Ignatiadis, M., Sledge, G. W. & Jeffrey, S. S. Liquid biopsy enters the clinic—implementation issues and future challenges. Nat. Rev. Clin. Oncol. 18, 297–312 (2021).
PubMed
Article
Google Scholar
Weber, Z. T. et al. Modeling clonal structure over narrow time frames via circulating tumor DNA in metastatic breast cancer. Genome Med. 13, 89 (2021).
CAS
PubMed
PubMed Central
Article
Google Scholar
Abbosh, C. et al. Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution. Nature 545, 446–451 (2017).
ADS
CAS
PubMed
PubMed Central
Article
Google Scholar
Parikh, A. R. et al. Liquid versus tissue biopsy for detecting acquired resistance and tumor heterogeneity in gastrointestinal cancers. Nat. Med. 25, 1415–1421 (2019).
CAS
PubMed
PubMed Central
Article
Google Scholar
Cresswell, G. D. et al. Mapping the breast cancer metastatic cascade onto ctDNA using genetic and epigenetic clonal tracking. Nat. Commun. 11, 1446 (2020).
ADS
CAS
PubMed
PubMed Central
Article
Google Scholar
Annala, M. et al. Evolution of castration-resistant prostate cancer in ctDNA during sequential androgen receptor pathway inhibition. Clin. Cancer Res. 27, 4610–4623 (2021).
CAS
PubMed
Article
Google Scholar
Wyatt, A. W. et al. Concordance of circulating tumor DNA and matched metastatic tissue biopsy in prostate cancer. J. Natl Cancer Inst. 109, djx118 (2017).
PubMed Central
Article
CAS
Google Scholar
Razavi, P. et al. Alterations in PTEN and ESR1 promote clinical resistance to alpelisib plus aromatase inhibitors. Nat. Cancer 1, 382–393 (2020).
CAS
PubMed
PubMed Central
Article
Google Scholar
Siravegna, G. et al. Radiologic and genomic evolution of individual metastases during HER2 blockade in colorectal cancer. Cancer Cell 34, 148–162 (2018).
CAS
PubMed
Article
Google Scholar
O’Leary, B. et al. The genetic landscape and clonal evolution of breast cancer resistance to palbociclib plus fulvestrant in the PALOMA-3 trial. Cancer Discov. 8, 1390–1403 (2018).
PubMed
PubMed Central
Article
Google Scholar
Noorani, A. et al. Genomic evidence supports a clonal diaspora model for metastases of esophageal adenocarcinoma. Nat. Genet. 52, 74–83 (2020).
CAS
PubMed
PubMed Central
Article
Google Scholar
Woodcock, D. J. et al. Prostate cancer evolution from multilineage primary to single lineage metastases with implications for liquid biopsy. Nat. Commun. 11, 5070 (2020).
ADS
CAS
PubMed
PubMed Central
Article
Google Scholar
Snyder, M. W., Kircher, M., Hill, A. J., Daza, R. M. & Shendure, J. Cell-free DNA comprises an in vivo nucleosome footprint that informs its tissues-of-origin. Cell 164, 57–68 (2016).
CAS
PubMed
PubMed Central
Article
Google Scholar
Ulz, P. et al. Inference of transcription factor binding from cell-free DNA enables tumor subtype prediction and early detection. Nat. Commun. 10, 4666 (2019).
ADS
CAS
PubMed
PubMed Central
Article
Google Scholar
Zhu, G. et al. Tissue-specific cell-free DNA degradation quantifies circulating tumor DNA burden. Nat. Commun. 12, 1–11 (2021).
ADS
CAS
Article
Google Scholar
Ulz, P. et al. Inferring expressed genes by whole-genome sequencing of plasma DNA. Nat. Genet. 48, 1273–1278 (2016).
CAS
PubMed
Article
Google Scholar
Peneder, P. et al. Multimodal analysis of cell-free DNA whole-genome sequencing for pediatric cancers with low mutational burden. Nat. Commun. 12, 3230 (2021).
ADS
CAS
PubMed
PubMed Central
Article
Google Scholar
Sun, K. et al. Orientation-aware plasma cell-free DNA fragmentation analysis in open chromatin regions informs tissue of origin. Genome Res. 29, 418–427 (2019).
CAS
PubMed
PubMed Central
Article
Google Scholar
Khalaf, D. J. et al. Optimal sequencing of enzalutamide and abiraterone acetate plus prednisone in metastatic castration-resistant prostate cancer: a multicentre, randomised, open-label, phase 2, crossover trial. Lancet Oncol. 20, 1730–1739 (2019).
CAS
PubMed
Article
Google Scholar
Quigley, D. A. et al. Genomic hallmarks and structural variation in metastatic prostate cancer. Cell 174, 758–769 (2018).
CAS
PubMed
PubMed Central
Article
Google Scholar
Abida, W. et al. Genomic correlates of clinical outcome in advanced prostate cancer. Proc. Natl Acad. Sci. USA. 116, 11428–11436 (2019).
CAS
PubMed
PubMed Central
Article
Google Scholar
van Dessel, L. F. et al. The genomic landscape of metastatic castration-resistant prostate cancers reveals multiple distinct genotypes with potential clinical impact. Nat. Commun. 10, 5251 (2019).
ADS
PubMed
PubMed Central
Article
CAS
Google Scholar
Alexandrov, L. B. et al. The repertoire of mutational signatures in human cancer. Nature 578, 94–101 (2020).
ADS
CAS
PubMed
PubMed Central
Article
Google Scholar
Wu, Y.-M. et al. Inactivation of CDK12 delineates a distinct immunogenic class of advanced prostate cancer. Cell 173, 1770–1782 (2018).
CAS
PubMed
Article
Google Scholar
Black, J. R. M. & McGranahan, N. Genetic and non-genetic clonal diversity in cancer evolution. Nat. Rev. Cancer 21, 379–392 (2021).
CAS
PubMed
Article
Google Scholar
Dentro, S. C. et al. Characterizing genetic intra-tumor heterogeneity across 2,658 human cancer genomes. Cell 184, 2239–2254 (2021).
CAS
PubMed
PubMed Central
Article
Google Scholar
Tarabichi, M. et al. A practical guide to cancer subclonal reconstruction from DNA sequencing. Nat. Methods 18, 144–155 (2021).
CAS
PubMed
PubMed Central
Article
Google Scholar
Bielski, C. M. et al. Genome doubling shapes the evolution and prognosis of advanced cancers. Nat. Genet. 50, 1189–1195 (2018).
CAS
PubMed
PubMed Central
Article
Google Scholar
Quinton, R. J. et al. Whole-genome doubling confers unique genetic vulnerabilities on tumour cells. Nature 590, 492–497 (2021).
ADS
CAS
PubMed
PubMed Central
Article
Google Scholar
Cohen-Sharir, Y. et al. Aneuploidy renders cancer cells vulnerable to mitotic checkpoint inhibition. Nature 590, 486–491 (2021).
ADS
CAS
PubMed
PubMed Central
Article
Google Scholar
Zaccaria, S. & Raphael, B. J. Accurate quantification of copy-number aberrations and whole-genome duplications in multi-sample tumor sequencing data. Nat. Commun. 11, 4301 (2020).
ADS
CAS
PubMed
PubMed Central
Article
Google Scholar
Chen, C. D. et al. Molecular determinants of resistance to antiandrogen therapy. Nat. Med. 10, 33–39 (2004).
PubMed
Article
CAS
Google Scholar
Henzler, C. et al. Truncation and constitutive activation of the androgen receptor by diverse genomic rearrangements in prostate cancer. Nat. Commun. 7, 13668 (2016).
ADS
CAS
PubMed
PubMed Central
Article
Google Scholar
Takeda, D. Y. et al. A somatically acquired enhancer of the androgen receptor is a noncoding driver in advanced prostate cancer. Cell 174, 422–432 (2018).
CAS
PubMed
PubMed Central
Article
Google Scholar
Li, Y. et al. Diverse AR gene rearrangements mediate resistance to androgen receptor inhibitors in metastatic prostate cancer. Clin. Cancer Res. 26, 1965–1976 (2020).
CAS
PubMed
PubMed Central
Article
Google Scholar
Annala, M. et al. Circulating tumor dna genomics correlate with resistance to abiraterone and enzalutamide in prostate cancer. Cancer Discov. 8, 444–457 (2018).
CAS
PubMed
Article
Google Scholar
Baca, S. C. et al. Punctuated evolution of prostate cancer genomes. Cell 153, 666–677 (2013).
CAS
PubMed
PubMed Central
Article
Google Scholar
Viswanathan, S. R. et al. Structural alterations driving castration-resistant prostate cancer revealed by linked-read genome sequencing. Cell 174, 433–447 (2018).
CAS
PubMed
PubMed Central
Article
Google Scholar
Esfahani, M. S. et al. Inferring gene expression from cell-free DNA fragmentation profiles. Nat. Biotechnol. 40, 585–597 (2022).
CAS
PubMed
Article
Google Scholar
Davies, A. H., Beltran, H. & Zoubeidi, A. Cellular plasticity and the neuroendocrine phenotype in prostate cancer. Nat. Rev. Urol. 15, 271–286 (2018).
CAS
PubMed
Article
Google Scholar
Pomerantz, M. M. et al. The androgen receptor cistrome is extensively reprogrammed in human prostate tumorigenesis. Nat. Genet. 47, 1346–1351 (2015).
CAS
PubMed
PubMed Central
Article
Google Scholar
Morova, T. et al. Androgen receptor-binding sites are highly mutated in prostate cancer. Nat. Commun. 11, 832 (2020).
ADS
CAS
PubMed
PubMed Central
Article
Google Scholar
Rebello, R. J. et al. Prostate cancer. Nat Rev. Dis. Primers 7, 9 (2021).
PubMed
Article
Google Scholar
Chi, K. N. et al. A prognostic index model for predicting overall survival in patients with metastatic castration-resistant prostate cancer treated with abiraterone acetate after docetaxel. Ann. Oncol. 27, 454–460 (2016).
CAS
PubMed
Article
Google Scholar
Turajlic, S. et al. Deterministic evolutionary trajectories influence primary tumor growth: TRACERx Renal. Cell 173, 595–610 (2018).
CAS
PubMed
PubMed Central
Article
Google Scholar
Gundem, G. et al. The evolutionary history of lethal metastatic prostate cancer. Nature 520, 353–357 (2015).
CAS
PubMed
PubMed Central
Article
Google Scholar
Kumar, A. et al. Substantial interindividual and limited intraindividual genomic diversity among tumors from men with metastatic prostate cancer. Nat. Med. 22, 369–378 (2016).
CAS
PubMed
PubMed Central
Article
Google Scholar
Quigley, D. et al. Analysis of circulating cell-free DNA identifies multiclonal heterogeneity of reversion mutations associated with resistance to PARP inhibitors. Cancer Discov. 7, 999–1005 (2017).
CAS
PubMed
PubMed Central
Article
Google Scholar
Unterrainer, M. et al. Recent advances of PET imaging in clinical radiation oncology. Radiat. Oncol. 15, 88 (2020).
CAS
PubMed
PubMed Central
Article
Google Scholar
Brandão, M., Caparica, R., Eiger, D. & de Azambuja, E. Biomarkers of response and resistance to PI3K inhibitors in estrogen receptor-positive breast cancer patients and combination therapies involving PI3K inhibitors. Ann. Oncol. 30, x27–x42 (2019).
PubMed
PubMed Central
Article
Google Scholar
Parikh, A. et al. Systematic liquid biopsy identifies novel and heterogeneous mechanisms of acquired resistance in gastrointestinal (GI) cancer patients. Ann. Oncol. 28, iii137 (2017).
Article
Google Scholar
Balanis, N. G. et al. Pan-cancer Convergence to a small-cell neuroendocrine phenotype that shares susceptibilities with hematological malignancies. Cancer Cell 36, 17–34 (2019).
CAS
PubMed
PubMed Central
Article
Google Scholar
Herberts, C. & Wyatt, A. W. Technical and biological constraints on ctDNA-based genotyping. Trends Cancer Res. 7, 995–1009 (2021).
CAS
Article
Google Scholar
Turajlic, S., Sottoriva, A., Graham, T. & Swanton, C. Resolving genetic heterogeneity in cancer. Nat. Rev. Genet. 20, 404–416 (2019).
CAS
PubMed
Article
Google Scholar
Scher, H. I. et al. Trial design and objectives for castration-resistant prostate cancer: updated recommendations from the prostate cancer clinical trials working group 3. J. Clin. Oncol. 34, 1402–1418 (2016).
PubMed
PubMed Central
Article
Google Scholar
Warner, E. et al. BRCA2, ATM, and CDK12 defects differentially shape prostate tumor driver genomics and clinical aggression. Clin. Cancer Res. 27, 1650–1662 (2021).
CAS
PubMed
Article
Google Scholar
Martin, M. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J. 17, 10 (2011).
Article
Google Scholar
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
CAS
PubMed
PubMed Central
Article
Google Scholar
Faust, G. G. & Hall, I. M. SAMBLASTER: fast duplicate marking and structural variant read extraction. Bioinformatics 30, 2503–2505 (2014).
CAS
PubMed
PubMed Central
Article
Google Scholar
Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).
CAS
PubMed
PubMed Central
Article
Google Scholar
Wang, K., Li, M. & Hakonarson, H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 38, e164 (2010).
PubMed
PubMed Central
Article
CAS
Google Scholar
Rosenthal, R., McGranahan, N., Herrero, J., Taylor, B. S. & Swanton, C. DeconstructSigs: delineating mutational processes in single tumors distinguishes DNA repair deficiencies and patterns of carcinoma evolution. Genome Biol. 17, 31 (2016).
PubMed
PubMed Central
Article
CAS
Google Scholar
Bergstrom, E. N. et al. SigProfilerMatrixGenerator: a tool for visualizing and exploring patterns of small mutational events. BMC Genomics 20, 685 (2019).
PubMed
PubMed Central
Article
Google Scholar
Landrum, M. J. et al. ClinVar: improving access to variant interpretations and supporting evidence. Nucleic Acids Res. 46, D1062–D1067 (2018).
CAS
PubMed
Article
Google Scholar
Danecek, P. et al. Twelve years of SAMtools and BCFtools. Gigascience 10, giab008 (2021).
PubMed
PubMed Central
Article
CAS
Google Scholar
Eisenberg, E. & Levanon, E. Y. Human housekeeping genes, revisited. Trends Genet. 29, 569–574 (2013).
CAS
PubMed
Article
Google Scholar