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How chemotherapy affects carcinoma genomes is largely unknown. Here we report whole-exome and deep sequencing of 30 paired oesophageal adenocarcinomas sampled before and after neo-adjuvant chemotherapy. Most, but not all, good responders pass through genetic bottlenecks, a feature associated with higher mutation burden pre-treatment. Some poor responders pass through bottlenecks, but re-grow by the time of surgical resection, suggesting a missed therapeutic opportunity. Cancers often show major changes in driver mutation presence or frequency after treatment, owing to outgrowth persistence or loss of sub-clones, copy number changes, polyclonality and/or spatial genetic heterogeneity. Post-therapy mutation spectrum shifts are also common, particularly C>A and TT>CT changes in good responders or bottleneckers. Post-treatment samples may also acquire mutations in known cancer driver genes (for example, SF3B1, TAF1 and CCND2) that are absent from the paired pre-treatment sample. Neo-adjuvant chemotherapy can rapidly and profoundly affect the oesophageal adenocarcinoma genome. Monitoring molecular changes during treatment may be clinically useful.

Original publication




Journal article


Nature communications

Publication Date





11111 - 11111


Genomic Medicine Theme, Oxford NIHR Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.


Humans, Adenocarcinoma, Esophageal Neoplasms, Neoplasm Recurrence, Local, Ribonucleoprotein, U2 Small Nuclear, TATA-Binding Protein Associated Factors, Transcription Factor TFIID, Neoplasm Proteins, Phosphoproteins, DNA, Neoplasm, Antineoplastic Agents, Neoadjuvant Therapy, Sequence Analysis, DNA, Gene Expression Regulation, Neoplastic, Genetic Heterogeneity, Mutation, Adult, Aged, Middle Aged, Female, Male, Histone Acetyltransferases, Cyclin D2, DNA Copy Number Variations, Exome, Clonal Evolution, RNA Splicing Factors