Table of Contents Author Guidelines Submit a Manuscript
Analytical Cellular Pathology
Volume 2018, Article ID 2898962, 7 pages
https://doi.org/10.1155/2018/2898962
Research Article

Prospective Evaluation of Unprocessed Core Needle Biopsy DNA and RNA Yield from Lung, Liver, and Kidney Tumors: Implications for Cancer Genomics

1Interventional Radiology Section, Department of Radiology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
2Department of Surgery, Urology Service, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
3Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
4Division of Oncology, Department of Medicine, Washington University Medical School, USA
5Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA

Correspondence should be addressed to Jeremy C. Durack; gro.ccksm@jkcarud

Received 18 July 2018; Accepted 29 October 2018; Published 10 December 2018

Academic Editor: Maria M. Picken

Copyright © 2018 Mikhail T. Silk et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. P. B. Chapman, A. Hauschild, C. Robert et al., “Improved survival with vemurafenib in melanoma with BRAF V600E mutation,” The New England Journal of Medicine, vol. 364, no. 26, pp. 2507–2516, 2011. View at Publisher · View at Google Scholar · View at Scopus
  2. B. J. Druker, M. Talpaz, D. J. Resta et al., “Efficacy and safety of a specific inhibitor of the BCR-ABL tyrosine kinase in chronic myeloid leukemia,” The New England Journal of Medicine, vol. 344, no. 14, pp. 1031–1037, 2001. View at Publisher · View at Google Scholar · View at Scopus
  3. D. J. Slamon, B. Leyland-Jones, S. Shak et al., “Use of chemotherapy plus a monoclonal antibody against her2 for metastatic breast cancer that overexpresses HER2,” The New England Journal of Medicine, vol. 344, no. 11, pp. 783–792, 2001. View at Publisher · View at Google Scholar · View at Scopus
  4. D. Marshall, J. M. Laberge, B. Firetag, T. Miller, and R. K. Kerlan, “The changing face of percutaneous image-guided biopsy: molecular profiling and genomic analysis in current practice,” Journal of Vascular and Interventional Radiology, vol. 24, no. 8, pp. 1094–1103, 2013. View at Publisher · View at Google Scholar · View at Scopus
  5. S. Gupta, M. J. Wallace, J. F. Cardella et al., “Quality improvement guidelines for percutaneous needle biopsy,” Journal of Vascular and Interventional Radiology, vol. 21, no. 7, pp. 969–975, 2010. View at Publisher · View at Google Scholar · View at Scopus
  6. A. L. Tam, H. J. Lim, I. I. Wistuba et al., “Image-guided biopsy in the era of personalized cancer care: proceedings from the Society of Interventional Radiology Research Consensus Panel,” Journal of Vascular and Interventional Radiology, vol. 27, no. 1, pp. 8–19, 2016. View at Publisher · View at Google Scholar · View at Scopus
  7. A. Sankin, A. A. Hakimi, N. Mikkilineni et al., “The impact of genetic heterogeneity on biomarker development in kidney cancer assessed by multiregional sampling,” Cancer Medicine, vol. 3, no. 6, pp. 1485–1492, 2014. View at Publisher · View at Google Scholar · View at Scopus
  8. H. Chen, R. Luthra, R. S. Goswami, R. R. Singh, and S. Roy-Chowdhuri, “Analysis of pre-analytic factors affecting the success of clinical next-generation sequencing of solid organ malignancies,” Cancers, vol. 7, no. 3, pp. 1699–1715, 2015. View at Publisher · View at Google Scholar · View at Scopus
  9. S. Roy-Chowdhuri, R. S. Goswami, H. Chen et al., “Factors affecting the success of next-generation sequencing in cytology specimens,” Cancer Cytopathology, vol. 123, no. 11, pp. 659–668, 2015. View at Publisher · View at Google Scholar · View at Scopus
  10. P. R. Geraghty, S. T. Kee, G. McFarlane, M. K. Razavi, D. Y. Sze, and M. D. Dake, “CT-guided transthoracic needle aspiration biopsy of pulmonary nodules: needle size and pneumothorax rate,” Radiology, vol. 229, no. 2, pp. 475–481, 2003. View at Publisher · View at Google Scholar · View at Scopus
  11. G. R. Vijayaraghavan, S. Vedantham, V. Rangan et al., “Effect of needle gauge and lobe laterality on parenchymal liver biopsy outcome: a retrospective analysis,” Abdominal Imaging, vol. 40, no. 5, pp. 1223–1229, 2015. View at Publisher · View at Google Scholar · View at Scopus
  12. K. M. Corapi, J. L. T. Chen, E. M. Balk, and C. E. Gordon, “Bleeding complications of native kidney biopsy: a systematic review and meta-analysis,” American Journal of Kidney Diseases, vol. 60, no. 1, pp. 62–73, 2012. View at Publisher · View at Google Scholar · View at Scopus
  13. J. N. McCutcheon and G. Giaccone, “Next-generation sequencing: targeting targeted therapies,” Clinical Cancer Research, vol. 21, no. 16, pp. 3584-3585, 2015. View at Publisher · View at Google Scholar · View at Scopus
  14. M. Srinivasan, D. Sedmak, and S. Jewell, “Effect of fixatives and tissue processing on the content and integrity of nucleic acids,” The American Journal of Pathology, vol. 161, no. 6, pp. 1961–1971, 2002. View at Publisher · View at Google Scholar · View at Scopus
  15. R. L. Schmidt, B. L. Witt, L. E. Lopez-Calderon, and L. J. Layfield, “The influence of rapid onsite evaluation on the adequacy rate of fine-needle aspiration cytology: a systematic review and meta-analysis,” American Journal of Clinical Pathology, vol. 139, no. 3, pp. 300–308, 2013. View at Publisher · View at Google Scholar · View at Scopus
  16. M. C. Austin, C. Smith, C. C. Pritchard, and J. F. Tait, “DNA yield from tissue samples in surgical pathology and minimum tissue requirements for molecular testing,” Archives of Pathology & Laboratory Medicine, vol. 140, no. 2, pp. 130–133, 2016. View at Publisher · View at Google Scholar · View at Scopus
  17. N. Jamshidi, D. Huang, F. G. Abtin et al., “Genomic adequacy from solid tumor core needle biopsies of ex vivo tissue and in vivo lung masses: prospective study,” Radiology, vol. 282, no. 3, pp. 903–912, 2016. View at Publisher · View at Google Scholar · View at Scopus
  18. S. A. Fuhrman, L. C. Lasky, and C. Limas, “Prognostic significance of morphologic parameters in renal cell carcinoma,” American Journal of Surgical Pathology, vol. 6, no. 7, pp. 655–664, 1982. View at Publisher · View at Google Scholar
  19. T. Muto, H. J. R. Bussey, and B. C. Morson, “The evolution of cancer of the colon and rectum,” Cancer, vol. 36, no. 6, pp. 2251–2270, 1975. View at Publisher · View at Google Scholar · View at Scopus
  20. J. J. Elser, M. M. Kyle, M. S. Smith, and J. D. Nagy, “Biological stoichiometry in human cancer,” PLoS One, vol. 2, no. 10, article e1028, 2007. View at Publisher · View at Google Scholar · View at Scopus
  21. S. B. Solomon, M. F. Zakowski, W. Pao et al., “Core needle lung biopsy specimens: adequacy for EGFR and KRAS mutational analysis,” American Journal of Roentgenology, vol. 194, no. 1, pp. 266–269, 2010. View at Publisher · View at Google Scholar · View at Scopus
  22. W. J. Heerink, G. H. de Bock, G. J. de Jonge, H. J. M. Groen, R. Vliegenthart, and M. Oudkerk, “Complication rates of CT-guided transthoracic lung biopsy: meta-analysis,” European Radiology, vol. 27, no. 1, pp. 138–148, 2017. View at Publisher · View at Google Scholar · View at Scopus
  23. D. T. Cheng, T. N. Mitchell, A. Zehir et al., “Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable cancer Targets (MSK-IMPACT): a hybridization capture-based next-generation sequencing clinical assay for solid tumor molecular oncology,” The Journal of Molecular Diagnostics, vol. 17, no. 3, pp. 251–264, 2015. View at Publisher · View at Google Scholar · View at Scopus
  24. J. Shendure and H. Ji, “Next-generation DNA sequencing,” Nature Biotechnology, vol. 26, no. 10, pp. 1135–1145, 2008. View at Publisher · View at Google Scholar · View at Scopus
  25. M. L. Metzker, “Sequencing technologies—the next generation,” Nature Reviews. Genetics, vol. 11, no. 1, pp. 31–46, 2010. View at Publisher · View at Google Scholar · View at Scopus
  26. J. Li, C. Fu, T. P. Speed, W. Wang, and W. F. Symmans, “Accurate RNA sequencing from formalin-fixed cancer tissue to represent high-quality transcriptome from frozen tissue,” JCO Precision Oncology, vol. 2018, no. 2, pp. 1–9, 2018. View at Publisher · View at Google Scholar
  27. S. K. Tian, J. K. Killian, N. Rekhtman et al., “Optimizing workflows and processing of cytologic samples for comprehensive analysis by next-generation sequencing: Memorial Sloan Kettering Cancer Center experience,” Archives of Pathology & Laboratory Medicine, vol. 140, no. 11, pp. 1200–1205, 2016. View at Publisher · View at Google Scholar · View at Scopus
  28. M. T. Silk, S. Yazdanfar, D. V. Dylov, T. Silk, S. B. Solomon, and J. C. Durack, “Rapid determination of core needle biopsy adequacy using optical spectroscopy,” in SIR 39th annual scientific meeting, p. S117, San Diego, CA, USA, 2014.
  29. R. R. White, H. B. Xie, M. R. Gottfried et al., “Significance of histological response to preoperative chemoradiotherapy for pancreatic cancer,” Annals of Surgical Oncology, vol. 12, no. 3, pp. 214–221, 2005. View at Publisher · View at Google Scholar · View at Scopus
  30. R. Kalluri and M. Zeisberg, “Fibroblasts in cancer,” Nature Reviews. Cancer, vol. 6, no. 5, pp. 392–401, 2006. View at Publisher · View at Google Scholar · View at Scopus
  31. R. Kadaba, H. Birke, J. Wang et al., “Imbalance of desmoplastic stromal cell numbers drives aggressive cancer processes,” The Journal of Pathology, vol. 230, no. 1, pp. 107–117, 2013. View at Publisher · View at Google Scholar · View at Scopus
  32. J. F. Pan, P. C. Yang, D. B. Chang, Y. C. Lee, S. H. Kuo, and K. T. Luh, “Needle aspiration biopsy of malignant lung masses with necrotic centers: improved sensitivity with ultrasonic guidance,” Chest, vol. 103, no. 5, pp. 1452–1456, 1993. View at Publisher · View at Google Scholar · View at Scopus
  33. S. Sartori, I. Nielsen, L. Trevisani, P. Tombesi, P. Ceccotti, and V. Abbasciano, “Contrast-enhanced sonography as guidance for transthoracic biopsy of a peripheral lung lesion with large necrotic areas,” Journal of Ultrasound in Medicine, vol. 23, no. 1, pp. 133–136, 2004. View at Publisher · View at Google Scholar · View at Scopus
  34. K. De Jaeger, F. M. Merlo, M.-C. Kavanagh, A. W. Fyles, D. Hedley, and R. P. Hill, “Heterogeneity of tumor oxygenation: relationship to tumor necrosis, tumor size, and metastasis,” International Journal of Radiation Oncology, Biology, Physics, vol. 42, no. 4, pp. 717–721, 1998. View at Publisher · View at Google Scholar · View at Scopus
  35. Thermo Scientific, “260/280 and 260/230 Ratios,” T009-Technical Bulletin, pp. 1-2, 2008, http://www.nhm.ac.uk/content/dam/nhmwww/our-science/dpts-facilities-staff/Coreresearchlabs/nanodrop.pdf. View at Google Scholar