Alessandro Paniccia1, Patricio M Polanco2, Brian A Boone3, Abigail I Wald4, Kevin McGrath5, Randall E Brand5, Asif Khalid6, Nisa Kubiliun7, Anne Marie O'Broin-Lennon8, Walter G Park9, Jason Klapman10, Benjamin Tharian11, Sumant Inamdar11, Kenneth Fasanella5, John Nasr12, Jennifer Chennat5, Rohit Das5, John DeWitt13, Jeffrey J Easler13, Benjamin Bick13, Harkirat Singh5, Kimberly J Fairley14, Savreet Sarkaria5, Tarek Sawas7, Wasseem Skef15, Adam Slivka5, Anna Tavakkoli7, Shyam Thakkar14, Victoria Kim1, Hendrikus Dutch Vanderveldt7, Allyson Richardson9, Michael B Wallace16, Bhaumik Brahmbhatt17, Megan Engels17, Charles Gabbert5, Mohannad Dugum18, Samer El-Dika9, Yasser Bhat19, Sanjay Ramrakhiani19, Gennadiy Bakis20, Daniil Rolshud20, Gordon Millspaugh20, Thomas Tielleman7, Carl Schmidt3, John Mansour2, Wallis Marsh3, Melanie Ongchin1, Barbara Centeno21, Sara E Monaco22, N Paul Ohori4, Sigfred Lajara4, Elizabeth D Thompson23, Ralph H Hruban23, Phoenix D Bell4, Katelyn Smith4, Jennifer B Permuth10, Christopher Vandenbussche23, Wayne Ernst4, Maria Grupillo4, Cihan Kaya4, Melissa Hogg24, Jin He25, Christopher L Wolfgang26, Kenneth K Lee1, Herbert Zeh2, Amer Zureikat1, Marina N Nikiforova27, Aatur D Singhi28. 1. Department of Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA, USA. 2. Department of Clinical Sciences, Surgery, University of Texas Southwestern, Dallas, TX, USA. 3. Department of Surgery, West Virginia University Health Sciences Center, Morgantown, WV, USA. 4. Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA. 5. Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA. 6. Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, PA, USA; VA Pittsburgh Healthcare System, Pittsburgh, PA, USA. 7. Department of Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA. 8. The Sol Goldman Pancreatic Cancer Research Center, Department of Medicine, Johns Hopkins Medical Institutions, Baltimore, MD, USA. 9. Department of Medicine, Stanford University, Stanford, CA, USA. 10. Department of Gastrointestinal Oncology, Moffitt Cancer Center, Tampa, FL, USA. 11. Department of Internal Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA. 12. Department of Medicine, Wheeling Hospital, West Virginia University Health Sciences Center, Morgantown, WV, USA. 13. Department of Gastroenterology and Hepatology, Indiana University Health Medical Center, Indianapolis, IN, USA. 14. Department of Medicine, Section of Gastroenterology & Hepatology, West Virginia University Health Sciences Center, Morgantown, WV, USA. 15. Department of Medicine, Division of Gastroenterology and Hepatology, Loma Linda University Medical Center, Loma Linda, CA, USA. 16. Department of Medicine, Division of Gastroenterology and Hepatology, Mayo Clinic, Jacksonville, FL, USA; Sheikh Shakhbout Medical City, Abu Dhabi, UAE. 17. Department of Medicine, Division of Gastroenterology and Hepatology, Mayo Clinic, Jacksonville, FL, USA. 18. Digestive Health Center, Essentia Health-Duluth Clinic, Duluth, MN, USA. 19. Department of Gastroenterology, Palo Alto Medical Foundation (PAMF), Mountain View, CA, USA. 20. Portland Gastroenterology Center, Portland, ME, USA. 21. Department of Pathology, Moffitt Cancer Center, Tampa, FL, USA. 22. Department of Pathology, Geisinger Medical Center, Danville, PA, USA. 23. The Sol Goldman Pancreatic Cancer Research Center, Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, MD, USA. 24. Department of Surgery, NorthShore University Health System, Chicago, IL, USA. 25. The Sol Goldman Pancreatic Cancer Research Center, Department of Surgery, Johns Hopkins Medical Institutions, Baltimore, MD, USA. 26. The Sol Goldman Pancreatic Cancer Research Center, Department of Surgery, Johns Hopkins Medical Institutions, Baltimore, MD, USA; Department of Surgery, NYU Langone Health, New York, NY, USA. 27. Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA. Electronic address: nikiforovamn@upmc.edu. 28. Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA, USA. Electronic address: singhiad@upmc.edu.
Abstract
BACKGROUND AND AIMS: Next-generation sequencing (NGS) of pancreatic cyst fluid is a useful adjunct in the assessment of pancreatic cyst (PC) patients. 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 PC patients in real-time. METHODS: The performance of a 22-gene NGS panel (PancreaSeq) was first retrospectively confirmed and then within a two-year timeframe, PancreaSeq testing was prospectively used to evaluate endoscopic ultrasound (EUS)-guided fine-needle aspiration PC fluid from 31 institutions. PancreaSeq results were correlated with EUS 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, MAPK/GNAS mutations had 90% sensitivity and 100% specificity for a mucinous cyst (PPV, 100%; NPV, 77%). Upon exclusion of low-level variants, the combination of MAPK/GNAS and TP53/SMAD4/CTNNB1/mTOR 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 AGA and IAP/Fukuoka guidelines, show inferior diagnostic performance. The sensitivities and specificities of VHL and MEN1/LOH alterations were 71% and 100% for serous cystadenomas (SCAs) (PPV, 100%; NPV, 98%), and 68% and 98% for pancreatic neuroendocrine tumors (PanNETs) (PPV, 85%; NPV, 95%), respectively. Upon follow-up, SCAs with TP53/TERT mutations exhibited interval growth, while PanNETs with LOH 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 PC types and advanced neoplasia arising from mucinous cysts, but also reveals the diversity of genomic alterations seen in PCs and their clinical significance.
BACKGROUND AND AIMS: Next-generation sequencing (NGS) of pancreatic cyst fluid is a useful adjunct in the assessment of pancreatic cyst (PC) patients. 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 PC patients in real-time. METHODS: The performance of a 22-gene NGS panel (PancreaSeq) was first retrospectively confirmed and then within a two-year timeframe, PancreaSeq testing was prospectively used to evaluate endoscopic ultrasound (EUS)-guided fine-needle aspiration PC fluid from 31 institutions. PancreaSeq results were correlated with EUS 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, MAPK/GNAS mutations had 90% sensitivity and 100% specificity for a mucinous cyst (PPV, 100%; NPV, 77%). Upon exclusion of low-level variants, the combination of MAPK/GNAS and TP53/SMAD4/CTNNB1/mTOR 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 AGA and IAP/Fukuoka guidelines, show inferior diagnostic performance. The sensitivities and specificities of VHL and MEN1/LOH alterations were 71% and 100% for serous cystadenomas (SCAs) (PPV, 100%; NPV, 98%), and 68% and 98% for pancreatic neuroendocrine tumors (PanNETs) (PPV, 85%; NPV, 95%), respectively. Upon follow-up, SCAs with TP53/TERT mutations exhibited interval growth, while PanNETs with LOH 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 PC types and advanced neoplasia arising from mucinous cysts, but also reveals the diversity of genomic alterations seen in PCs and their clinical significance.