Lu S, Stein JE, Rimm DL, Wang DW, Bell JM, Johnson DB, et al. Comparison of biomarker modalities for predicting response to PD-1/PD-L1 checkpoint blockade. JAMA Oncol. 2019;5:1195–204.

Article  PubMed  PubMed Central  Google Scholar 

Tsao MS, Kerr KM, Kockx M, Beasley M-B, Borczuk AC, Botling J, et al. PD-L1 immunohistochemistry comparability study in real-life clinical samples: results of blueprint phase 2 project. J Thorac Oncol. 2018;13:1302–11.

Article  PubMed  PubMed Central  Google Scholar 

Lantuejoul S, Sound-Tsao M, Cooper WA, Girard N, Hirsch FR, Roden AC, et al. PD-L1 testing for lung cancer in 2019: perspective from the IASLC Pathology Committee. J Thorac Oncol. 2020;15:499–519.

Article  CAS  PubMed  Google Scholar 

Cristescu R, Mogg R, Ayers M, Albright A, Murphy E, Yearley J, et al. Pan-tumor genomic biomarkers for PD-1 checkpoint blockade-based immunotherapy. Science (New York NY). 2018. https://doi.org/10.1126/science.aar3593.

Article  Google Scholar 

Samstein RM, Lee C-H, Shoushtari AN, Hellmann MD, Shen R, Janjigian YY, et al. Tumor mutational load predicts survival after immunotherapy across multiple cancer types. Nat Genet. 2019;51:202–6.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Büttner R, Longshore JW, López-Ríos F, Merkelbach-Bruse S, Normanno N, Rouleau E, et al. Implementing TMB measurement in clinical practice: considerations on assay requirements. ESMO Open. 2019;4: e000442.

Article  PubMed  PubMed Central  Google Scholar 

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;30:44–56.

Article  CAS  PubMed  Google Scholar 

Kong Y, Rose CM, Cass AA, Williams AG, Darwish M, Lianoglou S, et al. Transposable element expression in tumors is associated with immune infiltration and increased antigenicity. Nat Commun. 2019;10:1–14.

Article  Google Scholar 

Rodriguez-Martin B, Alvarez EG, Baez-Ortega A, Zamora J, Supek F, Demeulemeester J, et al. Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition. Nat Genet. 2020;52:306–19.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Tubio JMC, Li Y, Ju YS, Martincorena I, Cooke SL, Tojo M, et al. Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes. Science. 2014;345:1251343.

Article  PubMed  PubMed Central  Google Scholar 

Shah NM, Jang HJ, Liang Y, Maeng JH, Tzeng S-C, Wu A, et al. Pan-cancer analysis identifies tumor-specific antigens derived from transposable elements. Nat Genet. 2023;55:631–9.

Article  CAS  PubMed  Google Scholar 

Yang K, Halima A, Chan TA. Antigen presentation in cancer—mechanisms and clinical implications for immunotherapy. Nat Rev Clin Oncol. 2023;20:604–23.

Article  CAS  PubMed  Google Scholar 

Han J, Dong Y, Zhu X, Reuben A, Zhang J, Xu J, et al. Assessment of human leukocyte antigen-based neoantigen presentation to determine pan-cancer response to immunotherapy. Nat Commun. 2024;15:1199.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bray F, Laversanne M, Sung H, Ferlay J, Siegel RL, Soerjomataram I, et al. Global cancer statistics 2022: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin. 2024;74:229–63.

Article  PubMed  Google Scholar 

Lopez-Beltran A, Cookson MS, Guercio BJ, Cheng L. Advances in diagnosis and treatment of bladder cancer. BMJ. 2024;384: e076743.

Article  CAS  PubMed  Google Scholar 

Fahmy O, Khairul-Asri MG, Schubert T, Renninger M, Malek R, Kübler H, et al. A systematic review and meta-analysis on the oncological long-term outcomes after trimodality therapy and radical cystectomy with or without neoadjuvant chemotherapy for muscle-invasive bladder cancer. Urol Oncol. 2018;36:43–53.

Article  PubMed  Google Scholar 

Reck M, Remon J, Hellmann MD. Special series: thoracic oncology: current and future therapy review articles. J Clin Oncol. 2022;40:586–97.

Article  CAS  PubMed  Google Scholar 

Hendriks LE, Kerr KM, Menis J, Mok TS, Nestle U, Passaro A, et al. Non-oncogene-addicted metastatic non-small-cell lung cancer: ESMO Clinical Practice Guideline for diagnosis, treatment and follow-up☆. Ann Oncol. 2023;34:358–76.

Article  CAS  PubMed  Google Scholar 

Powles T, Valderrama BP, Gupta S, Bedke J, Kikuchi E, Hoffman-Censits J, et al. Enfortumab vedotin and pembrolizumab in untreated advanced urothelial cancer. N Engl J Med. 2024;390:875–88.

Article  CAS  PubMed  Google Scholar 

Powles T, Kockx M, Rodriguez-Vida A, Duran I, Crabb SJ, Van Der Heijden MS, et al. Clinical efficacy and biomarker analysis of neoadjuvant atezolizumab in operable urothelial carcinoma in the ABACUS trial. Nat Med. 2019;25:1706–14.

Article  CAS  PubMed  Google Scholar 

Andrews S. FastQC: a quality control tool for high throughput sequence data. 2010. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/. Accessed 15 May 2024.

Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv: Genomics. 2013.

Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics (Oxford, England). 2009;25:1754–60.

CAS  PubMed  Google Scholar 

Danecek P, Bonfield JK, Liddle J, Marshall J, Ohan V, Pollard MO, et al. Twelve years of SAMtools and BCFtools. GigaScience. 2021;10:giab008.

Article  PubMed  PubMed Central  Google Scholar 

Broad Institute. Picard Tools. http://broadinstitute.github.io/picard/.

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;20:1297–303.

Article  CAS  PubMed  PubMed Central  Google Scholar 

GATK Broad Institute, Caetano-Anolles D. Somatic short variant discovery (SNVs + Indels) https://gatk.broadinstitute.org/hc/en-us/articles/360035894731-Somatic-short-variant-discovery-SNVs-Indels.

Benjamin D, Sato T, Cibulskis K, Getz G, Stewart C, Lichtenstein L. Calling somatic SNVs and Indels with Mutect2. bioRxiv; 2019. p. 861054. https://www.biorxiv.org/content/https://doi.org/10.1101/861054v1.

McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GRS, Thormann A, et al. The ensembl variant effect predictor. Genome Biol. 2016;17:122.

Article  PubMed  PubMed Central  Google Scholar 

Kumar P, Henikoff S, Ng PC. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc. 2009;4:1073–81.

Article  CAS  PubMed  Google Scholar 

Adzhubei I, Jordan DM, Sunyaev SR. Predicting functional effect of human missense mutations using PolyPhen-2. Curr Protoc Hum Genet. 2013. https://doi.org/10.1002/0471142905.hg0720s76.

Article  PubMed  PubMed Central  Google Scholar 

Kandoth C. mskcc/vcf2maf: vcf2maf v1.6.19. 2020. https://doi.org/10.5281/zenodo.593251.

Mayakonda A, Lin D-C, Assenov Y, Plass C, Koeffler HP. Maftools: efficient and comprehensive analysis of somatic variants in cancer. Genome Res. 2018;28:1747–56.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lappalainen I, Lopez J, Skipper L, Hefferon T, Spalding JD, Garner J, et al. dbVar and DGVa: public archives for genomic structural variation. Nucleic Acids Res. 2013;41:D936–41.

Article  CAS  PubMed  Google Scholar 

Amemiya HM, Kundaje A, Boyle AP. The ENCODE Blacklist: identification of problematic regions of the genome. Sci Rep. 2019;9:9354.

Article  PubMed  PubMed Central