Interpreting Sequence Variation in PDAC-Predisposing Genes Using a Multi-Tier Annotation Approach Performed at the Gene, Patient, and Cohort Level

Abstract

We investigated germline variation in pancreatic ductal adenocarcinoma (PDAC) predisposition genes in 535 patients, using a custom-built panel and a new complementary bioinformatic approach. Our panel assessed genes belonging to DNA repair, cell cycle checkpoints, migration, and preneoplastic pancreatic conditions. Our bioinformatics approach integrated annotations of variants by using data derived from both germline and somatic references. This integrated approach with expanded evidence enabled us to consider patterns even among private mutations, supporting a functional role for certain alleles, which we believe enhances individualized medicine beyond classic gene-centric approaches. Concurrent evaluation of three levels of evidence, at the gene, sample, and cohort level, has not been previously done. Overall, we identified in PDAC patient germline samples, 12% with mutations previously observed in pancreatic cancers, 23% with mutations previously discovered by sequencing other human tumors, and 46% with mutations with germline associations to cancer. Non-polymorphic protein-coding pathogenic variants were found in 18.4% of patient samples. Moreover, among patients with metastatic PDAC, 16% carried at least one pathogenic variant, and this subgroup was found to have an improved overall survival (22.0 months versus 9.8; p=0.008) despite a higher pre-treatment CA19-9 level (p=0.02). Genetic alterations in DNA damage repair genes were associated with longer overall survival among patients who underwent resection surgery (92 months vs. 46; p=0.06). ATM alterations were associated with more frequent metastatic stage (p = 0.04) while patients with BRCA1 or BRCA2 alterations had improved overall survival (79 months vs. 39; p=0.05). We found that mutations in genes associated with chronic pancreatitis were more common in non-white patients (p<0.001) and associated with longer overall survival (52 months vs. 26; p=0.004), indicating the need for greater study of the relationship among these factors. More than 90% of patients were found to have variants of uncertain significance, which is higher than previously reported. Furthermore, we generated 3D models for selected mutant proteins, which suggested distinct mechanisms underlying their dysfunction, likely caused by genetic alterations. Notably, this type of information is not predictable from sequence alone, underscoring the value of structural bioinformatics to improve genomic interpretation. In conclusion, the variation in PDAC predisposition genes appears to be more extensive than anticipated. This information adds to the growing body of literature on the genomic landscape of PDAC and brings us closer to a more widespread use of precision medicine for this challenging disease.

A systematic review and meta-analysis of germline BRCA mutations in pancreatic cancer patients identifies global and racial disparities in access to genetic testing

“… 78 2021 Greece/Cyprus 549 NR R Mixed White, 100% Yes Yes Zimmermann et al. 79 2021 USA 535 2009-2017 P Mixed White, 89% African American, 7% Hispanic, 2% Asian, 2% Other, 1% Native American, <1% Yes No Takai et al. 80 2020 Japan 81 2002-2015 R NR Japanese, 100% Yes Yes Earl et al.…”

Understanding the Genetic Landscape of Pancreatic Ductal Adenocarcinoma to Support Personalized Medicine: A Systematic Review

“…Among these, 527 studies were excluded for different reasons (articles not in English, PDAC patients without PVs/LPVs in the selected genes, patients carrying only somatic alterations in PDAC susceptibility genes), and 150 studies were excluded because the evaluated patients had endocrine pancreatic cancer. As a result, 169 published studies fulfilled the inclusion criteria [ 11 , 15 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 , 61 , 62 , 63 , 64 , 65 , 66 …”

“…Genetic testing was performed in PDAC individuals with or without a family history of different cancer types (i.e., pancreatic, breast, colorectal, or melanoma). Full details of all the genetic causative or likely causative variants reported are shown in Table S3 [ 11 , 15 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 , 61 , 62 , 63 , 64 , 65 , 66 ,…”

Circulating tumor DNA: toward evolving the clinical paradigm of pancreatic ductal adenocarcinoma

“…Germline mutations affecting key DNA damage repair genes, such as BRCA1/2 , as well as chronic pancreatitis, have been established as features that predispose individuals to developing PDAC. 65 – 67 Individuals bearing these features are therefore considered as a high-risk group and would benefit from screening procedures capable of accurately capturing early onset of PDAC. While an early study of mutation-based ctDNA screening for early PDAC development did not show improvement compared to using CA19-9 alone, 68 a more recent study demonstrated higher accuracy when ctDNA and protein biomarkers were used in combination (64% sensitivity, 99.5% specificity 69 ).…”