References
- Leroy K, Audigier Valette C, Alexandre J, Boussemart L, Chiesa J, Deldycke C, et al. Retrospective analysis of real-world data to evaluate actionability of a comprehensive molecular profiling panel in solid tumor tissue samples (REALM study). PLoS One. 2023;18(9):e0291495. doi:10.1371/journal.pone.0291495.
- Agarwala V, Khozin S, Singal G, O'Connell C, Kuk D, Li G, et al. Real-World Evidence In Support Of Precision Medicine: Clinico-Genomic Cancer Data As A Case Study. Health Aff (Millwood). 2018;37(5):765–772. doi:10.1377/hlthaff.2017.1579.
- Malone ER, Oliva M, Sabatini PJB, Stockley TL, Siu LL. Molecular profiling for precision cancer therapies. Genome Med. 2020;12(1):8. doi:10.1186/s13073-019-0703-1.
- Schwartzberg L, Kim ES, Liu D, Schrag D. Precision Oncology: Who, How, What, When, and When Not? Am Soc Clin Oncol Educ Book. 2017;37(37):160–169. doi:10.14694/EDBK_174176.
- Vijay P, McIntyre ABR, Mason CE, Greenfield JP, Li S. Clinical Genomics: Challenges and Opportunities. Crit Rev Eukaryot Gene Expr. 2016;26(2):97–113. doi:10.1615/CritRevEukaryotGeneExpr.2016015724.
- Garofalo A, Sholl L, Reardon B, Taylor-Weiner A, Amin-Mansour A, Miao D, et al. The impact of tumor profiling approaches and genomic data strategies for cancer precision medicine. Genome Med. 2016;8(1):79. doi:10.1186/s13073-016-0333-9.
- Halperin RF, Carpten JD, Manojlovic Z, Aldrich J, Keats J, Byron S, et al. A method to reduce ancestry related germline false positives in tumor only somatic variant calling. BMC Med Genomics. 2017;10(1):61. doi:10.1186/s12920-017-0296-8.
- Parikh K, Huether R, White K, Hoskinson D, Beaubier N, Dong H, et al. Tumor Mutational Burden From Tumor-Only Sequencing Compared With Germline Subtraction From Paired Tumor and Normal Specimens. JAMA Netw Open. 2020;3(2):e200202. doi:10.1001/jamanetworkopen.2020.0202.
- Faust GG, Hall IM. SAMBLASTER: fast duplicate marking and structural variant read extraction. Bioinformatics. 2014;30(17):2503–2505. doi:10.1093/bioinformatics/btu314.
- McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20(9):1297–1303. doi:10.1101/gr.107524.110.
- Kim S, Scheffler K, Halpern AL, Bekritsky MA, Noh E, Källberg M, et al. Strelka2: fast and accurate calling of germline and somatic variants. Nat Methods. 2018;15(8):591–594. doi:10.1038/s41592-018-0051-x.
- Chen X, Schulz-Trieglaff O, Shaw R, Barnes B, Schlesinger F, Källberg M, et al. Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications. Bioinformatics. 2016;32(8):1220–1222. doi:10.1093/bioinformatics/btv710.
- McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GRS, Thormann A, et al. The Ensembl Variant Effect Predictor. Genome Biol. 2016;17(1):122. doi:10.1186/s13059-016-0974-4.
- Niu B, Ye K, Zhang Q, Lu C, Xie M, McLellan MD, et al. MSIsensor: microsatellite instability detection using paired tumor-normal sequence data. Bioinformatics. 2014;30(7):1015–1016. doi:10.1093/bioinformatics/btt755.
- Hagemann IS, Devarakonda S, Lockwood CM, Spencer DH, Guebert K, Bredemeyer AJ, et al. Clinical next-generation sequencing in patients with non-small cell lung cancer. Cancer. 2015;121(4):631–639. doi:10.1002/cncr.29089.
- Simons M, Ramaekers B, Peeters A, Mankor J, Paats M, Aerts J, et al. Observed versus modelled lifetime overall survival of targeted therapies and immunotherapies for advanced non-small cell lung cancer patients – A systematic review. Crit Rev Oncol Hematol. 2020;153:103035. doi:10.1016/j.critrevonc.2020.103035.
- Steuten L, Goulart B, Meropol NJ, Pritchard D, Ramsey SD. Cost Effectiveness of Multigene Panel Sequencing for Patients With Advanced Non-Small-Cell Lung Cancer. JCO Clin Cancer Inform. 2019;3:1–10. doi:10.1200/CCI.19.00002.
- Chan TA, Yarchoan M, Jaffee E, Swanton C, Quezada SA, Stenzinger A, et al. Development of tumor mutation burden as an immunotherapy biomarker: utility for the oncology clinic. Ann Oncol. 2019;30(1):44–56. doi:10.1093/annonc/mdy495.