VanderLaan, P. A. et al. Success and failure rates of tumor genotyping techniques in routine pathological samples with non-small-cell lung cancer. Lung Cancer 84, 39–44 (2014).
Murtaza, M. et al. Multifocal clonal evolution characterized using circulating tumour DNA in a case of metastatic breast cancer. Nat. Commun. 6, 8760 (2015).
Phallen, J. et al. Direct detection of early-stage cancers using circulating tumor DNA. Sci. Transl. Med. 9, eaan2415 (2017).
Article PubMed PubMed Central Google Scholar
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
Ueda, M. et al. Somatic mutations in plasma cell-free DNA are diagnostic markers for esophageal squamous cell carcinoma recurrence. Oncotarget 7, 62280–62291 (2016).
Article PubMed PubMed Central Google Scholar
Adalsteinsson, V. A. et al. Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors. Nat. Commun. 8, 1324 (2017).
Article PubMed PubMed Central Google Scholar
Camus, V. et al. Digital PCR for quantification of recurrent and potentially actionable somatic mutations in circulating free DNA from patients with diffuse large B-cell lymphoma. Leuk. Lymphoma 57, 2171–2179 (2016).
Article CAS PubMed Google Scholar
Rothwell, D. G. et al. Utility of ctDNA to support patient selection for early phase clinical trials: the TARGET study. Nat. Med. 25, 738–743 (2019).
Article CAS PubMed Google Scholar
Li, S. et al. Sensitive detection of tumor mutations from blood and its application to immunotherapy prognosis. Nat. Commun. 12, 1–14 (2021).
Goldberg, S. B. et al. Early assessment of lung cancer immunotherapy response via circulating tumor DNA. Clin. Cancer Res. 24, 1872–1880 (2018).
Article CAS PubMed PubMed Central Google Scholar
Iwama, E. et al. Monitoring of somatic mutations in circulating cell-free DNA by digital PCR and next-generation sequencing during afatinib treatment in patients with lung adenocarcinoma positive for EGFR activating mutations. Ann. Oncol. 28, 136–141 (2017).
Article CAS PubMed Google Scholar
Fontanilles, M. et al. Non-invasive detection of somatic mutations using next-generation sequencing in primary central nervous system lymphoma. Oncotarget 8, 48157–48168 (2017).
Article PubMed PubMed Central Google Scholar
Chaudhuri, A. A. et al. Early detection of molecular residual disease in localized lung cancer by circulating tumor DNA profiling. Cancer Discov. 7, 1394–1403 (2017).
Article CAS PubMed PubMed Central Google Scholar
Li, S. et al. cfTrack, a method of exome-wide mutation analysis of cell-free DNA to simultaneously monitor the full spectrum of cancer treatment outcomes including MRD, recurrence, and evolution. Clin. Cancer Res. 28, 1841–1853 (2022).
Article CAS PubMed PubMed Central Google Scholar
Choudhury, A. D. et al. Tumor fraction in cell-free DNA as a biomarker in prostate cancer. JCI Insight 3, e122109 (2018).
Article PubMed PubMed Central Google Scholar
Li, S. et al. cfSNV: a software tool for the sensitive detection of somatic mutations from cell-free DNA. Jasminezhoulab/cfSNV_docker: cfSNV docker image. Available at https://github.com/jasminezhoulab/cfSNV_docker (2022).
Jiang, P. et al. Lengthening and shortening of plasma DNA in hepatocellular carcinoma patients. Proc. Natl Acad. Sci. USA 112, E1317–E1325 (2015).
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).
Abbosh, C. et al. Phylogenetic ctDNA analysis depicts early-stage lung cancer evolution. Nature 545, 446–461 (2017).
Article CAS PubMed PubMed Central Google Scholar
Cibulskis, K. et al. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat. Biotechnol. 31, 213–219 (2013).
Article CAS PubMed PubMed Central Google Scholar
Van der Auwera, G. A. et al. From FastQ data to high‐confidence variant calls: the genome analysis toolkit best practices pipeline. Curr. Protoc. Bioinforma. 43, 11.10.1–11.10.33 (2013).
DePristo, M. A. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 43, 491–498 (2011).
Article CAS PubMed PubMed Central Google Scholar
Pellini, B. & Chaudhuri, A. A. Circulating tumor DNA minimal residual disease detection of non–small-cell lung cancer treated with curative intent. J. Clin. Oncol. 40, 567–575 (2022).
Article CAS PubMed PubMed Central Google Scholar
Roth, A. et al. JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data. Bioinformatics 28, 907–913 (2012).
Article CAS PubMed PubMed Central Google Scholar
Kim, S. et al. Strelka2: fast and accurate calling of germline and somatic variants. Nat. Methods 15, 591–594 (2018).
Article CAS PubMed Google Scholar
Kothen-Hill, S. T. et al. Deep learning mutation prediction enables early stage lung cancer detection in liquid biopsy. Available at https://openreview.net/forum?id=H1DkN7ZCZ (2018).
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
Koboldt, D. C. Best practices for variant calling in clinical sequencing. Genome Med. 12, 1–13 (2020).
Chen, Z. et al. Systematic comparison of somatic variant calling performance among different sequencing depth and mutation frequency. Sci. Rep. 10, 3501 (2020).
Article CAS PubMed PubMed Central Google Scholar
Xu, C. et al. A review of somatic single nucleotide variant calling algorithms for next-generation sequencing data. Comput. Struct. Biotechnol. J. 16, 15–24 (2018).
Article CAS PubMed PubMed Central Google Scholar
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
Article CAS PubMed PubMed Central Google Scholar
Broad Institute. Picard tools. Available at https://broadinstitute.github.io/picard/ (2019).
Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
Article PubMed PubMed Central Google Scholar
Mose, L. E. et al. ABRA: improved coding indel detection via assembly-based realignment. Bioinformatics 30, 2813–2815 (2014).
Article CAS PubMed PubMed Central Google Scholar
Opasic, L. et al. How many samples are needed to infer truly clonal mutations from heterogenous tumours? BMC Cancer 19, 1–11 (2019).
Butler, T. M. et al. Exome sequencing of cell-free DNA from metastatic cancer patients identifies clinically actionable mutations distinct from primary disease. PloS One 10, e0136407 (2015).
Article 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. 39, 1537–1547 (2021).
Article CAS PubMed PubMed Central Google Scholar
Liebs, S. et al. Liquid biopsy assessment of synchronous malignancies: a case report and review of the literature. ESMO Open 4, e000528 (2019).
Article PubMed PubMed Central Google Scholar
Ramesh, N. et al. Decoding the evolutionary response to prostate cancer therapy by plasma genome sequencing. Genome Biol. 21, 1–22 (2020).
Magoč, T. & Salzberg, S. L. FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27, 2957–2963 (2011).
Article PubMed PubMed Central Google Scholar
Merkel, D. Docker: lightweight linux containers for consistent development and deployment. Linux J. 2014, 2 (2014).
Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).
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