Singal G et al (2019) Association of patient characteristics and tumor genomics with clinical outcomes among patients with non-small cell lung cancer using a clinicogenomic database. JAMA 321(14):1391–1399

Article  PubMed  PubMed Central  Google Scholar 

Levy SE, Myers RM (2016) Advancements in next-generation sequencing. Annu Rev Genomics Hum Genet 17:95–115

Article  PubMed  Google Scholar 

Satam H et al (2023) Next-generation sequencing technology: current trends and advancements. Biology (Basel) 12:7

Google Scholar 

Goodwin S, McPherson JD, McCombie WR (2016) Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet 17(6):333–351

Article  PubMed  PubMed Central  Google Scholar 

Rothberg JM et al (2011) An integrated semiconductor device enabling non-optical genome sequencing. Nature 475(7356):348–352

Article  PubMed  Google Scholar 

Uhlen M, Quake SR (2023) Sequential sequencing by synthesis and the next-generation sequencing revolution. Trends Biotechnol 41(12):1565–1572

van Dijk EL, Naquin D, Gorrichon K, Jaszczyszyn Y, Ouazahrou R, Thermes C, Hernandez C (2023) Genomics in the long-read sequencing era. Trends Genet 39(9):649–671

Rhoads A, Au KF (2015) PacBio sequencing and its applications. Genom Proteomics Bioinforma 13(5):278–289

Article  Google Scholar 

Eid J et al (2009) Real-time DNA sequencing from single polymerase molecules. Science 323(5910):133–138

Article  PubMed  Google Scholar 

Mikheyev AS, Tin MM (2014) A first look at the Oxford Nanopore MinION sequencer. Mol Ecol Resour 14(6):1097–1102

Article  PubMed  Google Scholar 

Quick J, Quinlan AR, Loman NJ (2014) A reference bacterial genome dataset generated on the MinION portable single-molecule nanopore sequencer. Gigascience 3:22

Article  PubMed  PubMed Central  Google Scholar 

Chaisson MJ et al (2015) Resolving the complexity of the human genome using single-molecule sequencing. Nature 517(7536):608–611

Article  PubMed  Google Scholar 

Wenger AM et al (2019) Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome. Nat Biotechnol 37(10):1155–1162

Article  PubMed  PubMed Central  Google Scholar 

Vollger MR et al (2020) Improved assembly and variant detection of a haploid human genome using single-molecule, high-fidelity long reads. Ann Hum Genet 84(2):125–140

Article  PubMed  Google Scholar 

Volden R et al (2018) Improving nanopore read accuracy with the R2C2 method enables the sequencing of highly multiplexed full-length single-cell cDNA. Proc Natl Acad Sci U S A 115(39):9726–9731

Article  PubMed  PubMed Central  Google Scholar 

Lee I et al (2020) Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing. Nat Methods 17(12):1191–1199

Article  PubMed  PubMed Central  Google Scholar 

Simpson JT et al (2017) Detecting DNA cytosine methylation using nanopore sequencing. Nat Methods 14(4):407–410

Article  PubMed  Google Scholar 

Vaser R et al (2017) Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res 27(5):737–746

Article  PubMed  PubMed Central  Google Scholar 

Bonenfant Q, Noe L, Touzet H (2023) Porechop_ABI: discovering unknown adapters in Oxford Nanopore Technology sequencing reads for downstream trimming. Bioinform Adv 3(1):vbac085

Article  PubMed  Google Scholar 

Salmela L, Rivals E (2014) LoRDEC: accurate and efficient long read error correction. Bioinformatics 30(24):3506–3514

Article  PubMed  PubMed Central  Google Scholar 

Yang X et al (2013) V-Phaser 2: variant inference for viral populations. BMC Genomics 14:674

Article  PubMed  PubMed Central  Google Scholar 

Boza V, Brejova B, Vinar T (2017) DeepNano: deep recurrent neural networks for base calling in MinION nanopore reads. PLoS ONE 12(6):e0178751

Article  PubMed  PubMed Central  Google Scholar 

Rang FJ, Kloosterman WP, de Ridder J (2018) From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy. Genome Biol 19(1):90

Article  PubMed  PubMed Central  Google Scholar 

Wang X, Liotta L (2011) Clinical bioinformatics: a new emerging science. J Clin Bioinforma 1(1):1

Article  PubMed  PubMed Central  Google Scholar 

Roy S et al (2018) Standards and guidelines for validating next-generation sequencing bioinformatics pipelines: a joint recommendation of the Association for Molecular Pathology and the College of American Pathologists. J Mol Diagn 20(1):4–27

Article  PubMed  Google Scholar 

Roy S et al (2016) Next-generation sequencing informatics: challenges and strategies for implementation in a clinical environment. Arch Pathol Lab Med 140(9):958–975

Article  PubMed  Google Scholar 

Thankaswamy-Kosalai S, Sen P, Nookaew I (2017) Evaluation and assessment of read-mapping by multiple next-generation sequencing aligners based on genome-wide characteristics. Genomics 109(3–4):186–191

Article  PubMed  Google Scholar 

Cibulskis K et al (2013) Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol 31(3):213–219

Article  PubMed  PubMed Central  Google Scholar 

Koboldt DC et al (2012) VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res 22(3):568–576

Article  PubMed  PubMed Central  Google Scholar 

Wang K, Li M, Hakonarson H (2010) ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res 38(16):e164

Article  PubMed  PubMed Central  Google Scholar 

den Dunnen JT et al (2016) HGVS recommendations for the description of sequence variants: 2016 update. Hum Mutat 37(6):564–569

Article  Google Scholar 

Li MM et al (2017) Standards and guidelines for the interpretation and reporting of sequence variants in cancer: a joint consensus recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists. J Mol Diagn 19(1):4–23

Article  PubMed  PubMed Central  Google Scholar 

Robinson JT et al (2011) Integrative genomics viewer. Nat Biotechnol 29(1):24–26

Article  PubMed  PubMed Central  Google Scholar 

Sayers EW, O’Sullivan C, Karsch-Mizrachi I (2022) Using GenBank and SRA methods. Mol Biol 2443:1–25

Google Scholar 

Kadri S et al (2022) Containers in bioinformatics: applications, practical considerations, and best practices in molecular pathology. J Mol Diagn 24(5):442–454

Article  PubMed  Google Scholar 

Conway JR, Warner JL, Rubinstein WS, Miller RS (2019) Next-generation sequencing and the clinical oncology workflow: data challenges, proposed solutions, and a call to action. JCO Precis Oncol 3:PO.19.00232

Heeke AL, Pishvaian MJ, Lynce F, Xiu J, Brody JR, Chen WJ, Baker TM, Marshall JL, Isaacs C (2018) Prevalence of homologous recombination-related gene mutations across multiple cancer types. JCO Precis Oncol 2018

Pratt D, Sahm F, Aldape K (2021) DNA methylation profiling as a model for discovery and precision diagnostics in neuro-oncology. Neuro Oncol 23(23 5):S16–S29

Article  PubMed  PubMed Central  Google Scholar 

Alexandrov LB et al (2020) The repertoire of mutational signatures in human cancer. Nature 578(7793):94–101

Article  PubMed  PubMed Central  Google Scholar 

Rekhtman N et al (2020) SMARCA4-deficient thoracic sarcomatoid tumors represent primarily smoking-related undifferentiated carcinomas rather than primary thoracic sarcomas. J Thorac Oncol 15(2):231–247

Article  PubMed  Google Scholar 

Fumet JD et al (2020) Tumour mutational burden as a biomarker for immunotherapy: Current data and emerging concepts. Eur J Cancer 131:40–50

Article  PubMed  PubMed Central  Google Scholar 

Rizvi NA et al (2015) Cancer immunology. Mutational landscape determines sensitivity to PD-1 blockade in non-small cell lung cancer. Science 348(6230):124–8

Article  PubMed  PubMed Central  Google Scholar 

Sha D et al (2020) Tumor mutational burden as a predictive biomarker in solid tumors. Cancer Discov 10(12):1808–1825

Article  PubMed  PubMed Central  Google Scholar 

Sholl LM et al (2020) The promises and challenges of tumor mutation burden as an immunotherapy biomarker: a perspective from the International Association for the Study of Lung Cancer Pathology Committee. J Thorac Oncol 15(9):1409–1424

Article  PubMed  PubMed Central  Google Scholar 

Jardim DL et al (2021) The challenges of tumor mutational burden as an immunotherapy biomarker. Cancer Cell 39(2):154–173

Article