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Investigation on the Role of PALB2 Gene in CDH1-Negative Patients With Hereditary Diffuse Gastric Cancer

Carreño, Marta MSc1; Pena-Couso, Laura PhD1; Mercadillo, Fátima1; Perea, José MD, PhD2,3; Urioste, Miguel MD, PhD1

Author Information
Clinical and Translational Gastroenterology: December 2020 - Volume 11 - Issue 12 - p e00280
doi: 10.14309/ctg.0000000000000280
  • Open



Gastric cancer is the third deadliest type of cancer worldwide (1). The best characterized inherited one is the hereditary diffuse gastric cancer (HDGC), which follows a pattern of autosomal dominant inheritance. This condition confers an increased risk to develop diffuse gastric cancer, together with lobular breast cancer in women. This entity is associated with germline pathogenic variants in the CDH1 gene that result in E-cadherin cell adhesion protein disfunction. The identification of these variants allows for a proper management of the disease, the establishment of the prognosis, and the correct genetic counseling, as total gastrectomy is currently the best prophylactic measure. However, up to 70% of the patients with HDGC lack germline alterations in the mentioned gene (2). Therefore, several efforts have been focused in the search for other genetic causes of HDGC to improve cancer prevention.

In this scenario, recent studies suggest that pathogenic variants in PALB2 could be the cause of HDGC in several families (3–6). PALB2 protein is involved in DNA repair through the Fanconi anemia and the homologous recombination repair pathways. Germline pathogenic variants in this gene are associated with hereditary breast and pancreatic cancers (7), but the role of PALB2 as susceptibility gene of HDGC is still unclear. Based on this, we decided to explore the possible implication of PALB2 in a new series of CDH1-negative HDGC patients.



The patients visited the familial cancer consultancy of the University Hospital of Fuenlabrada or other centers for genetic counseling and their samples were referred to the Spanish National Cancer Research Center for the study of the CDH1 gene. All patients signed an informed consent allowing further research and this project was approved by the University Hospital of Fuenlabrada ethics committee. The 58 patients selected for this study were unrelated individuals who met the HDGC clinical criteria (8) and in whom no pathogenic variants (point variants, deletions, or duplications) were found in CDH1 gene. Approximately 60% of the individuals were women (age range at diagnosis: 20–68 years, median age at diagnosis: 42 years) and 40% men (age range: 24–76, median: 52). Ninety-three percent of the patients were European Iberian individuals coming from Spain, together with 5% African (Moroccan) and 2% South American (Colombian) individuals. Signed informed consent was obtained from all patients. All data were anonymized.

Genetic studies

The genetic analyses were performed on DNA extracted from peripheral blood leukocytes samples. All patients had been previously screened for alterations in CDH1, by Sanger sequencing and by multiplex ligation-dependent probe amplification with SALSA P083-D1 (MRC Holland). Analysis of PALB2 was performed by Sanger sequencing. The primers were designed with Primer3Plus tool and are available on request. Presence of the selected variants of interest was confirmed in a second sample.

Variant interpretation

The selected variants in PALB2 were those with a minor allele frequency <1% (according to gnomAD). Decision on the variant interpretation was made considering the American College of Medical Genetics and Genomics guidelines (9), information from public databases (ClinVar, Leiden Open Variation Database, dbSNP, Ensembl, gnomAD, and Human Gene Mutation Database) and in silico pathogenicity predictors (PolyPhen, SIFT, and Condel).


No clearly pathogenic variants in PALB2 were identified in any of the 58 CDH1-negative HDGC patients in this study. We found 5 rare genetic variants in PALB2 (minor allele frequency <1%), 3 of them were classified as variants of uncertain significance (VUS) and the other 2 as likely benign variants. These variants were found in HDGC families without breast cancer cases (Table 1). DNA samples from the family relatives were not available; therefore, cosegregation studies could not be performed. Several aspects of the mentioned VUS such as their unreported frequency in general population or location near a splice site could suggest a pathogenic effect.

Table 1.
Table 1.:
Rare germline PALB2 variants found in CDH1-negative HDGC patients


The link between PALB2 pathogenic variants and HDGC was first found through whole exome sequencing and multiplexed targeted sequencing by other authors (3–6). This preliminary association was based in a reduced number of cases (10 families with HDGC) (3–6) with up to 1 identified case for every 100 CDH1-negative HDGC individuals tested. Similarly, our targeted study in 58 patients revealed a low number of PALB2 variants, and we were unable to demonstrate the pathogenicity of any of them. Therefore, this detection frequency seems minimal, and it is probably unsafe to consider PALB2 as an HDGC predisposition gene until larger series are studied. However, the possibility of testing a treatment with poly-ADP ribose polymerase inhibitors in the derived tumors in those patients carrying PALB2 pathogenic variants could be a promising alternative to gastrectomy (6), and thus, it is a good incentive to continue researching in this topic.


Guarantor of the article: Miguel Urioste, MD, PhD.

Specific author contributions: Marta Carreño and Laura Pena-Couso, share co-first authorship. Marta Carreño, MSc, and Laura Pena-Couso, PhD, contributed equally to this work. M.C., L.P.-C., and M.U. were involved in the design of the study. J.P. and M.U. were involved in patient recruitment. M.C., L.P.-C., and F.M. performed experiments and analyzed data. M.C., L.P.-C., F.M., and M.U. interpreted the results. M.C., L.P.-C., and M.U. elaborated the manuscript. All authors approved the final draft submitted.

Financial support: None to report.

Potential competing interests: None to report.

Study Highlights


  • ✓ Genetic testing is a crucial part in HDGC diagnosis to allow for optimal clinical management.
  • ✓ Germline pathogenic variants in CDH1 do not account for all patients with HDGC.
  • ✓ The implication of PALB2 in HDGC predisposition is poorly documented.


  • ✓ Targeted analysis of PALB2 in 58 CDH1-negative HDGC patients revealed only 3 VUS.
  • ✓ No strong evidence for PALB2 as a HDGC predisposition gene is found.


  • ✓ The diagnosis of HDGC patients might not benefit from including PALB2 genetic testing.


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© 2020 The Author(s). Published by Wolters Kluwer Health, Inc. on behalf of The American College of Gastroenterology