Germline Mutations in Pancreatic Adenocarcinoma (PaMPA)

Prevalence of Germline Pathogenic Mutations in Patients With Pancreatic Adenocarcinoma

This study will assess the hereditary component of pancreatic cancer in the largest series of patients up to date through the parallel analysis of 62 cancer-associated genes. The investigators will obtain germline DNA from blood samples that have been collected from 2000 to 2019 from patients with pancreatic cancer. The investigators plan to analyze germline DNA for mutations and single nucleotide polymorphisms (SNPs) in genes that have been previously linked to a predisposition towards cancer.

The outcome can provide useful insight on the overall understanding of pancreatic pathogenesis while possible associations with age of diagnosis, tumor stage and other cancer types might arise. In addition to that, it can lead to the characterization of new variants or even new genes that predispose to pancreatic cancer.

Confirmed deleterious mutations in established cancer genes can provide valuable clinical information that can lead to effective, individualized patient management. Furthermore, family relatives of the individuals found to carry mutations can also benefit from established screening protocols for various cancer types, such as frequent colonoscopies in the case of an MMR mutation predisposing for Lynch syndrome, or preventative surgeries in the case of a deleterious BRCA1 or BRCA2 mutation. In addition to that, specific therapies that have been previously shown to be effective in breast or ovarian cancer patients with BRCA1 & BRCA2 mutations, such as platinum-based chemotherapy and PARP inhibitors can be also effective in mutations carriers with pancreatic cancer.

Study Overview

• Status: Completed
• Conditions: Pancreatic Cancer; Hereditary Cancer; Predisposition, Genetic; Germline Mutation Abnormality
• Intervention / Treatment: Genetic: Mutations

Detailed Description

Background Pancreatic ductal adenocarcinoma has poor prognosis mainly highlighted by the low 5-year survival rate, which is estimated to be around 6%. Although pancreatic cancer incidence is approximately 0.5% in the general population, it has a high-mortality rate. It is being registered as the fourth leading cause of cancer-related deaths in the United States. Poor prognosis is mainly attributed to the lack of efficient treatment options.

With the majority of pancreatic adenocarcinoma cases being sporadic, familial clustering (defined by the presence of at least two first degree relatives with pancreatic cancer) is observed in ~20% of the cases, whereas a clear genetic cause is identified in approximately half of these cases. Pancreatic cancer is known to occur in a range of cancer predisposing syndromes, such as hereditary breast and ovarian cancer, Peutz-Jeghers, familial adenomatous polyposis, Lynch, Li-Fraumeni and familial atypical multiple mole syndromes, while there have been clear associations with loss-of-function mutations in non-syndromic cancer genes, such as PALB2 and ATM. In addition, individuals carrying mutations in PRSS1 gene that predisposes for hereditary pancreatitis are also considered to be at high-risk for pancreatic cancer. It is therefore clear that pancreatic cancer is not related with a single cancer predisposition gene, but with numerous known and probably yet to be discovered, cancer susceptibility genes.

On the other hand, the accurate fraction of genetic predisposition in pancreatic cancer hasn't been determined. Previous studies have evaluated the prevalence of loss-of-function mutations in known cancer predisposition genes in pancreatic cancer patients through the use of multi-gene panels. The mutation yield ranged from 3.8% to 9.7% in genes that were previously found relevant to pancreatic cancer predisposition.

Through these studies, it has been highlighted that family history and stage of pancreatic cancer or age at diagnosis is not always a predictor of an underlying genetic factor, while phenotypic heterogeneity is usually associated with mutation status. The search for novel predisposition genes in pancreatic cancer patients without family history is ongoing through candidate genes analysis or through whole exome sequencing.

Research methodology Clinicopathological characteristics

Genomic DNA from pancreatic cancer patients will be retrospectively and prospectively collected from the Hellenic Cooperative Oncology Group (HeCOG) Tumor Repository, through years 2000-2019. Written informed consent has already been obtained from all patients for the use and storage of their biologic material along with their approval for their participation in research studies. The study will be in agreement with the 1975 Helsinki statement, revised in 1983.

Clinicopathologic characteristics of patients with pancreatic cancer will be retrieved form their medical record. Diagnosis will be confirmed through pathology reports, which will also provide information about grade, proliferation rate, histological subtype and lymphovascular invasion. From the patient medical record, tumor size, nodal involvement as well as metastatic lesions (TNM staging) will be reported. Importantly, detailed family history will be collected. The collection of these information will be in compliance with the regulations of the Bioethics committees of participating hospitals. Clinicopathological characteristics will be correlated with the different genomic abnormalities identified by sequencing.

Germline DNA extraction

Blood samples will be collected from patients with pancreatic cancer. Germline DNA from white blood cells will be isolated using a commercially available blood DNA extraction kit. Germline DNA will then be subjected to mechanical fragmentation via sonication to reach a DNA size of approximately 200-250 bp for downstream next-generation sequencing (NGS) analysis.

Next-Generation Sequencing

Targeted capture enrichment NGS relies on in-solution hybridization of DNA libraries with TACS (Targeted Capture Enrichment Sequences) for the identification of germline mutations in cancer patients. First, TACS that target mutations associated with hereditary cancer (in a total of 62 cancer predisposing genes) are designed and prepared by PCR followed by biotinylation. Biotinylated TACS will then be immobilized on streptavidin coated magnetic beads for subsequent hybridisation with the DNA libraries. DNA libraries are prepared from patient derived-germline DNA that fulfill quality control criteria (DNA yield, DNA integrity and fragment size) according to established protocols. Library preparation involves the 3' end and 5' end adaptor ligation and each DNA library will be barcoded using unique oligonucleotide DNA sequences to allow subsequent discrimination after sequencing. Subsequent to barcoding, samples will undergo hybridization using custom made 5'-biotynylated TACS followed by PCR amplification. Finally, enriched DNA libraries will be normalised and pooled on a NGS platform prior to paired-end sequencing using manufacturer's protocols.

Bioinformatic and Data Analysis Sequence data from leucocyte (buffy coat) DNA will be demultiplexed and aligned to the human genome (hg19) using appropriate aligner algorithms (BWA) to generate a BAM file. A combination of variant calling algorithms will be used to call germline mutations. Local realignment will be performed for accurate detection of small insertions and deletions and appropriate algorithms to detect rearrangements. Bioinformatics tools for copy number alterations (CNAs) calling such as ASCAT-2, CNVkit or ANACONDA will be used for the assessment of focal gene amplification or deletion events. Read depth-based analysis will also be taken into consideration for assessment of gene-level CNAs. Appropriate variant annotators will be used to annotate the identified alterations to each gene. Germline variant databases such as ClinVar will be used for the classification of variants according to the ACMG guidelines.

• Study Type: Observational
• Enrollment (Actual): 549

Contacts and Locations

Study Locations

• Greece
  • Athens, Greece
    • Hellenic Oncology Cooperative Group

Participation Criteria

Eligibility Criteria

• Ages Eligible for Study: 16 years to 88 years (Adult, Older Adult)
• Accepts Healthy Volunteers: No
• Genders Eligible for Study: All

• Sampling Method: Non-Probability Sample

Study Population

Genomic DNA from patients with pancreatic cancer will be retrospectively and prospectively collected from the Hellenic Cooperative Oncology Group (HeCOG) Tumor Repository, through years 2000-2019. Written informed consent has already been obtained from all patients for the use and storage of their biologic material along with their approval for their participation in research studies. The study will be in agreement with the 1975 Helsinki statement, revised in 1983.

Description

Inclusion Criteria:

• Patients diagnosed with adenocarcinoma of the pancreas
• All disease stages

Exclusion criteria

• Patients with pancreatic cancer, other than adenocarcinoma
• Non-eligible blood samples

Study Plan

How is the study designed?

Design Details

• Observational Models: Cohort
• Time Perspectives: Retrospective

Number of groups / cohorts

2

Cohorts and Interventions

Group / Cohort	Intervention / Treatment
Patients with germline mutations; This group will comprise of patients with pancreatic cancer who carry pathogenic mutations in genes associated with a predisposition to cancer.	Genetic: Mutations
Patients without germline mutations; This group will comprise of patients with pancreatic cancer who did not carry pathogenic mutations in any of the genes tested, that have been previously shown to be associated with a predisposition to cancer.	Genetic: Mutations

What is the study measuring?

Primary Outcome Measures

Outcome Measure	Measure Description	Time Frame
Overall Survival	Evaluation of overall survival in patients with pancreatic cancer, from the date of treatment start until verified disease progression, death from any cause or date of last contact whichever occurred first	Time Frame: through the completion of the study, up to 2 years

Collaborators and Investigators

• Sponsor: Hellenic Cooperative Oncology Group

Publications and helpful links

General Publications

• Fountzilas E, Eliades A, Koliou GA, Achilleos A, Loizides C, Tsangaras K, Pectasides D, Sgouros J, Papakostas P, Rallis G, Psyrri A, Papadimitriou C, Oikonomopoulos G, Ferentinos K, Koumarianou A, Zarkavelis G, Dervenis C, Aravantinos G, Bafaloukos D, Kosmidis P, Papaxoinis G, Theochari M, Varthalitis I, Kentepozidis N, Rigakos G, Saridaki Z, Nikolaidi A, Christopoulou A, Fostira F, Samantas E, Kypri E, Ioannides M, Koumbaris G, Fountzilas G, Patsalis PC. Clinical Significance of Germline Cancer Predisposing Variants in Unselected Patients with Pancreatic Adenocarcinoma. Cancers (Basel). 2021 Jan 8;13(2):198. doi: 10.3390/cancers13020198.

Study record dates

Study Major Dates

• Study Start (Actual): March 1, 2016
• Primary Completion (Actual): November 1, 2019
• Study Completion (Actual): January 3, 2020

Study Registration Dates

• First Submitted: June 3, 2019
• First Submitted That Met QC Criteria: June 10, 2019
• First Posted (Actual): June 11, 2019

Study Record Updates

• Last Update Posted (Actual): February 12, 2021
• Last Update Submitted That Met QC Criteria: February 11, 2021
• Last Verified: February 1, 2020

More Information

Terms related to this study

• Additional Relevant MeSH Terms: Pathologic Processes; Neoplasms by Histologic Type; Neoplasms; Carcinoma; Neoplasms, Glandular and Epithelial; Disease Attributes; Adenocarcinoma; Disease Susceptibility; Genetic Predisposition to Disease
• Other Study ID Numbers: Germline_pancreas

Plan for Individual participant data (IPD)

• Plan to Share Individual Participant Data (IPD)?: No

Drug and device information, study documents

• Studies a U.S. FDA-regulated drug product: No
• Studies a U.S. FDA-regulated device product: No