L Calus
Publié dans:
G3 Genes|Genomes|Genetics, Numéro 17, 2022, Page(s) 12; 11; 2022, ISSN 2160-1836
Éditeur:
Genetics Society of America
DOI:
10.1093/g3journal/jkac258
Auteurs:
Fergal J Martin, M Ridwan Amode, Alisha Aneja, Olanrewaju Austine-Orimoloye, Andrey G Azov, If Barnes, Arne Becker, Ruth Bennett, Andrew Berry, Jyothish Bhai, Simarpreet Kaur Bhurji, Alexandra Bignell, Sanjay Boddu, Paulo R Branco Lins, Lucy Brooks, Shashank Budhanuru Ramaraju, Mehrnaz Charkhchi, Alexander Cockburn, Luca Da Rin Fiorretto, Claire Davidson, Kamalkumar Dodiya, Sarah Donaldson, Bilal
Publié dans:
Nucleic Acids Research, Numéro 18, 2022, ISSN 1362-4962
Éditeur:
Oxford University Press
DOI:
10.1093/nar/gkac958
Auteurs:
T. Jové-Juncà, D. Crespo-Piazuelo, O. González-Rodríguez, M. Pascual, C. Hernández-Banqué, J. Reixach, R. Quintanilla, M. Ballester
Publié dans:
Animal, 2023, ISSN 1751-7311
Éditeur:
Cambridge University Press
DOI:
10.1016/j.animal.2023.101043
Auteurs:
Peter W Harrison, Alisha Ahamed, Raheela Aslam, Blaise T F Alako, Josephine Burgin, Nicola Buso, Mélanie Courtot, Jun Fan, Dipayan Gupta, Muhammad Haseeb, Sam Holt, Talal Ibrahim, Eugene Ivanov, Suran Jayathilaka, Vishnukumar Balavenkataraman Kadhirvelu, Manish Kumar, Rodrigo Lopez, Simon Kay, Rasko Leinonen, Xin Liu, Colman O’Cathail, Amir Pakseresht, Youngmi Park, Stephane Pesant, Nadim Rahm
Publié dans:
Nucleic Acids Research, Numéro 49/D1, 2020, Page(s) D82-D85, ISSN 0305-1048
Éditeur:
Oxford University Press
DOI:
10.1093/nar/gkaa1028
Auteurs:
Mollandin, F., Rau, A., and Croiseau, P.
Publié dans:
G3 Genes|Genomes|Genetics, 2022, ISSN 2160-1836
Éditeur:
Genetics Society of America
DOI:
10.1093/g3journal/jkab225
Auteurs:
B. C. Perez, M. C. A. M. Bink, K. L. Svenson, G. A. Churchill and M. P. L. Calus
Publié dans:
G3 Genes|Genomes|Genetics, Numéro 12; 4; 2022, 2022, Page(s) jkac039, ISSN 2160-1836
Éditeur:
Genetics Society of America
DOI:
10.1093/g3journal/jkac039
Auteurs:
Sébastien Guizard; Katarzyna Miedzinska; Jacqueline Smith; Jonathan Smith; Richard I Kuo; Megan Davey; Alan Archibald; Mick Watson
Publié dans:
Bioinformatics, Numéro 4, 2023, Page(s) , vol. 39 , no. 5 , 24323 pp. 1-2, ISSN 1367-4811
Éditeur:
Oxford University Press
DOI:
10.1093/bioinformatics/btad150
Auteurs:
Acloque, Hervé; Harrison, P.W.; Lakhal, W.; Martin, F.; Archibald, A.L.; Beinat, M.; Davey, M.; Djebali, S.; Foissac, S.; Guizard, S.; Guyomar, C.; Kuo, R.; Kurylo, C.; Madsen, O.; Miedzinska, K.; Mongellaz, M.; Smith, J.; Smith, J.; Sokolov, A.; de Vos, J.; Giuffra, E.; Watson, M.
Publié dans:
"World Congress on Genetics Applied to Livestock Production, Jul 2022, Rotterdam, Netherlands. pp.2281-2284, ⟨10.3920/978-90-8686-940-4_550⟩", Numéro 1, 2022
Éditeur:
-
DOI:
10.3920/978-90-8686-940-4_550
Auteurs:
D. Crespo-Piazuelo, A. Reverter, Y. Ramayo-Caldas, R. Quintanilla, H. Acloque, M. J. Mercat, M.C.A.M. Bink, A.E. Huisman and M. Ballester
Publié dans:
Proceedings of the 39th International Conference on Animal Genetics, Cape Town, South Africa (2023), 2023, Page(s) 15
Éditeur:
-
Auteurs:
Mollandin, Fanny; Gilbert, Hélène; Croiseau, Pascal; Rau, Andrea
Publié dans:
12th World Congress on Genetics Applied to Livestock Production, Numéro 3, 2023, Page(s) 1275-1277
Éditeur:
-
DOI:
10.3920/978-90-8686-940-4_303
Auteurs:
D. Crespo-Piazuelo , O. González-Rodríguez, M. Mongellaz, H. Acloque, M.-J. Mercat, M. C. A. M. Bink, A. E. Huisman, Y. Ramayo-Caldas, J. P. Sánchez, and M. Ballester
Publié dans:
ISAG 2021 Book of abstracts, 2021, Page(s) 19; 113
Éditeur:
-
Auteurs:
Crespo-Piazuelo, D; González-Rodríguez, O; Mongellaz, M; Acloque, H; Mercat, M-J; Bink, M, C a M; Huisman, A, E; Ramayo-Caldas, Y; Sánchez, J, P; Ballester, M
Publié dans:
"World Congress on Genetics Applied to Livestock Production WCGALP 2022, Jul 2022, Rotterdam, Netherlands. ⟨10.3920/978-90-8686-940-4_524⟩", Numéro 10, 2023
Éditeur:
Wageningen Academic Publishers
DOI:
10.3920/978-90-8686-940-4
Auteurs:
Kurylo, Cyril; Guyomar, Cervin; Djebali, Sarah; Foissac, Sylvain
Publié dans:
ECCB 2022, Sep 2022, Sitges (Barcelona), France, Numéro 2, 2022
Éditeur:
-
Auteurs:
Amanda Jane Chamberlain, Hans H Cheng, Elisabetta Giuffra, Christa Kuehn, Christopher K Tuggle, Huaijun Zhou
Publié dans:
Frontiers in Genetics, 2021, ISSN 1664-8021
Éditeur:
Frontiers Media
DOI:
10.3389/fgene.2021.768626
Auteurs:
Mollandin, F.
Publié dans:
2022
Éditeur:
-
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