Somatic variant calls from TETRIS-seq duplex sequencing of longitudinal blood samples preceding acute myeloid leukaemia (UKCTOCS)

The final, filtered somatic variant calls from TETRIS-seq error-corrected duplex sequencing of longitudinal peripheral blood DNA from participants in the UK Collaborative Trial of Ovarian Cancer Screening (UKCTOCS), comprising individuals who went on to develop acute myeloid leukaemia and matched controls. 959 somatic variants are provided: 958 as per-sample VCF records across 382 files (842 single-nucleotide variants, 74 deletions, 40 insertions, 2 complex), plus one FLT3 internal tandem duplication supplied as the Pindel caller's own output in both single-strand and duplex consensus form. Coordinates are GRCh37/hg19. These are post-filtering calls. Single-nucleotide variants were called against a position-specific beta-binomial error model fitted across each sequencing lane and then post-processed; indels were called with VarDictJava and post-processed; the FLT3-ITD was called with Pindel and required in both consensus arms. Full filtering criteria are in the bundled README and in the paper's Methods and Supplementary Note. The files contain no ages and no clinical data. The same calls, with gene/transcript annotation and rounded participant ages, are given in Supplementary Table 6 of the paper. Raw sequencing reads and germline variant calls are available under controlled access via the European Genome-phenome Archive.