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Clonal fitness inferred from timeseries modeling of single cell cancer genomes

Progress in defining genomic fitness landscapes in cancer by copy number alterations (CNA) has been impeded by lack of single cell and timeseries sampling. We generated 42,000 single cell whole genomes (scWGS) from breast epithelium and primary triple negative breast cancer (TNBC) patient-derived xenografts (PDX) collected during multi-year time series. Using a Wright-Fisher population genetics model, we inferred reproducible CNA-defined clonal fitness dynamics induced by TP53 mutation and cisplatin chemotherapy, with accurate forecasting of experimentally enforced clonal competition dynamics. Drug treatment in three long-term serially passaged TNBC PDX resulted in cisplatin resistant clones that had shown low fitness in the untreated setting. By contrast high fitness clones from treatment naive controls were eradicated reflecting an inversion of the fitness landscape. Upon drug release selective pressure dynamics were reversed indicating a fitness cost of treatment resistance. Taken together, our findings reveal clonal fitness dynamics linked to CNA and therapeutic resistance in polyclonal tumours.

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Dataset ID Description Technology Samples
EGAD00001006460 Illumina HiSeq 2500 1
EGAD00001006461 Illumina HiSeq 2500 1
EGAD00001006462 Illumina HiSeq 2500 1
EGAD00001006463 Illumina HiSeq 2500 1
EGAD00001006464 Illumina HiSeq 2500 1
EGAD00001006465 Illumina HiSeq 2500 1
EGAD00001006466 Illumina HiSeq 2500 1
EGAD00001006467 Illumina HiSeq 2500 1
EGAD00001006468 Illumina HiSeq 2500 1
EGAD00001006469 Illumina HiSeq 2500 1
EGAD00001006470 Illumina HiSeq 2500 1
EGAD00001006471 Illumina HiSeq 2500 1
EGAD00001006472 Illumina HiSeq 2500 1
EGAD00001006473 Illumina HiSeq 2500 1
EGAD00001006474 Illumina HiSeq 2500 1
EGAD00001006475 Illumina HiSeq 2500 1
EGAD00001006476 Illumina HiSeq 2500 1
EGAD00001006477 Illumina HiSeq 2500 1
EGAD00001006478 Illumina HiSeq 2500 1
EGAD00001006479 Illumina HiSeq 2500 1
EGAD00001006480 Illumina HiSeq 2500 1
EGAD00001006481 Illumina HiSeq 2500 1
EGAD00001006482 Illumina HiSeq 2500 1
EGAD00001006483 NextSeq 550 1
EGAD00001006939 HiSeq X Five 5
EGAD00001006940 HiSeq X Five 5
EGAD00001006941 NextSeq 550 9
EGAD00001006942 HiSeq X Five 5
EGAD00001006943 HiSeq X Five 5
EGAD00001006944 HiSeq X Five 5
EGAD00001006945 HiSeq X Five 6
EGAD00001006946 HiSeq X Five 7
EGAD00001006947 HiSeq X Five 7
EGAD00001007086 HiSeq X Five 5
EGAD00001007087 HiSeq X Five 5
EGAD00001007088 HiSeq X Five 5
EGAD00001007089 HiSeq X Five 5
EGAD00001007090 HiSeq X Five 5
EGAD00001007091 HiSeq X Five 5
EGAD00001007092 HiSeq X Five 5
EGAD00001007093 HiSeq X Five 5
EGAD00001007094 HiSeq X Five 5
EGAD00001007095 HiSeq X Five 5
EGAD00001007096 HiSeq X Five 5
EGAD00001007097 HiSeq X Five 5
EGAD00001007098 HiSeq X Five 5
EGAD00001007099 HiSeq X Five 5
EGAD00001007100 HiSeq X Five 5
EGAD00001007101 Illumina HiSeq 2500 5
EGAD00001007102 Illumina HiSeq 2500 5
EGAD00001007103 HiSeq X Five 5
EGAD00001007104 NextSeq 550 7
EGAD00001007105 HiSeq X Five 5
EGAD00001007106 HiSeq X Five 5
EGAD00001007107 HiSeq X Five 5
EGAD00001007108 HiSeq X Five 7
EGAD00001007109 HiSeq X Five 5
EGAD00001007110 HiSeq X Five 5
EGAD00001007111 HiSeq X Five 7
EGAD00001007112 HiSeq X Five 5
EGAD00001007113 HiSeq X Five 5
EGAD00001007114 HiSeq X Five 5
EGAD00001007115 HiSeq X Five 5
EGAD00001007116 HiSeq X Five 5
EGAD00001007117 HiSeq X Five 5
EGAD00001007118 HiSeq X Five 4
EGAD00001007119 HiSeq X Five 4
EGAD00001007120 HiSeq X Five 4
EGAD00001007121 HiSeq X Five 5
EGAD00001007122 HiSeq X Five 5
EGAD00001007123 HiSeq X Five 5
EGAD00001007124 HiSeq X Five 5
EGAD00001007125 HiSeq X Five 5
EGAD00001007126 HiSeq X Five 5
EGAD00001007127 HiSeq X Five 5
EGAD00001007128 HiSeq X Five 5
EGAD00001007129 HiSeq X Five 5
EGAD00001007130 HiSeq X Five 5
EGAD00001007131 HiSeq X Five 5
EGAD00001007132 HiSeq X Five 5
EGAD00001007306 HiSeq X Five 5
EGAD00001007592 HiSeq X Five 7
EGAD00001007593 NextSeq 550 5
EGAD00001007594 HiSeq X Five 7
EGAD00001007595 HiSeq X Five 5
EGAD00001007596 HiSeq X Five 5
EGAD00001007597 HiSeq X Five 5
EGAD00001007598 HiSeq X Five 5
EGAD00001007599 HiSeq X Five 5
EGAD00001007600 HiSeq X Five 5
EGAD00001007601 HiSeq X Five 5
EGAD00001007602 HiSeq X Five 5
EGAD00001007603 HiSeq X Five 5
EGAD00001007604 HiSeq X Five 5
EGAD00001007605 HiSeq X Five 5
EGAD00001007606 HiSeq X Five 5
EGAD00001007607 HiSeq X Five 5
EGAD00001007608 HiSeq X Five 5
EGAD00001007609 HiSeq X Five 5
EGAD00001007610 HiSeq X Five 20
EGAD00001007611 HiSeq X Five 5
EGAD00001007612 NextSeq 550 5
EGAD00001007613 HiSeq X Five 5
EGAD00001007614 HiSeq X Five 5
EGAD00001007615 NextSeq 550 5
EGAD00001007616 HiSeq X Five 5
EGAD00001007617 HiSeq X Five 5
EGAD00001007618 HiSeq X Five 5
EGAD00001007619 HiSeq X Five 5
EGAD00001007620 HiSeq X Five 5
EGAD00001007621 HiSeq X Five 7
EGAD00001007622 HiSeq X Five 5
EGAD00001007623 HiSeq X Five 5
EGAD00001007624 HiSeq X Five 5
EGAD00001007625 HiSeq X Five 5
EGAD00001007626 HiSeq X Five 5
EGAD00001007627 HiSeq X Five 5
EGAD00001007628 HiSeq X Five 7
EGAD00001007629 HiSeq X Five 5
EGAD00001007630 HiSeq X Five 5
EGAD00001007631 HiSeq X Five 7
EGAD00001007632 HiSeq X Five 5
EGAD00001007633 HiSeq X Five 5
EGAD00001007634 HiSeq X Five 5
EGAD00001007635 HiSeq X Five 5
EGAD00001007636 HiSeq X Five 7
EGAD00001007637 HiSeq X Five 5
EGAD00001007640 HiSeq X Five 11
EGAD00001007641 HiSeq X Five 5
EGAD00001008218 HiSeq X Five 6
EGAD00001008219 Illumina HiSeq 2500 4
EGAD00001008220 HiSeq X Five 9
EGAD00001008221 HiSeq X Five 5
EGAD00001008222 Illumina HiSeq 2500 5
EGAD00001008223 Illumina HiSeq 2500 4
EGAD00001008224 Illumina HiSeq 2500 5
EGAD00001008225 HiSeq X Five 5
EGAD00001008226 Illumina HiSeq 2500 5
EGAD00001008227 Illumina HiSeq 2500 5
EGAD00001008228 HiSeq X Five 9
EGAD00001008229 NextSeq 550 5
EGAD00001008230 NextSeq 550 5
EGAD00001008231 HiSeq X Five 5
EGAD00001008232 HiSeq X Five 9
EGAD00001008233 HiSeq X Five 5
EGAD00001008234 HiSeq X Five 5
EGAD00001008235 HiSeq X Five 5
EGAD00001008236 HiSeq X Five 5
EGAD00001008237 HiSeq X Five 7
EGAD00001008238 HiSeq X Five 7
EGAD00001008239 HiSeq X Five 7
EGAD00001008240 HiSeq X Five 7
EGAD00001008241 HiSeq X Five 5
EGAD00001008242 HiSeq X Five 7
EGAD00001008243 HiSeq X Five 5
EGAD00001008244 HiSeq X Five 9
EGAD00001008245 HiSeq X Five 7
EGAD00001008246 HiSeq X Five 5
EGAD00001008247 HiSeq X Five 5
EGAD00001008248 HiSeq X Five 7
EGAD00001008249 HiSeq X Five 5
EGAD00001008250 HiSeq X Five 5
EGAD00001008251 HiSeq X Five 5
EGAD00001008252 HiSeq X Five 5
EGAD00001008253 HiSeq X Five 7
EGAD00001008254 HiSeq X Five 5
EGAD00001008255 HiSeq X Five 5
EGAD00001008256 HiSeq X Five 5
EGAD00001008257 HiSeq X Five 9
EGAD00001008258 HiSeq X Five 5
EGAD00001008259 HiSeq X Five 5
EGAD00001008260 HiSeq X Five 5
EGAD00001008261 HiSeq X Five 5
EGAD00001008262 HiSeq X Five 4
EGAD00001008263 HiSeq X Five 2
EGAD00001008264 HiSeq X Five 5
EGAD00001008265 HiSeq X Five 5
EGAD00001008266 HiSeq X Five 5
Publications Citations
Clonal fitness inferred from time-series modelling of single-cell cancer genomes.
Nature 595: 2021 585-590
55
Single-cell genomic variation induced by mutational processes in cancer.
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36
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