Pancreatic Cyst Fluid NGS Analysis - PancreaSeq®

Targeted Mutation Detection by Next Generation Sequencing

Test Details

PancreaSeq® – Targeted mutation detection by next generation sequencing in PANCREATIC cyst fluid fine needle aspiration (FNA) specimens. PancreaSeq® panel offers simultaneous sequencing and detection of mutations in 8 pancreatic cancer-related genes.

Genes Tested for Mutations

AKT1, CTNNB1, GNAS, KRAS, PIK3CA, PTEN, TP53, VHL

Background

Pancreatic cysts are becoming increasing encountered in clinical practice. While many pancreatic cysts, such as pseudocysts and serous cystadenomas (SCAs), have a benign clinical course; others, such as intraductal papillary mucinous neoplasms (IPMNs) and mucinous cystic neoplasms (MCNs), represent precursor lesions to invasive pancreatic adenocarcinoma. However, preoperatively distinguishing pancreatic cysts from one another can be diagnostically challenging. Recent whole-exome sequencing of pancreatic cysts has identified a limited number of genetic mutations that may be used diagnostically to classify pancreatic cysts.

IPMNs are frequently characterized by mutations in the GNAS (codon 201) and/or KRAS (codons 12, 13 and/or 61) genes. MCNs can also harbor mutations in KRAS, but not GNAS. In contrast, SCAs have mutations in VHL and/or loss of heterozygosity in or adjacent to VHL and do not contain mutations in GNAS or KRAS. Lastly, solid-pseudopapillary neoplasms are characterized by mutations in CTNNB1 and lack GNAS, KRAS, and VHL mutations. In addition to accurately identifying IPMNs, not all IPMNs follow a malignant course. Studies have shown that IPMNs harboring mutations in p53 and the phosphatidyl-3 kinase (PI3K) pathway including PIK3CA, PTEN, and AKT1 can be associated with high-grade dysplasia and early invasive pancreatic cancers.

References

  1. Khalid, et al. Molecular diagnosis of solid and cystic lesions of the pancreas. Clin Lab Med 2005 Mar; 25(1):101-16.
  2. Furukawa, et al. Whole-exome sequencing uncovers frequent GNAS mutations in intraductal papillary mucinous neoplasms of the Pancreas. Sci Rep. 2011 1: 161.
  3. Wu, et al. Whole-exome sequencing of neoplastic cysts of the pancreas reveals recurrent mutations in components of ubiquitin-dependent pathways. PNAS 2011 108(52): 21188-93.
  4. Nikiforova, et al. Integration of KRAS testing in the diagnosis of pancreatic cystic lesions: a clinical experience of 618 pancreatic cysts. Mod Pathol 2013 Nov; 26(11):1478-87.
  5. Garcia-Carracedo, et al. Loss of PTEN expression is associated with poor prognosis in patients with intraductal papillary mucinous neoplasms of the pancreas. Clin Cancer Res 2013 Dec; 19(24): 6830-41.

Methodology

PancreaSeq® NGS Panel is performed on DNA isolated from cyst fluid FNA material collected into preservative solution (please contact MGP laboratory at 412-864-6162 for collection protocol and solution tubes), fixed FNA specimens, or formalin-fixed, paraffin-embedded (FFPE) tumor tissue. The analysis is performed using next-generation, semiconductor-based sequencing (Ion Torrent PGM/Proton platform). Input DNA is amplified using the AmpliSeq technology (Ion Torrent), after which the amplicons are modified with adaptors, re-amplified, and subjected to emulsion PCR. The final products are sequenced on a 318 or P1 chip. The analytical sensitivity is 3-5% of mutant alleles for detection of mutations. The minimal required sequencing depth is 500x.

  • Input DNA: 10 ng

Pancreatic Cyst Fluid Requirements

Pancreatic cyst fluid should be collected in a sterile screw cap collection tube. These tubes may be provided by the laboratory upon request.

Other Specimen Types Requirements

Please contact the laboratory to discuss other specimen types that may be acceptable.

Shipping Conditions

Please contact the laboratory to discuss if shipping other specimen types.

Turnaround Time

7 – 14 days

Billing Information

For insurance or Institutional Prices, please call.

A REQUISITION FORM MUST ACCOMPANY ALL SAMPLES. Please include detailed clinical information.