Prospective, Multi-Institutional, Real-Time Next-Generation Sequencing of Pancreatic Cyst Fluid Reveals Diverse Genomic Alterations That Improve the Clinical Management of Pancreatic Cysts

Alessandro Paniccia, Patricio M. Polanco, Brian A. Boone, Abigail I. Wald, Kevin McGrath, Randall E. Brand, Asif Khalid, Nisa Kubiliun, Anne Marie O'Broin-Lennon, Walter G. Park, Jason Klapman, Benjamin Tharian, Sumant Inamdar, Kenneth Fasanella, John Nasr, Jennifer Chennat, Rohit Das, John DeWitt, Jeffrey J. Easler, Benjamin BickHarkirat Singh, Kimberly J. Fairley, Savreet Sarkaria, Tarek Sawas, Wasseem Skef, Adam Slivka, Anna Tavakkoli, Shyam Thakkar, Victoria Kim, Hendrikus Dutch Vanderveldt, Allyson Richardson, Michael B. Wallace, Bhaumik Brahmbhatt, Megan Engels, Charles Gabbert, Mohannad Dugum, Samer El-Dika, Yasser Bhat, Sanjay Ramrakhiani, Gennadiy Bakis, Daniil Rolshud, Gordon Millspaugh, Thomas Tielleman, Carl Schmidt, John Mansour, Wallis Marsh, Melanie Ongchin, Barbara Centeno, Sara E. Monaco, N. Paul Ohori, Sigfred Lajara, Elizabeth D. Thompson, Ralph H. Hruban, Phoenix D. Bell, Katelyn Smith, Jennifer B. Permuth, Christopher Vandenbussche, Wayne Ernst, Maria Grupillo, Cihan Kaya, Melissa Hogg, Jin He, Christopher L. Wolfgang, Kenneth K. Lee, Herbert Zeh, Amer Zureikat, Marina N. Nikiforova, Aatur D. Singhi

Research output: Contribution to journalArticlepeer-review


Background & Aims: Next-generation sequencing (NGS) of pancreatic cyst fluid is a useful adjunct in the assessment of patients with pancreatic cyst. However, previous studies have been retrospective or single institutional experiences. The aim of this study was to prospectively evaluate NGS on a multi-institutional cohort of patients with pancreatic cyst in real time. Methods: The performance of a 22-gene NGS panel (PancreaSeq) was first retrospectively confirmed and then within a 2-year timeframe, PancreaSeq testing was prospectively used to evaluate endoscopic ultrasound–guided fine-needle aspiration pancreatic cyst fluid from 31 institutions. PancreaSeq results were correlated with endoscopic ultrasound findings, ancillary studies, current pancreatic cyst guidelines, follow-up, and expanded testing (Oncomine) of postoperative specimens. Results: Among 1933 PCs prospectively tested, 1887 (98%) specimens from 1832 patients were satisfactory for PancreaSeq testing. Follow-up was available for 1216 (66%) patients (median, 23 months). Based on 251 (21%) patients with surgical pathology, mitogen-activated protein kinase/GNAS mutations had 90% sensitivity and 100% specificity for a mucinous cyst (positive predictive value [PPV], 100%; negative predictive value [NPV], 77%). On exclusion of low-level variants, the combination of mitogen-activated protein kinase/GNAS and TP53/SMAD4/CTNNB1/mammalian target of rapamycin alterations had 88% sensitivity and 98% specificity for advanced neoplasia (PPV, 97%; NPV, 93%). Inclusion of cytopathologic evaluation to PancreaSeq testing improved the sensitivity to 93% and maintained a high specificity of 95% (PPV, 92%; NPV, 95%). In comparison, other modalities and current pancreatic cyst guidelines, such as the American Gastroenterology Association and International Association of Pancreatology/Fukuoka guidelines, show inferior diagnostic performance. The sensitivities and specificities of VHL and MEN1/loss of heterozygosity alterations were 71% and 100% for serous cystadenomas (PPV, 100%; NPV, 98%), and 68% and 98% for pancreatic neuroendocrine tumors (PPV, 85%; NPV, 95%), respectively. On follow-up, serous cystadenomas with TP53/TERT mutations exhibited interval growth, whereas pancreatic neuroendocrine tumors with loss of heterozygosity of ≥3 genes tended to have distant metastasis. None of the 965 patients who did not undergo surgery developed malignancy. Postoperative Oncomine testing identified mucinous cysts with BRAF fusions and ERBB2 amplification, and advanced neoplasia with CDKN2A alterations. Conclusions: PancreaSeq was not only sensitive and specific for various pancreatic cyst types and advanced neoplasia arising from mucinous cysts, but also reveals the diversity of genomic alterations seen in pancreatic cysts and their clinical significance.

Original languageEnglish (US)
Pages (from-to)117-133.e7
Issue number1
StatePublished - Jan 2023


  • Diagnosis
  • Early Detection
  • Pancreas
  • Pancreatic Cancer
  • Pancreatic Neoplasm

ASJC Scopus subject areas

  • Hepatology
  • Gastroenterology


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