Deep whole genome ctDNA chronology of treatment-resistant prostate cancer
Circulating tumor DNA (ctDNA) in blood plasma is an emerging tool for clinical cancer genotyping and longitudinal disease monitoring. We performed deep whole-genome sequencing of serial plasma and synchronous metastases in patients with aggressive prostate cancer. We comprehensively assess all classes of genomic alterations and demonstrate that ctDNA harbors multiple dominant populations whose evolutionary histories frequently indicate whole-genome doubling and shifts in mutational processes. Although tissue and ctDNA showed concordant clonally-expanded cancer driver alterations, each individual metastasis contributed only a minor share of total ctDNA. By comparing serial ctDNA before and after clinical progression on potent androgen receptor (AR) pathway inhibitors, we reveal population restructuring converging solely on AR augmentation as the dominant genomic driver of acquired treatment-resistance. Finally we leverage nucleosome footprints in ctDNA to infer mRNA abundance in synchronously biopsied metastases, including treatment-induced changes in AR pathway transcriptional activity.
- 117 samples
- DAC: EGAC00001002479
- Technology: unspecified
Data Access Policy for the DNA sequencing data generated in the study "Somatic chronology of treatment-resistant prostate cancer via deep whole-genome ctDNA sequencing"
The following data access agreement (DAA) must be filled out by the requester, to be granted access to the data: https://docs.google.com/forms/d/e/1FAIpQLScy4KzxU8JA_3gU3hmHgZYE7mVgvBKYmpZkwBB0vASA9zqAQQ/viewform?usp=sf_link
Studies are experimental investigations of a particular phenomenon, e.g., case-control studies on a particular trait or cancer research projects reporting matching cancer normal genomes from patients.
| Study ID | Study Title | Study Type |
|---|---|---|
| EGAS00001005783 | Cancer Genomics |
This table displays only public information pertaining to the files in the dataset. If you wish to access this dataset, please submit a request. If you already have access to these data files, please consult the download documentation.
| ID | File Type | Size | Located in | |
|---|---|---|---|---|
| EGAF00005761909 | fq.gz | 227.4 GB | ||
| EGAF00005761910 | fq.gz | 240.1 GB | ||
| EGAF00005761911 | fq.gz | 242.0 GB | ||
| EGAF00005761912 | fq.gz | 269.6 GB | ||
| EGAF00005761913 | fq.gz | 29.7 GB | ||
| EGAF00005761914 | fq.gz | 31.0 GB | ||
| EGAF00005761915 | fq.gz | 222.2 GB | ||
| EGAF00005761916 | fq.gz | 245.0 GB | ||
| EGAF00005761917 | fq.gz | 212.6 GB | ||
| EGAF00005761918 | fq.gz | 231.4 GB | ||
| EGAF00005761919 | fq.gz | 213.9 GB | ||
| EGAF00005761920 | fq.gz | 234.6 GB | ||
| EGAF00005761921 | fq.gz | 183.3 GB | ||
| EGAF00005761922 | fq.gz | 203.1 GB | ||
| EGAF00005761923 | fq.gz | 192.9 GB | ||
| EGAF00005761924 | fq.gz | 211.1 GB | ||
| EGAF00005761925 | fq.gz | 33.0 GB | ||
| EGAF00005761926 | fq.gz | 34.9 GB | ||
| EGAF00005761927 | fq.gz | 169.5 GB | ||
| EGAF00005761928 | fq.gz | 186.3 GB | ||
| EGAF00005761929 | fq.gz | 34.7 GB | ||
| EGAF00005761930 | fq.gz | 37.7 GB | ||
| EGAF00005761931 | fq.gz | 228.7 GB | ||
| EGAF00005761932 | fq.gz | 232.3 GB | ||
| EGAF00005761933 | fq.gz | 32.7 GB | ||
| EGAF00005761934 | fq.gz | 34.5 GB | ||
| EGAF00005761935 | fq.gz | 204.8 GB | ||
| EGAF00005761936 | fq.gz | 205.1 GB | ||
| EGAF00005761937 | fq.gz | 212.7 GB | ||
| EGAF00005761938 | fq.gz | 220.4 GB | ||
| EGAF00005761939 | fq.gz | 34.8 GB | ||
| EGAF00005761940 | fq.gz | 36.7 GB | ||
| EGAF00005761941 | fq.gz | 161.6 GB | ||
| EGAF00005761942 | fq.gz | 159.5 GB | ||
| EGAF00005761943 | fq.gz | 34.8 GB | ||
| EGAF00005761944 | fq.gz | 34.0 GB | ||
| EGAF00006127311 | fq.gz | 45.3 GB | ||
| EGAF00006127312 | fq.gz | 46.2 GB | ||
| EGAF00006127313 | fq.gz | 206.0 GB | ||
| EGAF00006127314 | fq.gz | 221.3 GB | ||
| EGAF00006127315 | fq.gz | 213.9 GB | ||
| EGAF00006127316 | fq.gz | 232.7 GB | ||
| EGAF00006127317 | fq.gz | 56.8 GB | ||
| EGAF00006127318 | fq.gz | 59.1 GB | ||
| EGAF00006127319 | fq.gz | 198.3 GB | ||
| EGAF00006127320 | fq.gz | 207.2 GB | ||
| EGAF00006127321 | fq.gz | 203.2 GB | ||
| EGAF00006127322 | fq.gz | 229.5 GB | ||
| EGAF00006127323 | fq.gz | 31.6 GB | ||
| EGAF00006127324 | fq.gz | 31.9 GB | ||
| EGAF00006127325 | fq.gz | 214.6 GB | ||
| EGAF00006127326 | fq.gz | 228.0 GB | ||
| EGAF00006127327 | fq.gz | 57.7 GB | ||
| EGAF00006127328 | fq.gz | 60.2 GB | ||
| EGAF00006127329 | fq.gz | 203.8 GB | ||
| EGAF00006127330 | fq.gz | 215.3 GB | ||
| EGAF00006127331 | fq.gz | 200.6 GB | ||
| EGAF00006127332 | fq.gz | 213.1 GB | ||
| EGAF00006127333 | fq.gz | 211.1 GB | ||
| EGAF00006127334 | fq.gz | 214.5 GB | ||
| EGAF00006127335 | fq.gz | 246.3 GB | ||
| EGAF00006127336 | fq.gz | 268.7 GB | ||
| EGAF00006127337 | fq.gz | 208.0 GB | ||
| EGAF00006127338 | fq.gz | 226.1 GB | ||
| EGAF00006127339 | fq.gz | 239.1 GB | ||
| EGAF00006127340 | fq.gz | 267.9 GB | ||
| EGAF00006127341 | fq.gz | 201.7 GB | ||
| EGAF00006127342 | fq.gz | 223.3 GB | ||
| EGAF00006127343 | fq.gz | 32.2 GB | ||
| EGAF00006127344 | fq.gz | 33.1 GB | ||
| EGAF00006127345 | fq.gz | 33.9 GB | ||
| EGAF00006127346 | fq.gz | 36.2 GB | ||
| EGAF00006127347 | fq.gz | 34.8 GB | ||
| EGAF00006127348 | fq.gz | 37.2 GB | ||
| EGAF00006127349 | fq.gz | 204.3 GB | ||
| EGAF00006127350 | fq.gz | 217.3 GB | ||
| EGAF00006127351 | fq.gz | 40.4 GB | ||
| EGAF00006127352 | fq.gz | 40.1 GB | ||
| EGAF00006127353 | fq.gz | 65.4 GB | ||
| EGAF00006127354 | fq.gz | 64.8 GB | ||
| EGAF00006127355 | fq.gz | 61.4 GB | ||
| EGAF00006127356 | fq.gz | 65.4 GB | ||
| EGAF00006127357 | fq.gz | 203.2 GB | ||
| EGAF00006127358 | fq.gz | 212.8 GB | ||
| EGAF00006127359 | fq.gz | 47.5 GB | ||
| EGAF00006127360 | fq.gz | 48.2 GB | ||
| EGAF00006127361 | fq.gz | 193.9 GB | ||
| EGAF00006127362 | fq.gz | 197.5 GB | ||
| EGAF00006127363 | fq.gz | 233.2 GB | ||
| EGAF00006127364 | fq.gz | 254.4 GB | ||
| EGAF00006127365 | fq.gz | 245.8 GB | ||
| EGAF00006127366 | fq.gz | 271.8 GB | ||
| EGAF00006127367 | fq.gz | 189.4 GB | ||
| EGAF00006127368 | fq.gz | 190.6 GB | ||
| EGAF00006127369 | fq.gz | 49.6 GB | ||
| EGAF00006127370 | fq.gz | 54.5 GB | ||
| EGAF00006127371 | fq.gz | 34.6 GB | ||
| EGAF00006127372 | fq.gz | 35.7 GB | ||
| EGAF00006127373 | fq.gz | 209.9 GB | ||
| EGAF00006127374 | fq.gz | 226.9 GB | ||
| EGAF00006144270 | fq.gz | 189.1 GB | ||
| EGAF00006144271 | fq.gz | 203.6 GB | ||
| EGAF00006144272 | fq.gz | 199.2 GB | ||
| EGAF00006144273 | fq.gz | 213.2 GB | ||
| EGAF00006144274 | fq.gz | 189.0 GB | ||
| EGAF00006144275 | fq.gz | 196.5 GB | ||
| EGAF00006144276 | fq.gz | 185.7 GB | ||
| EGAF00006144277 | fq.gz | 203.6 GB | ||
| EGAF00006144278 | fq.gz | 208.2 GB | ||
| EGAF00006144279 | fq.gz | 221.9 GB | ||
| EGAF00006144280 | fq.gz | 34.8 GB | ||
| EGAF00006144281 | fq.gz | 37.1 GB | ||
| EGAF00006144282 | fq.gz | 204.0 GB | ||
| EGAF00006144283 | fq.gz | 226.5 GB | ||
| EGAF00006144284 | fq.gz | 207.0 GB | ||
| EGAF00006144285 | fq.gz | 221.4 GB | ||
| EGAF00006144286 | fq.gz | 222.0 GB | ||
| EGAF00006144287 | fq.gz | 238.3 GB | ||
| EGAF00006144288 | fq.gz | 33.5 GB | ||
| EGAF00006144289 | fq.gz | 35.2 GB | ||
| EGAF00006144290 | fq.gz | 216.0 GB | ||
| EGAF00006144291 | fq.gz | 233.6 GB | ||
| EGAF00006144292 | fq.gz | 31.3 GB | ||
| EGAF00006144293 | fq.gz | 35.3 GB | ||
| EGAF00006144294 | fq.gz | 198.9 GB | ||
| EGAF00006144295 | fq.gz | 216.2 GB | ||
| EGAF00006144296 | fq.gz | 64.3 GB | ||
| EGAF00006144297 | fq.gz | 72.0 GB | ||
| EGAF00006144298 | fq.gz | 152.0 GB | ||
| EGAF00006144299 | fq.gz | 168.1 GB | ||
| EGAF00006144300 | fq.gz | 169.6 GB | ||
| EGAF00006144301 | fq.gz | 191.8 GB | ||
| EGAF00006144302 | fq.gz | 203.8 GB | ||
| EGAF00006144303 | fq.gz | 220.2 GB | ||
| EGAF00006144304 | fq.gz | 34.2 GB | ||
| EGAF00006144305 | fq.gz | 36.1 GB | ||
| EGAF00006144306 | fq.gz | 61.6 GB | ||
| EGAF00006144307 | fq.gz | 71.5 GB | ||
| EGAF00006144308 | fq.gz | 223.7 GB | ||
| EGAF00006144309 | fq.gz | 244.1 GB | ||
| EGAF00006144310 | fq.gz | 32.6 GB | ||
| EGAF00006144311 | fq.gz | 32.3 GB | ||
| EGAF00006144312 | fq.gz | 210.0 GB | ||
| EGAF00006144313 | fq.gz | 224.6 GB | ||
| EGAF00006144314 | fq.gz | 32.5 GB | ||
| EGAF00006144315 | fq.gz | 34.5 GB | ||
| EGAF00006144316 | fq.gz | 162.8 GB | ||
| EGAF00006144317 | fq.gz | 179.2 GB | ||
| EGAF00006144318 | fq.gz | 155.1 GB | ||
| EGAF00006144319 | fq.gz | 169.5 GB | ||
| EGAF00006144320 | fq.gz | 31.5 GB | ||
| EGAF00006144321 | fq.gz | 35.2 GB | ||
| EGAF00006144322 | fq.gz | 178.6 GB | ||
| EGAF00006144323 | fq.gz | 187.2 GB | ||
| EGAF00006144324 | fq.gz | 34.1 GB | ||
| EGAF00006144325 | fq.gz | 36.0 GB | ||
| EGAF00006144326 | fq.gz | 33.4 GB | ||
| EGAF00006144327 | fq.gz | 36.1 GB | ||
| EGAF00006144328 | fq.gz | 34.7 GB | ||
| EGAF00006144329 | fq.gz | 34.5 GB | ||
| EGAF00006144330 | fq.gz | 170.4 GB | ||
| EGAF00006144331 | fq.gz | 186.8 GB | ||
| EGAF00006144332 | fq.gz | 31.5 GB | ||
| EGAF00006144333 | fq.gz | 34.5 GB | ||
| EGAF00006144334 | fq.gz | 33.7 GB | ||
| EGAF00006144335 | fq.gz | 36.6 GB | ||
| EGAF00006144336 | fq.gz | 33.0 GB | ||
| EGAF00006144337 | fq.gz | 35.2 GB | ||
| EGAF00006144342 | fq.gz | 63.9 GB | ||
| EGAF00006144343 | fq.gz | 69.5 GB | ||
| EGAF00006201206 | fq.gz | 117.5 GB | ||
| EGAF00006201207 | fq.gz | 134.8 GB | ||
| EGAF00006201208 | fq.gz | 65.6 GB | ||
| EGAF00006201209 | fq.gz | 87.1 GB | ||
| EGAF00006201210 | fq.gz | 70.3 GB | ||
| EGAF00006201211 | fq.gz | 99.3 GB | ||
| EGAF00006201212 | fq.gz | 66.7 GB | ||
| EGAF00006201213 | fq.gz | 93.3 GB | ||
| EGAF00006201214 | fq.gz | 62.6 GB | ||
| EGAF00006201215 | fq.gz | 80.6 GB | ||
| EGAF00006201216 | fq.gz | 74.4 GB | ||
| EGAF00006201217 | fq.gz | 98.8 GB | ||
| EGAF00006201218 | fq.gz | 200.4 GB | ||
| EGAF00006201219 | fq.gz | 212.3 GB | ||
| EGAF00006201220 | fq.gz | 61.6 GB | ||
| EGAF00006201221 | fq.gz | 85.3 GB | ||
| EGAF00006201222 | fq.gz | 207.3 GB | ||
| EGAF00006201223 | fq.gz | 207.2 GB | ||
| EGAF00006201224 | fq.gz | 67.5 GB | ||
| EGAF00006201225 | fq.gz | 94.3 GB | ||
| EGAF00006201226 | fq.gz | 220.9 GB | ||
| EGAF00006201227 | fq.gz | 230.2 GB | ||
| EGAF00006201228 | fq.gz | 68.2 GB | ||
| EGAF00006201229 | fq.gz | 89.2 GB | ||
| EGAF00006201230 | fq.gz | 176.9 GB | ||
| EGAF00006201231 | fq.gz | 172.0 GB | ||
| EGAF00006201232 | fq.gz | 67.8 GB | ||
| EGAF00006201233 | fq.gz | 93.7 GB | ||
| EGAF00006201234 | fq.gz | 171.4 GB | ||
| EGAF00006201235 | fq.gz | 189.1 GB | ||
| EGAF00006201236 | fq.gz | 65.7 GB | ||
| EGAF00006201237 | fq.gz | 86.5 GB | ||
| EGAF00006201238 | fq.gz | 229.6 GB | ||
| EGAF00006201239 | fq.gz | 238.0 GB | ||
| EGAF00006201240 | fq.gz | 70.2 GB | ||
| EGAF00006201241 | fq.gz | 94.6 GB | ||
| EGAF00006201242 | fq.gz | 68.6 GB | ||
| EGAF00006201243 | fq.gz | 95.6 GB | ||
| EGAF00006201244 | fq.gz | 66.5 GB | ||
| EGAF00006201245 | fq.gz | 87.3 GB | ||
| EGAF00006201246 | fq.gz | 66.1 GB | ||
| EGAF00006201247 | fq.gz | 87.4 GB | ||
| EGAF00006204849 | fq.gz | 31.4 GB | ||
| EGAF00006204850 | fq.gz | 32.5 GB | ||
| EGAF00006204851 | fq.gz | 30.6 GB | ||
| EGAF00006204852 | fq.gz | 32.1 GB | ||
| EGAF00006204853 | fq.gz | 33.3 GB | ||
| EGAF00006204854 | fq.gz | 37.8 GB | ||
| EGAF00006204855 | fq.gz | 165.4 GB | ||
| EGAF00006204856 | fq.gz | 171.4 GB | ||
| EGAF00006204857 | fq.gz | 162.5 GB | ||
| EGAF00006204858 | fq.gz | 180.0 GB | ||
| EGAF00006204859 | fq.gz | 28.7 GB | ||
| EGAF00006204860 | fq.gz | 33.8 GB | ||
| EGAF00006204861 | fq.gz | 196.7 GB | ||
| EGAF00006204862 | fq.gz | 217.9 GB | ||
| EGAF00006204863 | fq.gz | 30.9 GB | ||
| EGAF00006204864 | fq.gz | 35.3 GB | ||
| EGAF00006204865 | fq.gz | 217.5 GB | ||
| EGAF00006204866 | fq.gz | 235.8 GB | ||
| EGAF00006204867 | fq.gz | 33.3 GB | ||
| EGAF00006204868 | fq.gz | 38.3 GB | ||
| EGAF00006204869 | fq.gz | 212.4 GB | ||
| EGAF00006204870 | fq.gz | 237.2 GB | ||
| 234 Files (31.3 TB) | ||||