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Subclonal diversification of primary breast cancer

Cancers are ecosystems of genetically related clones, competing across space and time for limited resources. To understand the clonal structure of primary breast cancer, we applied genome and targeted sequencing to 295 samples from 49 patients’ tumors. The extent of subclonal diversification varied considerably among patients and encompassed many spatial patterns, including local growth, intraductal dissemination and clonal intermixture. Landmarks of disease progression, such as acquiring invasive or metastatic potential, arose within detectable subclones of antecedent lesions, suggesting that subclonal mutations could be relevant if actionable. No defined temporal order of mutation was evident, with the commonest genes, including PIK3CA, TP53, BRCA2, PTEN and MYC, mutated early in some, late in others, often exhibiting parallel evolution across subclones. Signatures of homologous recombination deficiency correlated with response to neoadjuvant chemotherapy. Thus, the interplay of mutation, growth and competition drives clonal structures of breast cancer that are complex, variable across patients and clinically relevant.

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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
EGAS00001000195 Cancer Genomics
EGAS00001000300 Cancer Genomics
EGAS00001000890 Cancer Genomics
EGAS00001000902 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
EGAF00000138910 bam 17.2 GB
EGAF00000138911 bam 15.8 GB
EGAF00000138912 bam 21.3 GB
EGAF00000138913 bam 27.2 GB
EGAF00000138914 bam 24.9 GB
EGAF00000138915 bam 16.4 GB
EGAF00000138916 bam 20.2 GB
EGAF00000141002 bam 15.9 GB
EGAF00000141003 bam 30.4 GB
EGAF00000141004 bam 25.0 GB
EGAF00000141005 bam 15.8 GB
EGAF00000147448 bam 31.7 GB
EGAF00000149529 bam 35.0 GB
EGAF00000151371 bam 22.3 GB
EGAF00000151372 bam 23.7 GB
EGAF00000151373 bam 18.8 GB
EGAF00000152725 bam 17.7 GB
EGAF00000153152 bam 25.7 GB
EGAF00000153153 bam 23.7 GB
EGAF00000153155 bam 22.7 GB
EGAF00000153157 bam 26.4 GB
EGAF00000153158 bam 25.4 GB
EGAF00000153159 bam 29.0 GB
EGAF00000153160 bam 25.9 GB
EGAF00000155864 bam 27.7 GB
EGAF00000155865 bam 23.3 GB
EGAF00000155866 bam 30.6 GB
EGAF00000155867 bam 28.9 GB
EGAF00000155868 bam 30.9 GB
EGAF00000155869 bam 28.1 GB
EGAF00000155870 bam 22.1 GB
EGAF00000155871 bam 24.8 GB
EGAF00000155872 bam 30.8 GB
EGAF00000155873 bam 28.1 GB
EGAF00000155877 bam 37.0 GB
EGAF00000155878 bam 37.9 GB
EGAF00000155879 bam 23.1 GB
EGAF00000155880 bam 22.0 GB
EGAF00000161499 bam 28.6 GB
EGAF00000162958 bam 36.9 GB
EGAF00000162959 bam 38.3 GB
EGAF00000162960 bam 40.0 GB
EGAF00000162961 bam 39.9 GB
EGAF00000162962 bam 38.1 GB
EGAF00000162963 bam 38.6 GB
EGAF00000162964 bam 46.6 GB
EGAF00000163586 bam 38.7 GB
EGAF00000163587 bam 35.4 GB
EGAF00000163588 bam 37.2 GB
EGAF00000163589 bam 37.5 GB
EGAF00000163590 bam 34.6 GB
EGAF00000163591 bam 34.6 GB
EGAF00000163592 bam 33.3 GB
EGAF00000163593 bam 32.8 GB
EGAF00000164378 bam 31.9 GB
EGAF00000164379 bam 32.4 GB
EGAF00000164853 bam 31.6 GB
EGAF00000164854 bam 32.6 GB
EGAF00000164855 bam 25.1 GB
EGAF00000164857 bam 32.4 GB
EGAF00000164858 bam 30.5 GB
EGAF00000164859 bam 25.6 GB
EGAF00000164860 bam 32.9 GB
EGAF00000164861 bam 33.1 GB
EGAF00000164862 bam 28.1 GB
EGAF00000164863 bam 28.1 GB
EGAF00000164864 bam 27.9 GB
EGAF00000164865 bam 26.6 GB
EGAF00000164866 bam 26.1 GB
EGAF00000167151 bam 40.6 GB
EGAF00000167152 bam 21.4 GB
EGAF00000168077 bam 32.1 GB
EGAF00000168078 bam 32.1 GB
EGAF00000168079 bam 24.5 GB
EGAF00000168687 bam 24.6 GB
EGAF00000168688 bam 26.3 GB
EGAF00000168689 bam 26.3 GB
EGAF00000168690 bam 25.9 GB
EGAF00000169196 bam 33.0 GB
EGAF00000170572 bam 34.9 GB
EGAF00000170573 bam 33.2 GB
EGAF00000170574 bam 34.0 GB
EGAF00000170575 bam 18.1 GB
EGAF00000170576 bam 23.7 GB
EGAF00000170577 bam 23.3 GB
EGAF00000170578 bam 23.5 GB
EGAF00000170579 bam 27.5 GB
EGAF00000171832 bam 32.1 GB
EGAF00000171833 bam 32.1 GB
EGAF00000172477 bam 29.5 GB
EGAF00000172478 bam 25.1 GB
EGAF00000172479 bam 25.4 GB
EGAF00000172480 bam 25.9 GB
EGAF00000172481 bam 25.7 GB
EGAF00000172482 bam 26.0 GB
EGAF00000172483 bam 26.2 GB
EGAF00000172484 bam 25.9 GB
EGAF00000172485 bam 27.1 GB
EGAF00000172486 bam 26.8 GB
EGAF00000177814 bam 34.5 GB
EGAF00000177815 bam 34.5 GB
EGAF00000177816 bam 29.6 GB
EGAF00000177817 bam 29.3 GB
EGAF00000177818 bam 29.6 GB
EGAF00000177819 bam 33.0 GB
EGAF00000177820 bam 32.8 GB
EGAF00000177821 bam 32.7 GB
EGAF00000181225 bam 30.3 GB
EGAF00000187957 bam 35.7 GB
EGAF00000188353 bam 36.1 GB
EGAF00000188354 bam 36.1 GB
EGAF00000188356 bam 20.1 GB
EGAF00000188357 bam 22.4 GB
EGAF00000222303 bam 25.2 GB
EGAF00000231521 bam 31.9 GB
EGAF00000231522 bam 31.9 GB
EGAF00000231523 bam 32.1 GB
EGAF00000231524 bam 33.2 GB
EGAF00000231525 bam 35.2 GB
EGAF00000231526 bam 35.2 GB
EGAF00000231527 bam 34.8 GB
EGAF00000231528 bam 35.9 GB
EGAF00000234291 bam 32.2 GB
EGAF00000234292 bam 33.8 GB
EGAF00000234293 bam 33.3 GB
EGAF00000234294 bam 33.7 GB
EGAF00000234295 bam 34.5 GB
EGAF00000234296 bam 34.1 GB
EGAF00000234297 bam 33.4 GB
EGAF00000234298 bam 33.8 GB
EGAF00000234299 bam 18.4 GB
EGAF00000234300 bam 13.0 GB
EGAF00000234301 bam 34.8 GB
EGAF00000240813 bam 24.7 GB
EGAF00000242184 bam 32.3 GB
EGAF00000242185 bam 33.7 GB
EGAF00000242186 bam 32.6 GB
EGAF00000242187 bam 34.1 GB
EGAF00000242188 bam 34.9 GB
EGAF00000584965 bam 14.0 GB
EGAF00000584966 bam 13.4 GB
EGAF00000584967 bam 20.1 GB
EGAF00000584968 bam 26.1 GB
EGAF00000584969 bam 26.1 GB
EGAF00000584970 bam 25.4 GB
EGAF00000584971 bam 25.7 GB
EGAF00000584972 bam 25.5 GB
EGAF00000584973 bam 25.2 GB
EGAF00000584974 bam 24.8 GB
EGAF00000584975 bam 24.8 GB
EGAF00000584976 bam 24.7 GB
EGAF00000584977 bam 24.3 GB
EGAF00000584978 bam 27.2 GB
EGAF00000584979 bam 27.6 GB
EGAF00000584980 bam 27.5 GB
EGAF00000584981 bam 27.1 GB
EGAF00000584982 bam 32.9 GB
EGAF00000584983 bam 33.5 GB
EGAF00000584984 bam 37.5 GB
EGAF00000584985 bam 37.6 GB
EGAF00000584986 bam 36.5 GB
EGAF00000584987 bam 19.2 GB
EGAF00000584988 bam 28.4 GB
EGAF00000584989 bam 28.2 GB
EGAF00000584990 bam 28.3 GB
EGAF00000584991 bam 35.9 GB
EGAF00000584992 bam 36.4 GB
EGAF00000584993 bam 36.0 GB
EGAF00000584994 bam 36.4 GB
EGAF00000584995 bam 36.6 GB
EGAF00000584996 bam 29.4 GB
EGAF00000584997 bam 38.6 GB
EGAF00000584998 bam 39.0 GB
EGAF00000584999 bam 22.3 GB
EGAF00000585000 bam 17.9 GB
EGAF00000585001 bam 15.3 GB
EGAF00000585002 bam 25.4 GB
EGAF00000585003 bam 25.9 GB
178 Files (5.2 TB)