Dataset for: DNMT3A-R882 mutation intrinsically mimics maladaptive myelopoiesis from human haematopoietic stem cells
Description
This dataset supports the manuscript: DNMT3A-R882 mutation intrinsically mimics maladaptive myelopoiesis from human haematopoietic stem cells Giovanna Mantica1*, Aditi Vedi1,2*, Amos Tuval3§, Hector Huerga-Encabo4§, Daniel Hayler1§, Aleksandra Krzywon1,5, Emily Mitchell6, William Dunn1, Tamir Biezuner3, Kendig Sham1, Antonella Santoro1, Joe Lee6, Adi Danin3, Noa Chapal3, Yoni Moskovitz3,7, Andrea Arruda8, Edoardo Fiorillo9, Valeria Orru9, Michele Marongiu9, Eoin McKinney10, Francesco Cucca9,11, Matthew Collin12, Mark Minden8, Peter Campbell6, George S Vassiliou1, Margarete Fabre1, Jyoti Nangalia1,6, Dominique Bonnet4, Liran Shlush3,7,8, Elisa Laurenti1 * These authors contributed equally. § These authors contributed equally. Affiliations: 1 Department of Haematology and Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK. 2 Department of Paediatric Oncology, Cambridge University Hospitals NHS Foundation Trust 3 Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel. 4 Haematopoietic Stem Cell Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK 5 Department of Biostatistics and Bioinformatics, Maria Sklodowska-Curie National Research Institute of Oncology, Gliwice Branch, Gliwice, Poland 6 Wellcome Sanger Institute, Hinxton, CB10 1SA, UK 7 Division of Haematology Rambam Healthcare Campus, Haifa 31096, Israel. 8 Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada. 9 Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Lanusei, Italy. 10 Cambridge Institute of Therapeutic Immunology & Infectious Disease, University of Cambridge, Cambridge, UK 11 Dipartimento di Scienze Biomediche, Università degli Studi di Sassari, Sassari, Italy 12 Translational and Clinical Research Institute, Newcastle University, Newcastle-upon-Tyne, UK
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Steps to reproduce
Variant calling and phylogenetic reconstruction has been performed following the previously published protocol: Coorens, T.H.H., Spencer Chapman, M., Williams, N. et al. Reconstructing phylogenetic trees from genome-wide somatic mutations in clonal samples. Nat Protoc 19, 1866–1886 (2024). https://doi.org/10.1038/s41596-024-00962-8 ./vcf_files/ Contains all variant call files (vcf) output for each single-cell derived colony. ./CHIP1_tree/ a) annotated_mut_set_LEUK4_1_01_standard_rho01 This is an R data object and is uploaded into an R workspace using load() The genotype matrix used for MPBoot tree building is available in the matrix: filtered_muts$Genotype_shared_bin The dna strings used as input for MPboot are available in the vector: filtered_muts$dna_strings The annotated variant calls with tree node information are available in the matrix: filtered_muts$COMB_mats.tree.build$mat The genotype matrix of mutations calls per sample is available in: filtered_muts$COMB_mats.tree.build$Genotype_bin Information on whether the variant is an SNV or indel is available in: filtered_muts$COMB_mats.tree.build$mat$Mut_type A summary of total numbers of shared and private SNVs and indels is available in: filtered_muts$summary b) tree_LEUK4_1_01_standard_rho01.tree The raw tree with branch lengths equal to number of mutations assigned.