Exome sequencing identifies nonsegregating nonsense ATM and PALB2 variants in familial pancreatic cancer.

We sequenced 11 germline exomes from five families with familial pancreatic cancer (FPC). One proband had a germline nonsense variant in ATM with somatic loss of the variant allele. Another proband had a nonsense variant in PALB2 with somatic loss of the variant allele. Both variants were absent in a relative with FPC. These findings question the causal mechanisms of ATM and PALB2 in these families and highlight challenges in identifying the causes of familial cancer syndromes using exome sequencing

Genomics-Driven Precision Medicine for Advanced Pancreatic Cancer: Early Results from the COMPASS Trial

Purpose: To perform real-time whole genome sequencing (WGS) and RNA sequencing (RNASeq) of advanced pancreatic ductal adenocarcinoma (PDAC) to identify predictive mutational and transcriptional features for better treatment selection.Experimental Design: Patients with advanced PDAC were prospectively recruited prior to first-line combination chemotherapy. Fresh tumor tissue was acquired by image-guided percutaneous core biopsy for WGS and RNASeq. Laser capture microdissection was performed for all cases. Primary endpoint was feasibility to report WGS results prior to first disease assessment CT scan at 8 weeks. The main secondary endpoint was discovery of patient subsets with predictive mutational and transcriptional signatures.Results: Sixty-three patients underwent a tumor biopsy between December 2015 and June 2017. WGS and RNASeq were successful in 62 (98%) and 60 (95%), respectively. Genomic results were reported at a median of 35 days (range, 19-52 days) from biopsy, meeting the primary feasibility endpoint. Objective responses to first-line chemotherapy were significantly better in patients with the classical PDAC RNA subtype compared with those with the basal-like subtype (P = 0.004). The best progression-free survival was observed in those with classical subtype treated with m-FOLFIRINOX. GATA6 expression in tumor measured by RNA in situ hybridization was found to be a robust surrogate biomarker for differentiating classical and basal-like PDAC subtypes. Potentially actionable genetic alterations were found in 30% of patients.Conclusions: Prospective genomic profiling of advanced PDAC is feasible, and our early data indicate that chemotherapy response differs among patients with different genomic/transcriptomic subtype

Abstract 3157: Loss of heterozygosity as a molecular ‘second hit’ In familial pancreatic cancer.

Abstract BACKGROUND/HYPOTHESIS: Familial Pancreatic Cancer (FPC) has an autosomal dominant, variable penetrant mode of inheritance with &amp;gt;80% of its genetic cause yet to be discovered. We hypothesize that a high density DNA microarray analysis of Formalin-Fixed Paraffin Embedded (FFPE) FPC tumors will yield novel regions of genomic loss harboring disease causing FPC gene(s). METHODS: 158 FFPE FPC tumor specimens with matched normal tissue were reviewed by a pancreatic pathologist and tumors with &amp;lt;70% cellularity underwent laser capture microdissection. The samples with &amp;gt;70% cellularity were microdissected directly from marked unstained slides. A total of 74 samples were DNA extracted, whole genome amplified and processed on the Affymetrix 660K Oncoscan Microarray. Copy number analysis was performed using Nexus Copy Number Variation Version 6.1 software employing the SNP-FASST2 segmentation and Allele Specific Copy Number Analysis of Tumors (ASCAT) algorithms. PRELIMINARY RESULTS: A pair-wise analysis of 55 FPC samples with matched normal tissue was performed. Recurrent regions of loss of heterozygosity (LOH) were known loci of importance in pancreatic tumorigenesis, including CDKN2A, p53 and SMAD4. Copy neutral/gain LOH was observed throughout the genome and may account for &amp;gt;35% of chromosomal loss. Recurrent novel genetic loci displaying LOH was observed on chromosomes: 3p(25%), 5q(18%), 6p(22%), 12q(18%) and Xq (42%). Examination of 2 FPC siblings elucidates shared loss regions spanning the 3p22.2-3p22.3 and 17p13.3 loci. Candidate tumor suppressor genes (TSGs) of interest include DCLK3, SERPINF1, SERPINF2 and SMYD4. CONCLUSION: We have described for the first time the presence of copy neutral/gain LOH in FPC highlighting previously unknown regions displaying genetic loss. Further confirmation with quantitative PCR, integrating with germline exome sequencing data, and validation of putative TSGs shared by members of high risk FPC kindreds will help uncover novel genes associated with this disease. Citation Format: Zaheer S. Kanji, Stefano Serra, Spring Holter, Ayelet Borgida, Robert Grant, Steven Gallinger. Loss of heterozygosity as a molecular ‘second hit’ In familial pancreatic cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3157. doi:10.1158/1538-7445.AM2013-3157</jats:p

Abstract 12: Germline BRCA mutations in an unselected cohort of patients with pancreatic adenocarcinoma

Abstract This is the first prospective study to determine the frequency of BRCA1 and BRCA2 germline mutations in an unselected series of patients with pancreatic adenocarcinoma. Patients with histologically or clinically confirmed pancreatic adenocarcinoma were approached at a single cancer centre to enroll in the IRB-approved Ontario Pancreas Cancer Study. Patients provided informed consent and cancer family history data was obtained. Blood was collected and analyzed by Sanger sequencing and MLPA for germline variants in BRCA1 and BRCA2. All predicted deleterious germline variants were confirmed by a clinical laboratory on an independent blood sample. Pathogenic germline mutations were identified in 12/234 (5%) of unselected incident pancreatic adenocarcinomas. BRCA1 mutations accounted for 1.2% (3/234) and BRCA2 accounted for 3.8% (9/234) cases. For the cohort, average age of pancreatic adenocarcinoma diagnosis was 65 years (27-91) and 46% were female. Previous primary cancer was reported in 24% of cases and 12% were of Ashkenazi Jewish descent. A family history of breast and/or ovarian cancer was reported in 25% of cases; however, of these with a family history, 1/3 did not meet NCCN guidelines to warrant germline BRCA analysis. Pancreatic cancer in another relative was reported in 12% of cases. A personal history of a previous primary cancer diagnosis and a family history of breast and/or ovarian cancer were significantly associated with germline BRCA mutations. Previous studies of BRCA mutations in pancreatic adenocarcinoma have been limited to retrospective case series and incomplete germline analysis. Our study shows that germline BRCA mutations account for a significant proportion of pancreatic adenocarcinoma, regardless of family history of breast and ovarian cancer. Increased identification of patients with germline BRCA mutations and pancreatic adenocarcinoma may allow for tailored chemotherapy through the use of platinum agents or PARP inhibitors. Citation Format: Spring Holter, Ayelet Borgida, Anna Dodd, Steven Narod, Mohammad Akbari, Malcolm Moore, Steven Gallinger. Germline BRCA mutations in an unselected cohort of patients with pancreatic adenocarcinoma. [abstract]. In: Proceedings of the AACR Special Conference: Cancer Susceptibility and Cancer Susceptibility Syndromes; Jan 29-Feb 1, 2014; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(23 Suppl):Abstract nr 12. doi:10.1158/1538-7445.CANSUSC14-12</jats:p