Advertisement

Analytical Principles of Cancer Next Generation Sequencing

Published:August 22, 2022DOI:https://doi.org/10.1016/j.cll.2022.04.003

      Keywords

      To read this article in full you will need to make a payment

      Purchase one-time access:

      Academic & Personal: 24 hour online accessCorporate R&D Professionals: 24 hour online access
      One-time access price info
      • For academic or personal research use, select 'Academic and Personal'
      • For corporate R&D use, select 'Corporate R&D Professionals'

      Subscribers receive full online access to your subscription and archive of back issues up to and including 2002.

      Content published before 2002 is available via pay-per-view purchase only.

      Subscribe:

      Subscribe to Clinics in Laboratory Medicine
      Already a print subscriber? Claim online access
      Already an online subscriber? Sign in
      Institutional Access: Sign in to ScienceDirect

      References

        • Hellmann M.D.
        • Paz-Ares L.
        • Bernabe Caro R.
        • et al.
        Nivolumab plus ipilimumab in advanced non-small-cell lung cancer.
        N Engl J Med. 2019; 381: 2020-2031
        • Hellmann M.D.
        • Ciuleanu T.E.
        • Pluzanski A.
        • et al.
        Nivolumab plus ipilimumab in lung cancer with a high tumor mutational burden.
        N Engl J Med. 2018; 378: 2093-2104
        • Snyder A.
        • Makarov V.
        • Merghoub T.
        • et al.
        Genetic basis for clinical response to CTLA-4 blockade in melanoma.
        N Engl J Med. 2014; 371: 2189-2199
        • Samstein R.M.
        • Lee C.H.
        • Shoushtari A.N.
        • et al.
        Tumor mutational load predicts survival after immunotherapy across multiple cancer types.
        Nat Genet. 2019; 51: 202-206
        • Ferruelo A.
        • El-Assar M.
        • Lorente J.A.
        • et al.
        Transcriptional profiling and genotyping of degraded nucleic acids from autopsy tissue samples after prolonged formalin fixation times.
        Int J Clin Exp Pathol. 2011; 4: 156-161
        • Do H.
        • Dobrovic A.
        Sequence artifacts in DNA from formalin-fixed tissues: causes and strategies for minimization.
        Clin Chem. 2015; 61: 64-71
        • Rait V.K.
        • Zhang Q.
        • Fabris D.
        • et al.
        Conversions of formaldehyde-modified 2'-deoxyadenosine 5'-monophosphate in conditions modeling formalin-fixed tissue dehydration.
        J Histochem Cytochem. 2006; 54: 301-310
        • Jackson D.P.
        • Lewis F.A.
        • Taylor G.R.
        • et al.
        Tissue extraction of DNA and RNA and analysis by the polymerase chain reaction.
        J Clin Pathol. 1990; 43: 499-504
        • Lindahl T.
        Instability and decay of the primary structure of DNA.
        Nature. 1993; 362: 709-715
        • Robbe P.
        • Popitsch N.
        • Knight S.J.L.
        • et al.
        Clinical whole-genome sequencing from routine formalin-fixed, paraffin-embedded specimens: pilot study for the 100,000 Genomes Project.
        Genet Med. 2018; 20: 1196-1205
        • Berra C.M.
        • Torrezan G.T.
        • de Paula C.A.
        • et al.
        Use of uracil-DNA glycosylase enzyme to reduce DNA-related artifacts from formalin-fixed and paraffin-embedded tissues in diagnostic routine.
        Appl Cancer Res. 2019; 39: 7
        • Prentice L.M.
        • Miller R.R.
        • Knaggs J.
        • et al.
        Formalin fixation increases deamination mutation signature but should not lead to false positive mutations in clinical practice.
        PLoS One. 2018; 13: e0196434
        • David S.S.
        • O'Shea V.L.
        • Kundu S.
        Base-excision repair of oxidative DNA damage.
        Nature. 2007; 447: 941-950
        • de Leng W.W.
        • Gadellaa-van Hooijdonk C.G.
        • Barendregt-Smouter F.A.
        • et al.
        Targeted next generation sequencing as a reliable diagnostic assay for the detection of somatic mutations in tumours using minimal DNA amounts from formalin fixed paraffin embedded material.
        PLoS One. 2016; 11: e0149405
        • Prendergast E.N.
        • Elvin J.A.
        Genomic profiling of gynecologic cancers and implications for clinical practice.
        Curr Opin Obstet Gynecol. 2017; 29: 18-25
        • Zehir A.
        • Benayed R.
        • Shah R.H.
        • et al.
        Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients.
        Nat Med. 2017; 23: 703-713
        • Frampton G.M.
        • Fichtenholtz A.
        • Otto G.A.
        • et al.
        Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing.
        Nat Biotechnol. 2013; 31: 1023-1031
        • Williams H.L.
        • Walsh K.
        • Diamond A.
        • et al.
        Validation of the Oncomine focus panel for next-generation sequencing of clinical tumour samples.
        Virchows Arch. 2018; 473: 489-503
        • Aloraifi F.
        • McDevitt T.
        • Martiniano R.
        • et al.
        Detection of novel germline mutations for breast cancer in non-BRCA1/2 families.
        FEBS J. 2015; 282: 3424-3437
        • Farmer H.
        • McCabe N.
        • Lord C.J.
        • et al.
        Targeting the DNA repair defect in BRCA mutant cells as a therapeutic strategy.
        Nature. 2005; 434: 917-921
        • Sholl L.M.
        • Do K.
        • Shivdasani P.
        • et al.
        Institutional implementation of clinical tumor profiling on an unselected cancer population.
        JCI Insight. 2016; 1: e87062
        • Priestley P.
        • Baber J.
        • Lolkema M.P.
        • et al.
        Pan-cancer whole-genome analyses of metastatic solid tumours.
        Nature. 2019; 575: 210-216
        • Chrystoja C.C.
        • Diamandis E.P.
        Whole genome sequencing as a diagnostic test: challenges and opportunities.
        Clin Chem. 2014; 60: 724-733
        • Chen X.
        • Chang C.W.
        • Spoerke J.M.
        • et al.
        Low-pass whole-genome sequencing of circulating cell-free DNA demonstrates dynamic changes in genomic copy number in a squamous lung cancer clinical cohort.
        Clin Cancer Res. 2019; 25: 2254-2263
        • Ruhen O.
        • Mirzai B.
        • Clark M.E.
        • et al.
        Comparison of circulating tumour DNA and extracellular vesicle DNA by low-pass whole-genome sequencing reveals molecular drivers of disease in a breast cancer patient.
        Biomedicines. 2020; 9: 14
        • Smyth E.C.
        • Vlachogiannis G.
        • Hedayat S.
        • et al.
        EGFR amplification and outcome in a randomised phase III trial of chemotherapy alone or chemotherapy plus panitumumab for advanced gastro-oesophageal cancers.
        Gut. 2021; 70: 1632-1641
        • Samorodnitsky E.
        • Jewell B.M.
        • Hagopian R.
        • et al.
        Evaluation of hybridization capture versus amplicon-based methods for whole-exome sequencing.
        Hum Mutat. 2015; 36: 903-914
        • Mardis E.R.
        Next-generation sequencing platforms.
        Annu Rev Anal Chem (Palo Alto Calif). 2013; 6: 287-303
        • Kadri S.
        • Long B.C.
        • Mujacic I.
        • et al.
        Clinical validation of a next-generation sequencing genomic Oncology panel via cross-platform benchmarking against established amplicon sequencing assays.
        J Mol Diagn. 2017; 19: 43-56
        • Sakamoto Y.
        • Zaha S.
        • Suzuki Y.
        • et al.
        Application of long-read sequencing to the detection of structural variants in human cancer genomes.
        Comput Struct Biotechnol J. 2021; 19: 4207-4216
        • Leung S.K.
        • Jeffries A.R.
        • Castanho I.
        • et al.
        Full-length transcript sequencing of human and mouse cerebral cortex identifies widespread isoform diversity and alternative splicing.
        Cell Rep. 2021; 37: 110022
        • De Paoli-Iseppi R.
        • Gleeson J.
        • Clark M.B.
        Isoform age - splice isoform profiling using long-read technologies.
        Front Mol Biosci. 2021; 8: 711733
        • Wang Y.
        • Mashock M.
        • Tong Z.
        • et al.
        Changing technologies of RNA sequencing and Their applications in clinical Oncology.
        Front Oncol. 2020; 10: 447
        • Anastasiadou E.
        • Jacob L.S.
        • Slack F.J.
        Non-coding RNA networks in cancer.
        Nat Rev Cancer. 2018; 18: 5-18
        • Huarte M.
        • Rinn J.L.
        Large non-coding RNAs: missing links in cancer?.
        Hum Mol Genet. 2010; 19: R152-R161
        • Park H.J.
        • Baek I.
        • Cheang G.
        • et al.
        Comparison of RNA-based next-generation sequencing assays for the detection of NTRK gene fusions.
        J Mol Diagn. 2021; 23: 1443-1451
        • Davies K.D.
        • Lomboy A.
        • Lawrence C.A.
        • et al.
        DNA-based versus RNA-based detection of MET exon 14 skipping events in lung cancer.
        J Thorac Oncol. 2019; 14: 737-741
        • Varnier R.
        • Sajous C.
        • de Talhouet S.
        • et al.
        Using breast cancer gene expression signatures in clinical practice: unsolved issues, ongoing trials and future perspectives.
        Cancers (Basel). 2021; 13: 4840
        • Jensen M.B.
        • Laenkholm A.V.
        • Balslev E.
        • et al.
        The Prosigna 50-gene profile and responsiveness to adjuvant anthracycline-based chemotherapy in high-risk breast cancer patients.
        NPJ Breast Cancer. 2020; 6: 7
        • Roschewski M.
        • Phelan J.D.
        • Wilson W.H.
        Molecular classification and treatment of diffuse large B-cell lymphoma and primary Mediastinal B-cell lymphoma.
        Cancer J. 2020; 26: 195-205
        • Cacciotti C.
        • Fleming A.
        • Ramaswamy V.
        Advances in the molecular classification of pediatric brain tumors: a guide to the galaxy.
        J Pathol. 2020; 251: 249-261
        • Guerreiro Stucklin A.S.
        • Ramaswamy V.
        • Daniels C.
        • et al.
        Review of molecular classification and treatment implications of pediatric brain tumors.
        Curr Opin Pediatr. 2018; 30: 3-9
        • Rosati D.
        • Giordano A.
        Single-cell RNA sequencing and bioinformatics as tools to decipher cancer heterogenicity and mechanisms of drug resistance.
        Biochem Pharmacol. 2021; 195: 114811
        • Tang F.
        • Barbacioru C.
        • Wang Y.
        • et al.
        mRNA-Seq whole-transcriptome analysis of a single cell.
        Nat Methods. 2009; 6: 377-382
        • Andrews T.S.
        • Kiselev V.Y.
        • McCarthy D.
        • et al.
        Tutorial: guidelines for the computational analysis of single-cell RNA sequencing data.
        Nat Protoc. 2021; 16: 1-9
        • Alexandrov L.B.
        • Nik-Zainal S.
        • Wedge D.C.
        • et al.
        Signatures of mutational processes in human cancer.
        Nature. 2013; 500: 415-421
        • Seo K.Y.
        • Jelinsky S.A.
        • Loechler E.L.
        Factors that influence the mutagenic patterns of DNA adducts from chemical carcinogens.
        Mutat Res. 2000; 463: 215-246
        • Pang J.
        • Gindin T.
        • Mansukhani M.
        • et al.
        Microsatellite instability detection using a large next-generation sequencing cancer panel across diverse tumour types.
        J Clin Pathol. 2020; 73: 83-89
        • Bonneville R.
        • Krook M.A.
        • Chen H.Z.
        • et al.
        Detection of microsatellite instability biomarkers via next-generation sequencing.
        Methods Mol Biol. 2020; 2055: 119-132
        • Hause R.J.
        • Pritchard C.C.
        • Shendure J.
        • et al.
        Classification and characterization of microsatellite instability across 18 cancer types.
        Nat Med. 2016; 22: 1342-1350
        • Sahin I.H.
        • Akce M.
        • Alese O.
        • et al.
        Immune checkpoint inhibitors for the treatment of MSI-H/MMR-D colorectal cancer and a perspective on resistance mechanisms.
        Br J Cancer. 2019; 121: 809-818
        • Andre T.
        • Shiu K.K.
        • Kim T.W.
        • et al.
        Pembrolizumab in microsatellite-instability-high advanced colorectal cancer.
        N Engl J Med. 2020; 383: 2207-2218
        • Hellmann M.D.
        • Nathanson T.
        • Rizvi H.
        • et al.
        Genomic features of response to combination immunotherapy in patients with advanced non-small-cell lung cancer.
        Cancer Cell. 2018; 33: 843-852.e4
        • Van Allen E.M.
        • Miao D.
        • Schilling B.
        • et al.
        Genomic correlates of response to CTLA-4 blockade in metastatic melanoma.
        Science. 2015; 350: 207-211
        • Konstantinopoulos P.A.
        • Ceccaldi R.
        • Shapiro G.I.
        • et al.
        Homologous recombination deficiency: exploiting the fundamental vulnerability of ovarian cancer.
        Cancer Discov. 2015; 5: 1137-1154
        • Pennington K.P.
        • Walsh T.
        • Harrell M.I.
        • et al.
        Germline and somatic mutations in homologous recombination genes predict platinum response and survival in ovarian, fallopian tube, and peritoneal carcinomas.
        Clin Cancer Res. 2014; 20: 764-775
        • Vega D.M.
        • Yee L.M.
        • McShane L.M.
        • et al.
        Aligning tumor mutational burden (TMB) quantification across diagnostic platforms: phase II of the Friends of Cancer Research TMB Harmonization Project.
        Ann Oncol. 2021; 32: 1626-1636
        • Stenzinger A.
        • Endris V.
        • Budczies J.
        • et al.
        Harmonization and standardization of panel-based tumor mutational burden measurement: real-world results and recommendations of the quality in pathology study.
        J Thorac Oncol. 2020; 15: 1177-1189
        • Buchhalter I.
        • Rempel E.
        • Endris V.
        • et al.
        Size matters: dissecting key parameters for panel-based tumor mutational burden analysis.
        Int J Cancer. 2019; 144: 848-858
        • Zill O.A.
        • Banks K.C.
        • Fairclough S.R.
        • et al.
        The landscape of actionable genomic alterations in cell-free circulating tumor DNA from 21,807 advanced cancer patients.
        Clin Cancer Res. 2018; 24: 3528-3538
        • Jensen T.J.
        • Goodman A.M.
        • Kato S.
        • et al.
        Genome-wide sequencing of cell-free DNA identifies copy-number alterations that can Be used for monitoring response to immunotherapy in cancer patients.
        Mol Cancer Ther. 2019; 18: 448-458
        • Chae Y.K.
        • Oh M.S.
        Detection of minimal residual disease using ctDNA in lung cancer: current evidence and future directions.
        J Thorac Oncol. 2019; 14: 16-24
        • Khagi Y.
        • Goodman A.M.
        • Daniels G.A.
        • et al.
        Hypermutated circulating tumor DNA: correlation with response to checkpoint inhibitor-based immunotherapy.
        Clin Cancer Res. 2017; 23: 5729-5736
        • Gandara D.R.
        • Paul S.M.
        • Kowanetz M.
        • et al.
        Blood-based tumor mutational burden as a predictor of clinical benefit in non-small-cell lung cancer patients treated with atezolizumab.
        Nat Med. 2018; 24: 1441-1448
        • Schmitt M.W.
        • Kennedy S.R.
        • Salk J.J.
        • et al.
        Detection of ultra-rare mutations by next-generation sequencing.
        Proc Natl Acad Sci U S A. 2012; 109: 14508-14513
        • Young A.L.
        • Wong T.N.
        • Hughes A.E.
        • et al.
        Quantifying ultra-rare pre-leukemic clones via targeted error-corrected sequencing.
        Leukemia. 2015; 29: 1608-1611
        • Chen X.
        • Cherian S.
        Role of minimal residual disease testing in acute Myeloid leukemia.
        Clin Lab Med. 2021; 41: 467-483
        • Ball M.P.
        • Thakuria J.V.
        • Zaranek A.W.
        • et al.
        A public resource facilitating clinical use of genomes.
        Proc Natl Acad Sci U S A. 2012; 109: 11920-11927
        • Barretina J.
        • Caponigro G.
        • Stransky N.
        • et al.
        The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity.
        Nature. 2012; 483: 603-607
        • Zook J.M.
        • Catoe D.
        • McDaniel J.
        • et al.
        Extensive sequencing of seven human genomes to characterize benchmark reference materials.
        Sci Data. 2016; 3: 160025
        • Zook J.M.
        • McDaniel J.
        • Olson N.D.
        • et al.
        An open resource for accurately benchmarking small variant and reference calls.
        Nat Biotechnol. 2019; 37: 561-566