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Methodology

Identification of Tissue of Origin in Cancer of Unknown Primary using a Targeted Bisulfite Sequencing Panel

, , , , , , , & show all
Pages 615-628 | Received 19 Nov 2021, Accepted 07 Apr 2022, Published online: 27 Apr 2022

References

  • Rassy E , PavlidisN. Progress in refining the clinical management of cancer of unknown primary in the molecular era. Nat. Rev. Clin. Oncol.17(9), 541–554 (2020).
  • Kwee TC , KweeRM. Combined FDG-PET/CT for the detection of unknown primary tumors: systematic review and meta-analysis. Eur. Radiol.19(3), 731–744 (2009).
  • Rassy E , PavlidisN. The currently declining incidence of cancer of unknown primary. Cancer Epidemiol.61, 139–141 (2019).
  • Park SY , KimBH , KimJH , LeeS , KangGH. Panels of immunohistochemical markers help determine primary sites of metastatic adenocarcinoma. Arch. Pathol. Lab. Med.131(10), 1561–1567 (2007).
  • Kandalaft PL , GownAM. Practical applications in immunohistochemistry: carcinomas of unknown primary site. Arch. Pathol. Lab. Med.140(6), 508–523 (2016).
  • Kei S , AdeyiOA. Practical application of lineage-specific immunohistochemistry markers: transcription factors (sometimes) behaving badly. Arch. Pathol. Lab. Med.144(5), 626–643 (2020).
  • Tothill RW , KowalczykA , RischinDet al. An expression-based site of origin diagnostic method designed for clinical application to cancer of unknown origin. Cancer Res.65(10), 4031–4040 (2005).
  • Ferracin M , PedrialiM , VeroneseAet al. MicroRNA profiling for the identification of cancers with unknown primary tissue-of-origin. J. Pathol.225(1), 43–53 (2011).
  • Varadhachary GR , SpectorY , AbbruzzeseJLet al. Prospective gene signature study using microRNA to identify the tissue of origin in patients with carcinoma of unknown primary. Clin. Cancer Res.17(12), 4063–4070 (2011).
  • Hainsworth JD , RubinMS , SpigelDRet al. Molecular gene expression profiling to predict the tissue of origin and direct site-specific therapy in patients with carcinoma of unknown primary site: a prospective trial of the Sarah Cannon Research Institute. J. Clin. Oncol.31(2), 217–223 (2013).
  • Fernandez AF , AssenovY , Martin-SuberoJIet al. A DNA methylation fingerprint of 1628 human samples. Genome Res.22(2), 407–419 (2012).
  • Moran S , VizosoM , Martinez-CardúsAet al. Validation of DNA methylation profiling in formalin-fixed paraffin-embedded samples using the Infinium HumanMethylation450 Microarray. Epigenetics9(6), 829–833 (2014).
  • Moran S , Martinez-CardusA , SayolsSet al. Epigenetic profiling to classify cancer of unknown primary: a multicentre, retrospective analysis. Lancet Oncol.17(10), 1386–1395 (2016).
  • Capper D , JonesDTW , SillMet al. DNA methylation-based classification of central nervous system tumours. Nature555(7697), 469–474 (2018).
  • Xia D , LeonAJ , CabaneroMet al. Minimalist approaches to cancer tissue-of-origin classification by DNA methylation. Mod. Pathol.33(10), 1874–1888 (2020).
  • Lu MY , ChenTY , WilliamsonDFKet al. AI-based pathology predicts origins for cancers of unknown primary. Nature594(7861), 106–110 (2021).
  • Schubert M , LindgreenS , OrlandoL. AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Res. Notes9, 88 (2016).
  • Krueger F , AndrewsSR. Bismark: a flexible aligner and methylation caller for bisulfite-seq applications. Bioinformatics27(11), 1571–1572 (2011).
  • Virtanen P , GommersR , OliphantTEet al. SciPy 1.0: fundamental algorithms for scientific computing in Python. Nat. Methods17(3), 261–272 (2020).
  • Walt SVD , ColbertSC , VaroquauxG. The NumPy array: a structure for efficient numerical computation. Comput. Sci. Eng.13(2), 22–30 (2011).
  • Pedregosa F , VaroquauxG , GramfortAet al. Scikit-learn: machine learning in Python. J. Mach. Learn. Res.12(Oct), 2825–-2830 (2011).
  • Valero-Mora PM . ggplot2: elegant graphics for data analysis. J. Stat. Softw.35(1), 1–3 (2010).
  • McInnes L , HealyJ , MelvilleJ. UMAP: Uniform Manifold Approximation and Projection for dimension reduction. (2018).
  • Anderson GG , WeissLM. Determining tissue of origin for metastatic cancers: meta-analysis and literature review of immunohistochemistry performance. Appl. Immunohistochem. Mol. Morphol.18(1), 3–8 (2010).
  • Weiss LM , ChuP , SchroederBEet al. Blinded comparator study of immunohistochemical analysis versus a 92-gene cancer classifier in the diagnosis of the primary site in metastatic tumors. J. Mol. Diagn.15(2), 263–269 (2013).
  • Penson A , CamachoN , ZhengYet al. Development of genome-derived tumor type prediction to inform clinical cancer care. JAMA Oncol.6(1), 84–91 (2020).
  • Horlings HM , Van LaarRK , KerstJMet al. Gene expression profiling to identify the histogenetic origin of metastatic adenocarcinomas of unknown primary. J. Clin. Oncol.26(27), 4435–4441 (2008).
  • Varadhachary GR , TalantovD , RaberMNet al. Molecular profiling of carcinoma of unknown primary and correlation with clinical evaluation. J. Clin. Oncol.26(27), 4442–4448 (2008).
  • Kerr SE , SchnabelCA , SullivanPSet al. Multisite validation study to determine performance characteristics of a 92-gene molecular cancer classifier. Clin. Cancer Res.18(14), 3952–3960 (2012).
  • Fizazi K , MaillardA , PenelNet al. LBA15_PR – a phase III trial of empiric chemotherapy with cisplatin and gemcitabine or systemic treatment tailored by molecular gene expression analysis in patients with carcinomas of an unknown primary (CUP) site (GEFCAPI 04). Ann. Oncol.30, v851 (2019).
  • Hayashi H , KurataT , TakiguchiYet al. Randomized phase II trial comparing site-specific treatment based on gene expression profiling with carboplatin and paclitaxel for patients with cancer of unknown primary site. J. Clin. Oncol.37(7), 570–579 (2019).
  • Ross JS , WangK , GayLet al. Comprehensive genomic profiling of carcinoma of unknown primary site: new routes to targeted therapies. JAMA Oncol.1(1), 40–49 (2015).
  • Hayashi H , TakiguchiY , MinamiHet al. Site-specific and targeted therapy based on molecular profiling by next-generation sequencing for cancer of unknown primary site: a nonrandomized phase 2 clinical trial. JAMA Oncol.6(12), 1931–1938 (2020).
  • Kacmarczyk TJ , FallMP , ZhangXet al. ‘Same difference’: comprehensive evaluation of four DNA methylation measurement platforms. Epigenetics Chromatin11(1), 21 (2018).
  • Xia D , LeonAJ , CabaneroMet al. Minimalist approaches to cancer tissue-of-origin classification by DNA methylation. Mod. Pathol.33(10), 1874–1888 (2020).
  • Leitheiser M , CapperD , SeegererPet al. Machine learning models predict the primary sites of head and neck squamous cell carcinoma metastases based on DNA methylation. J. Pathol.256(4), 378–387 (2022).
  • Guo S , DiepD , PlongthongkumN , FungHL , ZhangK , ZhangK. Identification of methylation haplotype blocks aids in deconvolution of heterogeneous tissue samples and tumor tissue-of-origin mapping from plasma DNA. Nat. Genet.49(4), 635–642 (2017).
  • Kang S , LiQ , ChenQet al. CancerLocator: non-invasive cancer diagnosis and tissue-of-origin prediction using methylation profiles of cell-free DNA. Genome Biol.18(1), 53 (2017).
  • Shen SY , SinghaniaR , FehringerGet al. Sensitive tumour detection and classification using plasma cell-free DNA methylomes. Nature563(7732), 579–583 (2018).
  • Nassiri F , ChakravarthyA , FengSet al. Detection and discrimination of intracranial tumors using plasma cell-free DNA methylomes. Nat. Med.26(7), 1044–1047 (2020).
  • Nuzzo PV , BerchuckJE , KorthauerKet al. Detection of renal cell carcinoma using plasma and urine cell-free DNA methylomes. Nat. Med.26(7), 1041–1043 (2020).
  • Liu MC , OxnardGR , KleinEAet al. Sensitive and specific multi-cancer detection and localization using methylation signatures in cell-free DNA. Ann. Oncol.31(6), 745–759 (2020).
  • Sun Z , VaisvilaR , HussongLMet al. Nondestructive enzymatic deamination enables single-molecule long-read amplicon sequencing for the determination of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution. Genome Res.31(2), 291–300 (2021).

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