Data

Contains the data used in this work.
Demographic and clinical:
- FBC_biochem.txt - full blood counts and blood chemistry
- RDW.txt - red blood cell distribution width - smoke.txt - smoking behaviour of a few individuals
Longitudinal sequencing data:- ALLvariants_exclSynonymous_Xadj.txt - longitudinal sequencing data for all 56 CH genes - Recurrent_sites_finalPhase.txt - data for the 6th timepoint (available for only a few individuals)
Cross-sectional sequencing data and dN/dS:- dnds_aml_mds.csv - dNdS in AML and MDS for specific sites
- dnds_global.txt - global dNdS for this cohort - dnds_genes.txt - gene-wise analysis of dNdS in this cohort
- dnds_domains.txt - domain-wise analysis of dNdS in this cohort- dnds_site.txt - site-wise analysis of dNdS in this cohort

Phylogenetic data:- tree_id2259, tree_id3877, tree_id500 - phylogenetic trees for three individuals- details_id2259_CNcorrected, details_id3877, details_id500 - R objects containing information on the phylogenetic trees- Trees_emily.zip - files from Mitchell et al. (2021); must be uncompressed into "Trees_emily"
Metadata:- excluded_individuals - individuals excluded from this analysis
- excluded_individuals_lymphocyte - individuals excluded from this analysis due to abnormal lymphocyte counts- included_genes - genes included in this analysis
- variants_bedfile_withDomainAnnotation.xlsx - domain information
Incidence, AML risk and dN/dS from other studies:- aml_incidence.csv - incidence of acute myeloid leukaemia retrieved from CRUK- aml-risk-coef.csv - coefficients for AML risk from Abelson et al. (2018)- leukaemia_incidence.csv - leukaemia incidence retrieved from CRUK
Technical replicates:- Replicates_all.txt - technical replicate data for a few individuals
- TruQ.txt - sequencing technical replicates