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Deep whole-genome ctDNA chronology of treatment-resistant prostate most cancers


  • Ignatiadis, M., Sledge, G. W. & Jeffrey, S. S. Liquid biopsy enters the clinic—implementation points and future challenges. Nat. Rev. Clin. Oncol. 18, 297–312 (2021).

    PubMed 
    Article 

    Google Scholar
     

  • Weber, Z. T. et al. Modeling clonal construction over slender time frames through circulating tumor DNA in metastatic breast most cancers. Genome Med. 13, 89 (2021).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Abbosh, C. et al. Phylogenetic ctDNA evaluation depicts early-stage lung most cancers 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 most cancers metastatic cascade onto ctDNA utilizing genetic and epigenetic clonal monitoring. Nat. Commun. 11, 1446 (2020).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Annala, M. et al. Evolution of castration-resistant prostate most cancers in ctDNA throughout sequential androgen receptor pathway inhibition. Clin. Most cancers 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 most cancers. J. Natl Most cancers Inst. 109, djx118 (2017).

    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • Razavi, P. et al. Alterations in PTEN and ESR1 promote medical resistance to alpelisib plus aromatase inhibitors. Nat. Most cancers 1, 382–393 (2020).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Siravegna, G. et al. Radiologic and genomic evolution of particular person metastases throughout HER2 blockade in colorectal most cancers. Most cancers Cell 34, 148–162 (2018).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • O’Leary, B. et al. The genetic panorama and clonal evolution of breast most cancers resistance to palbociclib plus fulvestrant within the PALOMA-3 trial. Most cancers Discov. 8, 1390–1403 (2018).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Noorani, A. et al. Genomic proof helps a clonal diaspora mannequin for metastases of esophageal adenocarcinoma. Nat. Genet. 52, 74–83 (2020).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Woodcock, D. J. et al. Prostate most cancers evolution from multilineage major 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 includes 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 issue binding from cell-free DNA allows 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 evaluation 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
     

  • Solar, Ok. et al. Orientation-aware plasma cell-free DNA fragmentation evaluation in open chromatin areas informs tissue of origin. Genome Res. 29, 418–427 (2019).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Khalaf, D. J. et al. Optimum sequencing of enzalutamide and abiraterone acetate plus prednisone in metastatic castration-resistant prostate most cancers: a multicentre, randomised, open-label, section 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 most cancers. Cell 174, 758–769 (2018).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Abida, W. et al. Genomic correlates of medical final result in superior prostate most cancers. Proc. Natl Acad. Sci. USA. 116, 11428–11436 (2019).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • van Dessel, L. F. et al. The genomic panorama of metastatic castration-resistant prostate cancers reveals a number of distinct genotypes with potential medical affect. 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 most cancers. Nature 578, 94–101 (2020).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Wu, Y.-M. et al. Inactivation of CDK12 delineates a definite immunogenic class of superior prostate most cancers. Cell 173, 1770–1782 (2018).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Black, J. R. M. & McGranahan, N. Genetic and non-genetic clonal variety in most cancers evolution. Nat. Rev. Most cancers 21, 379–392 (2021).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Dentro, S. C. et al. Characterizing genetic intra-tumor heterogeneity throughout 2,658 human most cancers genomes. Cell 184, 2239–2254 (2021).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Tarabichi, M. et al. A sensible information to most cancers subclonal reconstruction from DNA sequencing. Nat. Strategies 18, 144–155 (2021).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Bielski, C. M. et al. Genome doubling shapes the evolution and prognosis of superior cancers. Nat. Genet. 50, 1189–1195 (2018).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Quinton, R. J. et al. Complete-genome doubling confers distinctive 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 most cancers cells weak to mitotic checkpoint inhibition. Nature 590, 486–491 (2021).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Zaccaria, S. & Raphael, B. J. Correct quantification of copy-number aberrations and whole-genome duplications in multi-sample tumor sequencing information. Nat. Commun. 11, 4301 (2020).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Chen, C. D. et al. Molecular determinants of resistance to antiandrogen remedy. Nat. Med. 10, 33–39 (2004).

    PubMed 
    Article 
    CAS 

    Google Scholar
     

  • Henzler, C. et al. Truncation and constitutive activation of the androgen receptor by various genomic rearrangements in prostate most cancers. 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 superior prostate most cancers. Cell 174, 422–432 (2018).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Li, Y. et al. Various AR gene rearrangements mediate resistance to androgen receptor inhibitors in metastatic prostate most cancers. Clin. Most cancers 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 most cancers. Most cancers Discov. 8, 444–457 (2018).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Baca, S. C. et al. Punctuated evolution of prostate most cancers genomes. Cell 153, 666–677 (2013).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Viswanathan, S. R. et al. Structural alterations driving castration-resistant prostate most cancers 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. Mobile plasticity and the neuroendocrine phenotype in prostate most cancers. 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 websites are extremely mutated in prostate most cancers. Nat. Commun. 11, 832 (2020).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Rebello, R. J. et al. Prostate most cancers. Nat Rev. Dis. Primers 7, 9 (2021).

    PubMed 
    Article 

    Google Scholar
     

  • Chi, Ok. N. et al. A prognostic index mannequin for predicting general survival in sufferers with metastatic castration-resistant prostate most cancers handled with abiraterone acetate after docetaxel. Ann. Oncol. 27, 454–460 (2016).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Turajlic, S. et al. Deterministic evolutionary trajectories affect major tumor development: TRACERx Renal. Cell 173, 595–610 (2018).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Gundem, G. et al. The evolutionary historical past of deadly metastatic prostate most cancers. Nature 520, 353–357 (2015).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Kumar, A. et al. Substantial interindividual and restricted intraindividual genomic variety amongst tumors from males with metastatic prostate most cancers. Nat. Med. 22, 369–378 (2016).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Quigley, D. et al. Evaluation of circulating cell-free DNA identifies multiclonal heterogeneity of reversion mutations related to resistance to PARP inhibitors. Most cancers Discov. 7, 999–1005 (2017).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Unterrainer, M. et al. Current advances of PET imaging in medical 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 most cancers sufferers and mixture 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) most cancers sufferers. 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. Most cancers Cell 36, 17–34 (2019).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Herberts, C. & Wyatt, A. W. Technical and organic constraints on ctDNA-based genotyping. Developments Most cancers Res. 7, 995–1009 (2021).

    CAS 
    Article 

    Google Scholar
     

  • Turajlic, S., Sottoriva, A., Graham, T. & Swanton, C. Resolving genetic heterogeneity in most cancers. Nat. Rev. Genet. 20, 404–416 (2019).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Scher, H. I. et al. Trial design and targets for castration-resistant prostate most cancers: up to date suggestions from the prostate most cancers medical 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 form prostate tumor driver genomics and medical aggression. Clin. Most cancers 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. Quick gapped-read alignment with Bowtie 2. Nat. Strategies 9, 357–359 (2012).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Faust, G. G. & Corridor, I. M. SAMBLASTER: quick duplicate marking and structural variant learn extraction. Bioinformatics 30, 2503–2505 (2014).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Quinlan, A. R. & Corridor, I. M. BEDTools: a versatile suite of utilities for evaluating genomic options. Bioinformatics 26, 841–842 (2010).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Wang, Ok., Li, M. & Hakonarson, H. ANNOVAR: purposeful annotation of genetic variants from high-throughput sequencing information. 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 restore 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 software for visualizing and exploring patterns of small mutational occasions. BMC Genomics 20, 685 (2019).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Landrum, M. J. et al. ClinVar: bettering entry to variant interpretations and supporting proof. 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. Developments Genet. 29, 569–574 (2013).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

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