Diagnostics, Software & Data
Diagnostics
The Unit of Animal Genomics (UAG) offers diagnostic tests for:
- Genetic defects in Belgian Blue Cattle
- Myostatin mutations in cattle
- Cholesterol deficiency in Holstein
- Congenital neurodegeneration (axonopathy) in Blonde d'Aquitaine
Software
- The RZooRoH package (Bertrand et al., Methods in Ecology and Evolution 2019) is available at:
- CHROMIBD (Druet and Farnir, Genetics 2011), GLASCOW (Zhang et al., Bioinformatics 2012), LINKPHASE3 (Druet and Georges, Bioinformatics 2015) and ZooROH (Druet and Gautier, Molecular Ecology 2017) are available at:
- Fine-mapping inflammatory bowel disease loci to single-variant resolution. Huang H, Fang M, Jostins L, Umićević Mirkov M, Boucher G, Anderson CA, Andersen V, Cleynen I, Cortes A, Crins F, D'Amato M, Deffontaine V, Dmitrieva J, Docampo E, Elansary M, Farh KK, Franke A, Gori AS, Goyette P, Halfvarson J, Haritunians T, Knight J, Lawrance IC, Lees CW, Louis E, Mariman R, Meuwissen T, Mni M, Momozawa Y, Parkes M, Spain SL, Théâtre E, Trynka G, Satsangi J, van Sommeren S, Vermeire S, Xavier RJ; International Inflammatory Bowel Disease Genetics Consortium; Weersma RK, Duerr RH, Mathew CG, Rioux JD, McGovern DPB, Cho JH, Georges M, Daly MJ, Barrett JC. Nature 547: 173-178 (2017).
- Software availability: The algorithm is implemented in the BayesFM program which can be downloaded from https://sourceforge.net/projects/bayesfm-mcmc-v1-0/
Data
- An organism-wide ATAC-Seq peak catalogue for the bovine and its use to identify regulatory variants. Yuan C, Tang L, Lopdell T, Petrov VA, Oget-Ebrard C, Costa Monteiro Moreira G, Gualdron Duarte JL, Sartelet A, Cheng Z, Salavati M, Wathes CD, Crows MA, GplusE, Coppieters W, Littlejohn M, Charlier C, Druet T, Georges M, Takeda H. Submitted.
- Custom track UCSC genome browser
- Data: EMBL-EBI ArrayExpress (https://www.ebi.ac.uk/biostudies/arrayexpress), accession numbers: E-MTAB-11825 and E-MTAB-11826.
- Analyses pipelines: https://github.com/can11sichuan/Bov-ATAC.
- The rate of de novo structural variation is increased in in vitro produced offspring and preferentially affects the paternal genome. Y-L Lee, AC Bouwman, C Harland, M Bosse, GC Monteiro Moreira, RF Veerkamp, E Mullaart, N Cambisano, MAM Groenen, L Karim, W Coppieters, M Georges, C Charlier. Submitted.
- Data: European Nucleotide Archive, accession number PRJEB53518/ERA15565221
- Comparing the transcriptome of developing native and iPSC-derived mouse retinae by single cell RNA sequencing. Georges, A.* , Lavergne, A., Mandai, M., Lepiemme, F., Karim, L., Demeulenaere, L., Aguilar Ortmans, D., Schyns, M., Nguyen, L., Rakic, J.-M., Takahashi, M., Georges, M.* , & Takeda, H.*. Scientific Reports, 13: 1223 (2023) [doi:10.1038/s41598-023-28429-y]
- Data: scRNA-Seq have been deposited (Array Express) under accession number E-MTAB-9395 (https://www.ebi.ac.uk/biostudies/arrayexpress/studies/E-MTAB-9395).
- Analyses pipelines: Other data and analysis pipelines are available at https://doi.org/10.5281/zenodo.7486356.
updated on 4/3/23
