Ultrasensitive plasma-based monitoring of tumor burden using machine-learning-guided signal enrichment

Powles, T. et al. ctDNA guiding adjuvant immunotherapy in urothelial carcinoma. Nature https://doi.org/10.1038/s41586-021-03642-9 (2021).

Bratman, S. V. et al. Personalized circulating tumor DNA analysis as a predictive biomarker in solid tumor patients treated with pembrolizumab. Nat. Cancer 1, 873–881 (2020).

Article  CAS  PubMed  Google Scholar 

Tie, J. et al. Circulating tumor DNA analysis guiding adjuvant therapy in stage II colon cancer. N. Engl. J. Med. 386, 2261–2272 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Phallen, J. et al. Direct detection of early-stage cancers using circulating tumor DNA. Sci. Transl. Med. https://doi.org/10.1126/scitranslmed.aan2415 (2017).

Newman, A. M. et al. An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage. Nat. Med. 20, 548–554 (2014).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Nabet, B. Y. et al. Noninvasive early identification of therapeutic benefit from immune checkpoint inhibition. Cell 183, 363–376 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Rose Brannon, A. et al. Enhanced specificity of clinical high-sensitivity tumor mutation profiling in cell-free DNA via paired normal sequencing using MSK-ACCESS. Nat. Commun. 12, 3770 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Magbanua, M. J. M. et al. Circulating tumor DNA in neoadjuvant-treated breast cancer reflects response and survival. Ann. Oncol. 32, 229–239 (2021).

Article  CAS  PubMed  Google Scholar 

Henriksen, T. V. et al. Circulating tumor DNA in stage III colorectal cancer, beyond minimal residual disease detection, towards assessment of adjuvant therapy efficacy and clinical behavior of recurrences. Clin. Cancer Res. https://doi.org/10.1158/1078-0432.CCR-21-2404 (2021).

Kotani, D. et al. Molecular residual disease and efficacy of adjuvant chemotherapy in patients with colorectal cancer. Nat. Med. 29, 127–134 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kurtz, D. M. et al. Enhanced detection of minimal residual disease by targeted sequencing of phased variants in circulating tumor DNA. Nat. Biotechnol. https://doi.org/10.1038/s41587-021-00981-w (2021).

Haque, I. S. & Elemento, O. Challenges in using ctDNA to achieve early detection of cancer. Preprint at bioRxiv https://doi.org/10.1101/237578 (2017).

Avanzini, S. et al. A mathematical model of ctDNA shedding predicts tumor detection size. Sci. Adv. 6, eabc4308 (2020).

Article  PubMed  PubMed Central  Google Scholar 

Zviran, A. et al. Genome-wide cell-free DNA mutational integration enables ultra-sensitive cancer monitoring. Nat. Med. 26, 1114–1124 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Newman, A. M. et al. Integrated digital error suppression for improved detection of circulating tumor DNA. Nat. Biotechnol. 34, 547–555 (2016).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wan, J. C. M. et al. ctDNA monitoring using patient-specific sequencing and integration of variant reads. Sci. Transl. Med. https://doi.org/10.1126/scitranslmed.aaz8084 (2020).

Gydush, G. et al. Massively parallel enrichment of low-frequency alleles enables duplex sequencing at low depth. Nat. Biomed. Eng. 6, 257–266 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Alexandrov, L. B. et al. Signatures of mutational processes in human cancer. Nature 500, 415–421 (2013).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Alexandrov, L. B. et al. Mutational signatures associated with tobacco smoking in human cancer. Science 354, 618–622 (2016).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Underhill, H. R. et al. Fragment length of circulating tumor DNA. PLoS Genet. 12, e1006162 (2016).

Article  PubMed  PubMed Central  Google Scholar 

Mouliere, F. et al. Enhanced detection of circulating tumor DNA by fragment size analysis. Sci. Transl. Med. 10, eaat4921 (2018).

Article  PubMed  PubMed Central  Google Scholar 

Guo, J. et al. Quantitative characterization of tumor cell-free DNA shortening. BMC Genomics 21, 473 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gonzalez-Perez, A., Sabarinathan, R. & Lopez-Bigas, N. Local determinants of the mutational landscape of the human genome. Cell 177, 101–114 (2019).

Article  CAS  PubMed  Google Scholar 

Woo, Y. H. & Li, W.-H. DNA replication timing and selection shape the landscape of nucleotide variation in cancer genomes. Nat. Commun. 3, 1004 (2012).

Article  PubMed  Google Scholar 

Haradhvala, N. J. et al. Mutational strand asymmetries in cancer genomes reveal mechanisms of DNA damage and repair. Cell 164, 538–549 (2016).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Donley, N. & Thayer, M. J. DNA replication timing, genome stability and cancer: late and/or delayed DNA replication timing is associated with increased genomic instability. Semin. Cancer Biol. 23, 80–89 (2013).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Polak, P. et al. Cell-of-origin chromatin organization shapes the mutational landscape of cancer. Nature 518, 360–364 (2015).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bruhm, D. C. et al. Single-molecule genome-wide mutation profiles of cell-free DNA for non-invasive detection of cancer. Nat. Genet. 55, 1301–1310 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Taylor, A. M. et al. Genomic and functional approaches to understanding cancer aneuploidy. Cancer Cell 33, 676–689.e3 (2018).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Deshpande, A., Walradt, T., Hu, Y., Koren, A. & Imielinski, M. Robust foreground detection in somatic copy number data. Preprint at bioRxiv https://doi.org/10.1101/847681 (2019).

Raine, K. M. et al. AscatNgs: identifying somatically acquired copy-number alterations from whole-genome sequencing data. Curr. Protoc. Bioinform. 56, 15.9.1–15.9.17 (2016).

Article  Google Scholar 

Carter, S. L. et al. Absolute quantification of somatic DNA alterations in human cancer. Nat. Biotechnol. 30, 413–421 (2012).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cristiano, S. et al. Genome-wide cell-free DNA fragmentation in patients with cancer. Nature 570, 385–389 (2019).

Article  CAS  PubMed  PubMed Central  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).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Jiang, P. et al. Preferred end coordinates and somatic variants as signatures of circulating tumor DNA associated with hepatocellular carcinoma. Proc. Natl Acad. Sci. USA 115, E10925–E10933 (2018).

Article 

留言 (0)

沒有登入
gif