Unexpected cancer-predisposition gene variants in Cowden syndrome and Bannayan-Riley-Ruvalcaba syndrome patients without underlying germline <i>PTEN</i> mutations

<div><p>Patients with heritable cancer syndromes characterized by germline <i>PTEN</i> mutations (termed <i>PTEN</i> hamartoma tumor syndrome, PHTS) benefit from <i>PTEN</i>-enabled cancer risk assessment and clinical management. <i>PTEN-</i>wildtype patients (~50%) remain at increased risk of developing certain cancers. Existence of germline mutations in other known cancer susceptibility genes has not been explored in these patients, with implications for different medical management. We conducted a 4-year multicenter prospective study of incident patients with features of Cowden/Cowden-like (CS/CS-like) and Bannayan-Riley-Ruvalcaba syndromes (BRRS) without <i>PTEN</i> mutations. Exome sequencing and targeted analysis were performed including 59 clinically actionable genes from the American College of Medical Genetics and Genomics (ACMG) and 24 additional genes associated with inherited cancer syndromes. Pathogenic or likely pathogenic cancer susceptibility gene alterations were found in 7 of the 87 (8%) CS/CS-like and BRRS patients and included <i>MUTYH</i>, <i>RET</i>, <i>TSC2</i>, <i>BRCA1</i>, <i>BRCA2</i>, <i>ERCC2</i> and <i>HRAS</i>. We found classic phenotypes associated with the identified genes in 5 of the 7 (71.4%) patients. Variant positive patients were enriched for the presence of second malignant neoplasms compared to patients without identified variants (OR = 6.101, 95% CI 1.143–35.98, p = 0.035). Germline variant spectrum and frequencies were compared to The Cancer Genome Atlas (TCGA), including 6 apparently sporadic cancers associated with PHTS. With comparable overall prevalence of germline variants, the spectrum of mutated genes was different in our patients compared to TCGA. Intriguingly, we also found notable enrichment of variants of uncertain significance (VUS) in our patients (OR = 2.3, 95% CI 1.5–3.5, p = 0.0002). Our data suggest that only a small subset of <i>PTEN-</i>wildtype CS/CS-like and BRRS patients could be accounted for by germline variants in some of the known cancer-related genes. Thus, the existence of alterations in other and more likely non-classic cancer-associated genes is plausible, reflecting the complexity of these heterogeneous hereditary cancer syndromes.</p></div

Clinicopathological characteristics of patients with identified germline alterations.

<p>Clinicopathological characteristics of patients with identified germline alterations.</p

Study design and testing strategy.

<p>ACMG indicates American College of Medical Genetics and Genomics. Component cancers represent malignancies observed in PHTS patients.</p

Demographic and clinical characteristics of 87 <i>PTEN</i> wildtype Cowden/Cowden-like syndrome and Bannayan-Riley-Ruvalcaba syndrome patients.

<p>Demographic and clinical characteristics of 87 <i>PTEN</i> wildtype Cowden/Cowden-like syndrome and Bannayan-Riley-Ruvalcaba syndrome patients.</p

Comparison of pathogenic and likely pathogenic germline variant spectra and frequencies in CS/CS-like/BRRS patients and TCGA apparently sporadic component cancer patients.

<p>Solid-filled bars represent identified variant positive CS/CS-like and BRRS patients. Striped bars represent TCGA cancer patients with different colors indicating different cancer types. TCGA cancer types were selected because each is a PHTS component cancer. Abbreviations: CS, Cowden syndrome; BRRS, Bannayan-Riley-Ruvalcaba syndrome; OR, odds ratio; CI, confidence interval.</p

Germline variants and copy number variation (CNVs) identified and associated syndromes.

<p>Germline variants and copy number variation (CNVs) identified and associated syndromes.</p

Gene-specific criteria for PTEN variant curation: Recommendations from the ClinGen PTEN Expert Panel

The ClinGen PTEN Expert Panel was organized by the ClinGen Hereditary Cancer Clinical Domain Working Group to assemble clinicians, researchers, and molecular diagnosticians with PTEN expertise to develop specifications to the 2015 ACMG/AMP Sequence Variant Interpretation Guidelines for PTEN variant interpretation. We describe finalized PTEN-specific variant classification criteria and outcomes from pilot testing of 42 variants with benign/likely benign (BEN/LBEN), pathogenic/likely pathogenic (PATH/LPATH), uncertain significance (VUS), and conflicting (CONF) ClinVar assertions. Utilizing these rules, classifications concordant with ClinVar assertions were achieved for 14/15 (93.3%) BEN/LBEN and 16/16 (100%) PATH/LPATH ClinVar consensus variants for an overall concordance of 96.8% (30/31). The variant where agreement was not reached was a synonymous variant near a splice donor with noncanonical sequence for which in silico models cannot predict the native site. Applying these rules to six VUS and five CONF variants, adding shared internal laboratory data enabled one VUS to be classified as LBEN and two CONF variants to be as classified as PATH and LPATH. This study highlights the benefit of gene-specific criteria and the value of sharing internal laboratory data for variant interpretation. Our PTEN-specific criteria and expertly reviewed assertions should prove helpful for laboratories and others curating PTEN variants.</p