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

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.

A Combined DNA/RNA-based Next-Generation Sequencing Platform to Improve the Classification of Pancreatic Cysts and Early Detection of Pancreatic Cancer Arising From Pancreatic Cysts.

OBJECTIVE: We report the development and validation of a combined DNA/RNA next-generation sequencing (NGS) platform to improve the evaluation of pancreatic cysts. BACKGROUND AND AIMS: Despite a multidisciplinary approach, pancreatic cyst classification, such as a cystic precursor neoplasm, and the detection of high-grade dysplasia and early adenocarcinoma (advanced neoplasia) can be challenging. NGS of preoperative pancreatic cyst fluid improves the clinical evaluation of pancreatic cysts, but the recent identification of novel genomic alterations necessitates the creation of a comprehensive panel and the development of a genomic classifier to integrate the complex molecular results. METHODS: An updated and unique 74-gene DNA/RNA-targeted NGS panel (PancreaSeq Genomic Classifier) was created to evaluate 5 classes of genomic alterations to include gene mutations (e.g., KRAS, GNAS, etc.), gene fusions and gene expression. Further, CEA mRNA ( CEACAM5 ) was integrated into the assay using RT-qPCR. Separate multi-institutional cohorts for training (n=108) and validation (n=77) were tested, and diagnostic performance was compared to clinical, imaging, cytopathologic, and guideline data. RESULTS: Upon creation of a genomic classifier system, PancreaSeq GC yielded a 95% sensitivity and 100% specificity for a cystic precursor neoplasm, and the sensitivity and specificity for advanced neoplasia were 82% and 100%, respectively. Associated symptoms, cyst size, duct dilatation, a mural nodule, increasing cyst size, and malignant cytopathology had lower sensitivities (41-59%) and lower specificities (56-96%) for advanced neoplasia. This test also increased the sensitivity of current pancreatic cyst guidelines (IAP/Fukuoka and AGA) by >10% and maintained their inherent specificity. CONCLUSIONS: PancreaSeq GC was not only accurate in predicting pancreatic cyst type and advanced neoplasia but also improved the sensitivity of current pancreatic cyst guidelines.

Risk of Gastric Adenocarcinoma in a Multiethnic Population Undergoing Routine Care: An Electronic Health Records Cohort Study.

BACKGROUND: Gastric adenocarcinoma (GAC) is often diagnosed at advanced stages and portends a poor prognosis. We hypothesized that electronic health records (EHR) could be leveraged to identify individuals at highest risk for GAC from the population seeking routine care. METHODS: This was a retrospective cohort study, with endpoint of GAC incidence as ascertained through linkage to an institutional tumor registry. We utilized 2010 to 2020 data from the Palo Alto Medical Foundation, a large multispecialty practice serving Northern California. The analytic cohort comprised individuals ages 40-75 receiving regular ambulatory care. Variables collected included demographic, medical, pharmaceutical, social, and familial data. Electronic phenotyping was based on rule-based methods. RESULTS: The cohort comprised 316,044 individuals and approximately 2 million person-years (p-y) of observation. 157 incident GACs occurred (incidence 7.9 per 100,000 p-y), of which 102 were non-cardia GACs (incidence 5.1 per 100,000 p-y). In multivariable analysis, male sex [HR: 2.2, 95% confidence interval (CI): 1.6-3.1], older age, Asian race (HR: 2.5, 95% CI: 1.7-3.7), Hispanic ethnicity (HR: 1.9, 95% CI: 1.1-3.3), atrophic gastritis (HR: 4.6, 95% CI: 2.2-9.3), and anemia (HR: 1.9, 95% CI: 1.3-2.6) were associated with GAC risk; use of NSAID was inversely associated (HR: 0.3, 95% CI: 0.2-0.5). Older age, Asian race, Hispanic ethnicity, atrophic gastritis, and anemia were associated with non-cardia GAC. CONCLUSIONS: Routine EHR data can stratify the general population for GAC risk. IMPACT: Such methods may help triage populations for targeted screening efforts, such as upper endoscopy.

A retrograde-viewing device improves detection of adenomas in the colon: a prospective efficacy evaluation (with videos).

BACKGROUND: Colonoscopy may fail to detect neoplasia located on the proximal sides of haustral folds and flexures. The Third Eye Retroscope (TER) provides a simultaneous retrograde view that complements the forward view of a standard colonoscope. OBJECTIVE: To evaluate the added benefit for polyp detection during colonoscopy of a retrograde-viewing device. DESIGN: Open-label, prospective, multicenter study evaluating colonoscopy by using a TER in combination with a standard colonoscope. SETTING: Eight U.S. sites, including university medical centers, ambulatory surgery centers, a community hospital, and a physician's office. PATIENTS: A total of 249 patients (age range 55-80 years) presenting for screening or surveillance colonoscopy. INTERVENTIONS: After cecal intubation, the disposable TER was inserted through the instrument channel of the colonoscope. During withdrawal, the forward and retrograde video images were observed simultaneously on a wide-screen monitor. MAIN OUTCOME MEASUREMENTS: The number and sizes of lesions (adenomas and all polyps) detected with the standard colonoscope and the number and sizes of lesions found only because they were first detected with the TER. RESULTS: In the 249 subjects, 257 polyps (including 136 adenomas) were identified with the colonoscope alone. The TER allowed detection of 34 additional polyps (a 13.2% increase; P < .0001) including 15 additional adenomas (an 11.0% increase; P < .0001). For lesions 6 mm or larger, the additional detection rates with the TER for all polyps and for adenomas were 18.2% and 25.0%, respectively. For lesions 10 mm or larger, the additional detection rates with the TER for all polyps and for adenomas were 30.8% and 33.3%, respectively. In 28 (11.2%) individuals, at least 1 additional polyp was found with the TER. In 8 (3.2%) patients, the polyp detected with the TER was the only one found. Every polyp that was detected with the TER was subsequently located with the colonoscope and removed. For all polyps and for adenomas, the additional detection rates for the TER were 9.7%/4.1% in the left colon (the splenic flexure to the rectum) and 16.5%/14.9% in the right colon (the cecum to the transverse colon), respectively. LIMITATIONS: There was no randomization or comparison with a separate control group. CONCLUSIONS: A retrograde-viewing device revealed areas that were hidden from the forward-viewing colonoscope and allowed detection of 13.2% additional polyps, including 11.0% additional adenomas. Additional detection rates with the TER for adenomas 6 mm or larger and 10 mm or larger were 25.0% and 33.3%, respectively. ( CLINICAL TRIAL REGISTRATION NUMBER: NCT00657371.).

Treatment of hepatitis B and C following liver transplantation.

Advanced liver disease from hepatitis B virus (HBV) and hepatitis C virus (HCV) is the leading indication for orthotopic liver transplantation (OLT) worldwide. Our understanding of recurrent liver disease related to HBV and HCV in the setting of OLT has evolved rapidly in the past decade. Recurrent viral hepatitis may lead to graft failure, death, or the need for retransplantation. Until about a decade ago, HBV was considered a contraindication to OLT due to its frequent recurrence and development of associated liver disease. Medical therapy with hepatitis B immune globulin and nucleoside analogues has diminished the risk of HBV recurrence and led to improvement in patient and graft survival. Consequently, OLT is now considered to be the standard of care in patients with end-stage liver disease related to HBV. HCV recurrence after OLT is almost universal. Although short-term survival in patients undergoing OLT for HCV is similar to survival for those transplanted for other indications, recurrent HCV may have an impact on long-term patient and graft survival. A specific and effective therapy has not been defined for recurrent HCV following transplantation, but the combination of interferon and ribavirin appears promising. Optimal strategies to eradicate these viruses or to slow disease progression are continually being investigated in light of the disparity between supply and demand in a diminishing organ pool for OLT candidates.

Orlistat in the treatment of NASH: a case series.

Nonalcoholic steatohepatitis is now recognized as a common chronic liver disorder. Up to 16% of affected patients may progress to cirrhosis. The incidence and prevalence of this disease are noted to be increasing, in parallel with the nationwide increase in obesity and diabetes. Treatment options for these patients remain quite limited, however. Weight reduction has been advocated, but there are little data to support this practice, as most patients are unable to comply with the proper dietary modifications. We report three obese patients with biopsy-proven nonalcoholic steatohepatitis treated for 6-12 months with a weight reduction medication, orlistat, who lost between 22-42 lb, and had significant clinical and histopathological improvement on follow-up.

Biliary-venous fistula complicating transjugular intrahepatic portosystemic shunt presenting with recurrent bacteremia, jaundice, anemia and fever.

A 50-year-old White man with noncirrhotic portal hypertension presented with bleeding from gastric varices. Bleeding was initially managed with band ligation and subsequent transjugular intrahepatic portosystemic shunt (TIPS). Over the next few months, the patient had recurrent episodes of anemia, jaundice, fever and polymicrobial bacteremia. Computed tomography (CT) of the abdomen and chest, upper and lower endoscopy, endoscopic retrograde cholangiopancreatography (ERCP), and echocardiography failed to explain the bacteremia and anemia. Follow-up CT scan and Doppler sonography 9 months after placement showed TIPS was occluded. Repeat ERCP showed a bile leak with free run-off of contrast from the left hepatic duct into a vascular structure. The patient's status was upgraded for liver transplantation with Regional Review Board agreement and subsequently received a liver transplant. Gross examination of the native liver demonstrated a fistula between the left bile duct and the middle hepatic vein. Pathologic evaluation confirmed focal necrosis of the left hepatic duct communicating with an occluded TIPS and nodular regenerative hyperplasia consistent with noncirrhotic portal hypertension. Infection is rarely reported in a totally occluded TIPS. Biliary fistulas in patent TIPS have been treated by endoluminal stent graft and endoscopic sphincterotomy with biliary stent placement. Liver transplantation may be the preferred treatment if TIPS becomes infected following its complete occlusion.

Evolution of hepatitis C viral quasispecies after liver transplantation.

BACKGROUND & AIMS: To determine whether HCV quasispecies diversity correlated positively with liver disease progression after orthotopic liver transplantation (OLT). METHODS: We studied 11 patients undergoing OLT for HCV-related cirrhosis with recurrent hepatitis C in 2 groups according to the stage of hepatic fibrosis on follow-up. The mild group had stage 1 or 2 fibrosis; the severe group, stage 3 or 4 fibrosis. HCV quasispecies diversity was assessed by cloning and sequencing in pretransplantation and posttransplantation serum samples. RESULTS: In the mild fibrosis group, intrasample hypervariable region 1 (HVR1) genetic distance and nonsynonymous substitutions increased after OLT, whereas in the severe fibrosis group, these parameters decreased in follow-up. In contrast, intrasample diversity progressed similarly in both groups in the adjacent sequences flanking HVR1. There was an inverse correlation between the stage of hepatic fibrosis and amino acid complexity after OLT. Among all patients, the estimated rate of amino acid change was greater initially and became more constant after 36 months. CONCLUSIONS: After OLT, a more complex HCV HVR1 quasispecies population was associated with mild disease recurrence. Among those patients with severe recurrent hepatitis C, HCV appeared to be under greater immune pressure. The greatest change in viral amino acid sequences occurred in the first 36 months after OLT.