Ignite Creation Date:
2024-05-06 @ 1:18 PM
Last Modification Date:
2024-10-26 @ 1:11 PM
Study NCT ID:
NCT03982446
Status:
COMPLETED
Last Update Posted:
2021-02-12
First Post:
2019-06-03
Brief Title:
Germline Mutations in Pancreatic Adenocarcinoma
Sponsor:
Hellenic Cooperative Oncology Group
Organization:
Hellenic Cooperative Oncology Group
Study Overview
Official Title:
Prevalence of Germline Pathogenic Mutations in Patients With Pancreatic Adenocarcinoma
Status:
COMPLETED
Status Verified Date:
2020-02
Last Known Status:
None
Delayed Posting:
No
If Stopped, Why?:
Not Stopped
Has Expanded Access:
False
If Expanded Access, NCT#:
N/A
Has Expanded Access, NCT# Status:
N/A
Acronym:
PaMPA
Brief Summary:
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
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
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 05 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 hasnt 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 38 to 97 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 manufacturers 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
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 hasnt 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 38 to 97 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 manufacturers 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 Oversight
Has Oversight DMC:
None
Is a FDA Regulated Drug?:
False
Is a FDA Regulated Device?:
False
Is an Unapproved Device?:
None
Is a PPSD?:
None
Is a US Export?:
None
Is an FDA AA801 Violation?:
None