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.

Type: Other
Archiver: European Genome-Phenome Archive (EGA)

178 Datasets 5 Publications

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID	Description	Technology	Samples
EGAD00001006460	Transcriptome profiling by high-throughput sequencing for single cells for library SCRNA10X_SA_CHIP0006_001 1 samples; filetype=fastq	Illumina HiSeq 2500	1
EGAD00001006461	Transcriptome profiling by high-throughput sequencing for single cells for library SCRNA10X_SA_CHIP0080_001 1 samples; filetype=fastq	Illumina HiSeq 2500	1
EGAD00001006462	Transcriptome profiling by high-throughput sequencing for single cells for library SCRNA10X_SA_CHIP0080_002 1 samples; filetype=fastq	Illumina HiSeq 2500	1
EGAD00001006463	Transcriptome profiling by high-throughput sequencing for single cells for library SCRNA10X_SA_CHIP0141_004 1 samples; filetype=fastq	Illumina HiSeq 2500	1
EGAD00001006464	Transcriptome profiling by high-throughput sequencing for single cells for library SCRNA10X_SA_CHIP0142_001 1 samples; filetype=fastq	Illumina HiSeq 2500	1
EGAD00001006465	Transcriptome profiling by high-throughput sequencing for single cells for library SCRNA10X_SA_CHIP0142_003 1 samples; filetype=fastq	Illumina HiSeq 2500	1
EGAD00001006466	Transcriptome profiling by high-throughput sequencing for single cells for library SCRNA10X_SA_CHIP0146_002 1 samples; filetype=fastq	Illumina HiSeq 2500	1
EGAD00001006467	Transcriptome profiling by high-throughput sequencing for single cells for library SCRNA10X_SA_CHIP0149_001 1 samples; filetype=fastq	Illumina HiSeq 2500	1
EGAD00001006468	Transcriptome profiling by high-throughput sequencing for single cells for library SCRNA10X_SA_CHIP0149_002 1 samples; filetype=fastq	Illumina HiSeq 2500	1
EGAD00001006469	Transcriptome profiling by high-throughput sequencing for single cells for library SCRNA10X_SA_CHIP0150_001 1 samples; filetype=fastq	Illumina HiSeq 2500	1
EGAD00001006470	Transcriptome profiling by high-throughput sequencing for single cells for library SCRNA10X_SA_CHIP0150_002 1 samples; filetype=fastq	Illumina HiSeq 2500	1
EGAD00001006471	Transcriptome profiling by high-throughput sequencing for single cells for library SCRNA10X_SA_CHIP0152_001 1 samples; filetype=fastq	Illumina HiSeq 2500	1
EGAD00001006472	Transcriptome profiling by high-throughput sequencing for single cells for library SCRNA10X_SA_CHIP0152_002 1 samples; filetype=fastq	Illumina HiSeq 2500	1
EGAD00001006473	Transcriptome profiling by high-throughput sequencing for single cells for library SCRNA10X_SA_CHIP0163_001 1 samples; filetype=fastq	Illumina HiSeq 2500	1
EGAD00001006474	Transcriptome profiling by high-throughput sequencing for single cells for library SCRNA10X_SA_CHIP0163_002 1 samples; filetype=fastq	Illumina HiSeq 2500	1
EGAD00001006475	Transcriptome profiling by high-throughput sequencing for single cells for library SCRNA10X_SA_CHIP0172_001 1 samples; filetype=fastq	Illumina HiSeq 2500	1
EGAD00001006476	Transcriptome profiling by high-throughput sequencing for single cells for library SCRNA10X_SA_CHIP0172_002 1 samples; filetype=fastq	Illumina HiSeq 2500	1
EGAD00001006477	Transcriptome profiling by high-throughput sequencing for single cells for library TENX062 1 samples; filetype=fastq	Illumina HiSeq 2500	1
EGAD00001006478	Transcriptome profiling by high-throughput sequencing for single cells for library SCRNA10X_SA_CHIP0063_000 1 samples; filetype=fastq	Illumina HiSeq 2500	1
EGAD00001006479	Transcriptome profiling by high-throughput sequencing for single cells for library TENX064 1 samples; filetype=fastq	Illumina HiSeq 2500	1
EGAD00001006480	Transcriptome profiling by high-throughput sequencing for single cells for library TENX065 1 samples; filetype=fastq	Illumina HiSeq 2500	1
EGAD00001006481	Transcriptome profiling by high-throughput sequencing for single cells for library TENX066 1 samples; filetype=fastq	Illumina HiSeq 2500	1
EGAD00001006482	Transcriptome profiling by high-throughput sequencing for single cells for library TENX068 1 samples; filetype=fastq	Illumina HiSeq 2500	1
EGAD00001006483	Transcriptome profiling by high-throughput sequencing for single cells for library TENX069 1 samples; filetype=fastq	NextSeq 550	1
EGAD00001006939	Whole genome sequencing for single cells for library A95629A 1023 cells; filetype=bam	HiSeq X Five	5
EGAD00001006940	Whole genome sequencing for single cells for library A95654B 1740 cells; filetype=bam	HiSeq X Five	5
EGAD00001006941	Whole genome sequencing for single cells for library A95673A 1446 cells; filetype=bam	NextSeq 550	9
EGAD00001006942	Whole genome sequencing for single cells for library A95703B 1267 cells; filetype=bam	HiSeq X Five	5
EGAD00001006943	Whole genome sequencing for single cells for library A95728A 876 cells; filetype=bam	HiSeq X Five	5
EGAD00001006944	Whole genome sequencing for single cells for library A96192B 1304 cells; filetype=bam	HiSeq X Five	5
EGAD00001006945	Whole genome sequencing for single cells for library A96217B 1616 cells; filetype=bam	HiSeq X Five	6
EGAD00001006946	Whole genome sequencing for single cells for library A96219B 1743 cells; filetype=bam	HiSeq X Five	7
EGAD00001006947	Whole genome sequencing for single cells for library A98269B 1609 cells; filetype=bam	HiSeq X Five	7
EGAD00001007086	Whole genome sequencing for single cells for library A108757B 1644 cells; filetype=bam	HiSeq X Five	5
EGAD00001007087	Whole genome sequencing for single cells for library A98299B 991 cells; filetype=bam	HiSeq X Five	5
EGAD00001007088	Whole genome sequencing for single cells for library A108759B 1134 cells; filetype=bam	HiSeq X Five	5
EGAD00001007089	Whole genome sequencing for single cells for library A108768B 1126 cells; filetype=bam	HiSeq X Five	5
EGAD00001007090	Whole genome sequencing for single cells for library A108837A 1435 cells; filetype=bam	HiSeq X Five	5
EGAD00001007091	Whole genome sequencing for single cells for library A108846A 1670 cells; filetype=bam	HiSeq X Five	5
EGAD00001007092	Whole genome sequencing for single cells for library A108846B 1636 cells; filetype=bam	HiSeq X Five	5
EGAD00001007093	Whole genome sequencing for single cells for library A108879A 1567 cells; filetype=bam	HiSeq X Five	5
EGAD00001007094	Whole genome sequencing for single cells for library A110632A 1151 cells; filetype=bam	HiSeq X Five	5
EGAD00001007095	Whole genome sequencing for single cells for library A110632B 892 cells; filetype=bam	HiSeq X Five	5
EGAD00001007096	Whole genome sequencing for single cells for library A118833A 919 cells; filetype=bam	HiSeq X Five	5
EGAD00001007097	Whole genome sequencing for single cells for library A118833B 1147 cells; filetype=bam	HiSeq X Five	5
EGAD00001007098	Whole genome sequencing for single cells for library A118845B 1209 cells; filetype=bam	HiSeq X Five	5
EGAD00001007099	Whole genome sequencing for single cells for library A118869A 1165 cells; filetype=bam	HiSeq X Five	5
EGAD00001007100	Whole genome sequencing for single cells for library A118869B 1124 cells; filetype=bam	HiSeq X Five	5
EGAD00001007101	Whole genome sequencing for single cells for library A73044B 2085 cells; filetype=bam	Illumina HiSeq 2500	5
EGAD00001007102	Whole genome sequencing for single cells for library A73047D 2091 cells; filetype=bam	Illumina HiSeq 2500	5
EGAD00001007103	Whole genome sequencing for single cells for library A95626A 1040 cells; filetype=bam	HiSeq X Five	5
EGAD00001007104	Whole genome sequencing for single cells for library A95633B 2259 cells; filetype=bam	NextSeq 550	7
EGAD00001007105	Whole genome sequencing for single cells for library A95634B 1335 cells; filetype=bam	HiSeq X Five	5
EGAD00001007106	Whole genome sequencing for single cells for library A95646A 1071 cells; filetype=bam	HiSeq X Five	5
EGAD00001007107	Whole genome sequencing for single cells for library A95653B 1342 cells; filetype=bam	HiSeq X Five	5
EGAD00001007108	Whole genome sequencing for single cells for library A95663B 1364 cells; filetype=bam	HiSeq X Five	7
EGAD00001007109	Whole genome sequencing for single cells for library A95675A 668 cells; filetype=bam	HiSeq X Five	5
EGAD00001007110	Whole genome sequencing for single cells for library A95731B 1307 cells; filetype=bam	HiSeq X Five	5
EGAD00001007111	Whole genome sequencing for single cells for library A96115A 1635 cells; filetype=bam	HiSeq X Five	7
EGAD00001007112	Whole genome sequencing for single cells for library A96115B 1201 cells; filetype=bam	HiSeq X Five	5
EGAD00001007113	Whole genome sequencing for single cells for library A96118A 1193 cells; filetype=bam	HiSeq X Five	5
EGAD00001007114	Whole genome sequencing for single cells for library A96130B 1267 cells; filetype=bam	HiSeq X Five	5
EGAD00001007115	Whole genome sequencing for single cells for library A96178A 788 cells; filetype=bam	HiSeq X Five	5
EGAD00001007116	Whole genome sequencing for single cells for library A96178B 846 cells; filetype=bam	HiSeq X Five	5
EGAD00001007117	Whole genome sequencing for single cells for library A96181C 1216 cells; filetype=bam	HiSeq X Five	5
EGAD00001007118	Whole genome sequencing for single cells for library A96193B 2410 cells; filetype=bam	HiSeq X Five	4
EGAD00001007119	Whole genome sequencing for single cells for library A96225B 959 cells; filetype=bam	HiSeq X Five	4
EGAD00001007120	Whole genome sequencing for single cells for library A96225C 1034 cells; filetype=bam	HiSeq X Five	4
EGAD00001007121	Whole genome sequencing for single cells for library A96240A 1493 cells; filetype=bam	HiSeq X Five	5
EGAD00001007122	Whole genome sequencing for single cells for library A96240B 1683 cells; filetype=bam	HiSeq X Five	5
EGAD00001007123	Whole genome sequencing for single cells for library A98172A 898 cells; filetype=bam	HiSeq X Five	5
EGAD00001007124	Whole genome sequencing for single cells for library A98256A 1372 cells; filetype=bam	HiSeq X Five	5
EGAD00001007125	Whole genome sequencing for single cells for library A98256B 1437 cells; filetype=bam	HiSeq X Five	5
EGAD00001007126	Whole genome sequencing for single cells for library A98257B 1286 cells; filetype=bam	HiSeq X Five	5
EGAD00001007127	Whole genome sequencing for single cells for library A98258B 1357 cells; filetype=bam	HiSeq X Five	5
EGAD00001007128	Whole genome sequencing for single cells for library A98274B 1295 cells; filetype=bam	HiSeq X Five	5
EGAD00001007129	Whole genome sequencing for single cells for library A98282A 1198 cells; filetype=bam	HiSeq X Five	5
EGAD00001007130	Whole genome sequencing for single cells for library A98283A 1137 cells; filetype=bam	HiSeq X Five	5
EGAD00001007131	Whole genome sequencing for single cells for library A98285A 1422 cells; filetype=bam	HiSeq X Five	5
EGAD00001007132	Whole genome sequencing for single cells for library A98295B 1381 cells; filetype=bam	HiSeq X Five	5
EGAD00001007306	Whole genome sequencing for single cells for library A95646B 507 cells; filetype=bam	HiSeq X Five	5
EGAD00001007592	Whole genome sequencing for single cells for library A108732A 1139 cells; filetype=bam	HiSeq X Five	7
EGAD00001007593	Whole genome sequencing for single cells for library A108735A 714 cells; filetype=bam	NextSeq 550	5
EGAD00001007594	Whole genome sequencing for single cells for library A108833B 866 cells; filetype=bam	HiSeq X Five	7
EGAD00001007595	Whole genome sequencing for single cells for library A108842A 1477 cells; filetype=bam	HiSeq X Five	5
EGAD00001007596	Whole genome sequencing for single cells for library A108851B 1681 cells; filetype=bam	HiSeq X Five	5
EGAD00001007597	Whole genome sequencing for single cells for library A108863A 1301 cells; filetype=bam	HiSeq X Five	5
EGAD00001007598	Whole genome sequencing for single cells for library A108870A 1795 cells; filetype=bam	HiSeq X Five	5
EGAD00001007599	Whole genome sequencing for single cells for library A110618A 1184 cells; filetype=bam	HiSeq X Five	5
EGAD00001007600	Whole genome sequencing for single cells for library A110618B 1047 cells; filetype=bam	HiSeq X Five	5
EGAD00001007601	Whole genome sequencing for single cells for library A110621A 1137 cells; filetype=bam	HiSeq X Five	5
EGAD00001007602	Whole genome sequencing for single cells for library A110673A 1089 cells; filetype=bam	HiSeq X Five	5
EGAD00001007603	Whole genome sequencing for single cells for library A110673B 1153 cells; filetype=bam	HiSeq X Five	5
EGAD00001007604	Whole genome sequencing for single cells for library A118830A 912 cells; filetype=bam	HiSeq X Five	5
EGAD00001007605	Whole genome sequencing for single cells for library A118862A 1070 cells; filetype=bam	HiSeq X Five	5
EGAD00001007606	Whole genome sequencing for single cells for library A118862B 1152 cells; filetype=bam	HiSeq X Five	5
EGAD00001007607	Whole genome sequencing for single cells for library A95623A 1897 cells; filetype=bam	HiSeq X Five	5
EGAD00001007608	Whole genome sequencing for single cells for library A95623B 1363 cells; filetype=bam	HiSeq X Five	5
EGAD00001007609	Whole genome sequencing for single cells for library A95668B 1905 cells; filetype=bam	HiSeq X Five	5
EGAD00001007610	Whole genome sequencing for single cells for library A95697B 1233 cells; filetype=bam	HiSeq X Five	20
EGAD00001007611	Whole genome sequencing for single cells for library A95700A 1172 cells; filetype=bam	HiSeq X Five	5
EGAD00001007612	Whole genome sequencing for single cells for library A95703A 740 cells; filetype=bam	NextSeq 550	5
EGAD00001007613	Whole genome sequencing for single cells for library A95720A 1467 cells; filetype=bam	HiSeq X Five	5
EGAD00001007614	Whole genome sequencing for single cells for library A95730A 739 cells; filetype=bam	HiSeq X Five	5
EGAD00001007615	Whole genome sequencing for single cells for library A96114A 798 cells; filetype=bam	NextSeq 550	5
EGAD00001007616	Whole genome sequencing for single cells for library A96124B 1241 cells; filetype=bam	HiSeq X Five	5
EGAD00001007617	Whole genome sequencing for single cells for library A96155C 1316 cells; filetype=bam	HiSeq X Five	5
EGAD00001007618	Whole genome sequencing for single cells for library A96162A 1505 cells; filetype=bam	HiSeq X Five	5
EGAD00001007619	Whole genome sequencing for single cells for library A96183B 1191 cells; filetype=bam	HiSeq X Five	5
EGAD00001007620	Whole genome sequencing for single cells for library A96190A 1833 cells; filetype=bam	HiSeq X Five	5
EGAD00001007621	Whole genome sequencing for single cells for library A96226B 1274 cells; filetype=bam	HiSeq X Five	7
EGAD00001007622	Whole genome sequencing for single cells for library A96233A 637 cells; filetype=bam	HiSeq X Five	5
EGAD00001007623	Whole genome sequencing for single cells for library A96233B 1601 cells; filetype=bam	HiSeq X Five	5
EGAD00001007624	Whole genome sequencing for single cells for library A98168A 1294 cells; filetype=bam	HiSeq X Five	5
EGAD00001007625	Whole genome sequencing for single cells for library A98168B 1290 cells; filetype=bam	HiSeq X Five	5
EGAD00001007626	Whole genome sequencing for single cells for library A98234A 1240 cells; filetype=bam	HiSeq X Five	5
EGAD00001007627	Whole genome sequencing for single cells for library A98234B 1600 cells; filetype=bam	HiSeq X Five	5
EGAD00001007628	Whole genome sequencing for single cells for library A98244A 1271 cells; filetype=bam	HiSeq X Five	7
EGAD00001007629	Whole genome sequencing for single cells for library A98253A 1250 cells; filetype=bam	HiSeq X Five	5
EGAD00001007630	Whole genome sequencing for single cells for library A98253B 1388 cells; filetype=bam	HiSeq X Five	5
EGAD00001007631	Whole genome sequencing for single cells for library A98254A 1490 cells; filetype=bam	HiSeq X Five	7
EGAD00001007632	Whole genome sequencing for single cells for library A98255B 1394 cells; filetype=bam	HiSeq X Five	5
EGAD00001007633	Whole genome sequencing for single cells for library A98271A 1190 cells; filetype=bam	HiSeq X Five	5
EGAD00001007634	Whole genome sequencing for single cells for library A98289A 1066 cells; filetype=bam	HiSeq X Five	5
EGAD00001007635	Whole genome sequencing for single cells for library A98290B 869 cells; filetype=bam	HiSeq X Five	5
EGAD00001007636	Whole genome sequencing for single cells for library A98304A 1560 cells; filetype=bam	HiSeq X Five	7
EGAD00001007637	Whole genome sequencing for single cells for library A98305A 986 cells; filetype=bam	HiSeq X Five	5
EGAD00001007640	Whole genome sequencing for single cells for library A96120A 1143 cells; filetype=bam	HiSeq X Five	11
EGAD00001007641	Whole genome sequencing for single cells for library A98172B 941 cells; filetype=bam	HiSeq X Five	5
EGAD00001008218	Whole genome sequencing for single cells for library A96228B 1125 samples; filetype=bam	HiSeq X Five	6
EGAD00001008219	Whole genome sequencing for single cells for library A90679 1034 samples; filetype=bam	Illumina HiSeq 2500	4
EGAD00001008220	Whole genome sequencing for single cells for library A95618A 876 samples; filetype=bam	HiSeq X Five	9
EGAD00001008221	Whole genome sequencing for single cells for library A95628B 1335 samples; filetype=bam	HiSeq X Five	5
EGAD00001008222	Whole genome sequencing for single cells for library A95632D 644 samples; filetype=bam	Illumina HiSeq 2500	5
EGAD00001008223	Whole genome sequencing for single cells for library A95635B 593 samples; filetype=bam	Illumina HiSeq 2500	4
EGAD00001008224	Whole genome sequencing for single cells for library A95635D 367 samples; filetype=bam	Illumina HiSeq 2500	5
EGAD00001008225	Whole genome sequencing for single cells for library A95654A 901 samples; filetype=bam	HiSeq X Five	5
EGAD00001008226	Whole genome sequencing for single cells for library A95662A 637 samples; filetype=bam	Illumina HiSeq 2500	5
EGAD00001008227	Whole genome sequencing for single cells for library A95664B 630 samples; filetype=bam	Illumina HiSeq 2500	5
EGAD00001008228	Whole genome sequencing for single cells for library A95707A 1359 samples; filetype=bam	HiSeq X Five	9
EGAD00001008229	Whole genome sequencing for single cells for library A95724A 503 samples; filetype=bam	NextSeq 550	5
EGAD00001008230	Whole genome sequencing for single cells for library A95724B 581 samples; filetype=bam	NextSeq 550	5
EGAD00001008231	Whole genome sequencing for single cells for library A95732B 655 samples; filetype=bam	HiSeq X Five	5
EGAD00001008232	Whole genome sequencing for single cells for library A96145A 642 samples; filetype=bam	HiSeq X Five	9
EGAD00001008233	Whole genome sequencing for single cells for library A96146A 1195 samples; filetype=bam	HiSeq X Five	5
EGAD00001008234	Whole genome sequencing for single cells for library A96149A 751 samples; filetype=bam	HiSeq X Five	5
EGAD00001008235	Whole genome sequencing for single cells for library A96149B 1792 samples; filetype=bam	HiSeq X Five	5
EGAD00001008236	Whole genome sequencing for single cells for library A96155B 1028 samples; filetype=bam	HiSeq X Five	5
EGAD00001008237	Whole genome sequencing for single cells for library A96157C 938 samples; filetype=bam	HiSeq X Five	7
EGAD00001008238	Whole genome sequencing for single cells for library A96162B 1316 samples; filetype=bam	HiSeq X Five	7
EGAD00001008239	Whole genome sequencing for single cells for library A96165A 779 samples; filetype=bam	HiSeq X Five	7
EGAD00001008240	Whole genome sequencing for single cells for library A96172A 1476 samples; filetype=bam	HiSeq X Five	7
EGAD00001008241	Whole genome sequencing for single cells for library A96172B 1694 samples; filetype=bam	HiSeq X Five	5
EGAD00001008242	Whole genome sequencing for single cells for library A96174B 1447 samples; filetype=bam	HiSeq X Five	7
EGAD00001008243	Whole genome sequencing for single cells for library A96175C 1473 samples; filetype=bam	HiSeq X Five	5
EGAD00001008244	Whole genome sequencing for single cells for library A96177B 683 samples; filetype=bam	HiSeq X Five	9
EGAD00001008245	Whole genome sequencing for single cells for library A96179B 1396 samples; filetype=bam	HiSeq X Five	7
EGAD00001008246	Whole genome sequencing for single cells for library A96180B 1189 samples; filetype=bam	HiSeq X Five	5
EGAD00001008247	Whole genome sequencing for single cells for library A96183C 1036 samples; filetype=bam	HiSeq X Five	5
EGAD00001008248	Whole genome sequencing for single cells for library A96184A 1733 samples; filetype=bam	HiSeq X Five	7
EGAD00001008249	Whole genome sequencing for single cells for library A96186A 850 samples; filetype=bam	HiSeq X Five	5
EGAD00001008250	Whole genome sequencing for single cells for library A96186C 525 samples; filetype=bam	HiSeq X Five	5
EGAD00001008251	Whole genome sequencing for single cells for library A96199B 1170 samples; filetype=bam	HiSeq X Five	5
EGAD00001008252	Whole genome sequencing for single cells for library A96201A 536 samples; filetype=bam	HiSeq X Five	5
EGAD00001008253	Whole genome sequencing for single cells for library A96205A 1907 samples; filetype=bam	HiSeq X Five	7
EGAD00001008254	Whole genome sequencing for single cells for library A96210C 1191 samples; filetype=bam	HiSeq X Five	5
EGAD00001008255	Whole genome sequencing for single cells for library A96211C 1397 samples; filetype=bam	HiSeq X Five	5
EGAD00001008256	Whole genome sequencing for single cells for library A96215A 1312 samples; filetype=bam	HiSeq X Five	5
EGAD00001008257	Whole genome sequencing for single cells for library A96216A 1001 samples; filetype=bam	HiSeq X Five	9
EGAD00001008258	Whole genome sequencing for single cells for library A96220B 1267 samples; filetype=bam	HiSeq X Five	5
EGAD00001008259	Whole genome sequencing for single cells for library A96244A 1374 samples; filetype=bam	HiSeq X Five	5
EGAD00001008260	Whole genome sequencing for single cells for library A98176A 1003 samples; filetype=bam	HiSeq X Five	5
EGAD00001008261	Whole genome sequencing for single cells for library A98176B 1389 samples; filetype=bam	HiSeq X Five	5
EGAD00001008262	Whole genome sequencing for single cells for library A98284A 1265 samples; filetype=bam	HiSeq X Five	4
EGAD00001008263	Whole genome sequencing for single cells for library A98284B 1582 samples; filetype=bam	HiSeq X Five	2
EGAD00001008264	Whole genome sequencing for single cells for library A98289B 1032 samples; filetype=bam	HiSeq X Five	5
EGAD00001008265	Whole genome sequencing for single cells for library A98293B 703 samples; filetype=bam	HiSeq X Five	5
EGAD00001008266	Whole genome sequencing for single cells for library A98294A 994 samples; filetype=bam	HiSeq X Five	5

Publications	Citations
Clonal fitness inferred from time-series modelling of single-cell cancer genomes. Salehi S, Kabeer F, Ceglia N, Andronescu M, Williams MJ, Campbell KR, Masud T, Wang B, Biele J, Brimhall J, Gee D, Lee H, Ting J, Zhang AW, Tran H, O'Flanagan C, Dorri F, Rusk N, de Algara TR, Lee SR, Cheng BYC, Eirew P, Kono T, Pham J, Grewal D, Lai D, Moore R, Mungall AJ, Marra MA, IMAXT Consortium, McPherson A, Bouchard-Côté A, Aparicio S, Shah SP. Nature 595: 2021 585-590	58
Single-cell genomic variation induced by mutational processes in cancer. Funnell T, O'Flanagan CH, Williams MJ, McPherson A, McKinney S, Kabeer F, Lee H, Salehi S, Vázquez-García I, Shi H, Leventhal E, Masud T, Eirew P, Yap D, Zhang AW, Lim JLP, Wang B, Brimhall J, Biele J, Ting J, Au V, Van Vliet M, Liu YF, Beatty S, Lai D, Pham J, Grewal D, Abrams D, Havasov E, Leung S, Bojilova V, Moore RA, Rusk N, Uhlitz F, Ceglia N, Weiner AC, Zaikova E, Douglas JM, Zamarin D, Weigelt B, Kim SH, Da Cruz Paula A, Reis-Filho JS, Martin SD, Li Y, Xu H, de Algara TR, Lee SR, Llanos VC, Huntsman DG, McAlpine JN, IMAXT Consortium, Shah SP, Aparicio S. Nature 612: 2022 106-115	41
Identification of transcriptional programs using dense vector representations defined by mutual information with GeneVector. Ceglia N, Sethna Z, Freeman SS, Uhlitz F, Bojilova V, Rusk N, Burman B, Chow A, Salehi S, Kabeer F, Aparicio S, Greenbaum BD, Shah SP, McPherson A. Nat Commun 14: 2023 4400	4
Single-cell mtDNA dynamics in tumors is driven by coregulation of nuclear and mitochondrial genomes. Kim M, Gorelick AN, Vàzquez-García I, Williams MJ, Salehi S, Shi H, Weiner AC, Ceglia N, Funnell T, Park T, Boscenco S, O'Flanagan CH, Jiang H, Grewal D, Tang C, Rusk N, Gammage PA, McPherson A, Aparicio S, Shah SP, Reznik E. Nat Genet 56: 2024 889-899	1
Inferring replication timing and proliferation dynamics from single-cell DNA sequencing data. Weiner AC, Williams MJ, Shi H, Vázquez-García I, Salehi S, Rusk N, Aparicio S, Shah SP, McPherson A. Nat Commun 15: 2024 8512	2