Colorectal cancer (CRC) in adolescents and young adults (AYA) is very rare. Known predisposition syndromes include Lynch syndrome (LS) due to highly penetrant MLH1 and MSH2 alleles, familial adenomatous polyposis (FAP), constitutional mismatch-repair deficiency (CMMRD), and polymerase proofreading-associated polyposis (PPAP). Yet, 60% of AYA-CRC cases remain unexplained. In two teenage siblings with multiple adenomas and CRC, we identified a maternally inherited heterozygous PMS2 exon 12 deletion, NM_000535.7:c.2007-786_2174+493del1447, and a paternally inherited POLD1 variant, NP_002682.2:p.Asp316Asn. Comprehensive molecular tumor analysis revealed ultra-mutation (>100 Mut/Mb) and a large contribution of COSMIC signature SBS20 in both siblings’ CRCs, confirming their predisposition to AYA-CRC results from a high propensity for somatic MMR deficiency (MMRd) compounded by a constitutional Pol δ proofreading defect. COSMIC signature SBS20 as well as SBS26 in the index patient’s CRC were associated with an early mutation burst, suggesting MMRd was an early event in tumorigenesis. The somatic second hits in PMS2 were through loss of heterozygosity (LOH) in both tumors, suggesting PPd-independent acquisition of MMRd. Taken together, these patients represent the first cases of cancer predisposition due to heterozygous variants in PMS2 and POLD1. Analysis of their CRCs supports that POLD1-mutated tumors acquire hypermutation only with concurrent MMRd.

Background: Homologous recombination deficiency (HRD) has evolved into a major diagnostic marker in high-grade ovarian cancer (HGOC), predicting the response to poly (adenosine diphosphate-ribose) polymerase inhibitors (PARPi) and also platinum-based therapy. In addition to HRD, the type of peritoneal tumor spread influences the treatment response and patient survival; miliary type tumor spread has a poorer predicted outcome than non-miliary type tumor spread. Methods: Known methods for HRD assessment were adapted for our technical requirements and the predictive-value integrated genomic instability score (PIGIS) for HRD assessment evolved as an outcome. PIGIS was validated in HGOC samples from 122 patients. We used PIGIS to analyze whether the type of tumor spread correlated with HRD status and whether this had an impact on survival. Results: We demonstrated that PIGIS can discriminate HRD-positive from HRD-negative samples. Tumors with a miliary tumor spread are HRD-negative and have a very bad prognosis with a progression-free survival (PFS) of 15.6 months and an overall survival (OS) of 3.9 years. However, HRD-negative non-miliary spreading tumors in our cohort had a much better prognosis (PFS 35.4 months, OS 8.9 years); similar to HRD-positive tumors (PFS 34.7 months, OS 8.9 years). Conclusions: Our results indicate that in a predominantly PARPi naïve cohort, the type of tumor spread and concomitant cytoreduction efficiency is a better predictor of survival than HRD and that HRD may be an accidental surrogate marker for tumor spread and concomitant cytoreduction efficiency. It remains to be determined whether this also applies for sensitivity to PARPi.

Secondary findings (SF) identified in massive parallel sequencing raise important clinical and healthcare related questions. To get an overview on current practices of European healthcare providers (HCP), we conducted a cross-sectional survey study among 39 stakeholders—predominantly senior medical and laboratory geneticists—from 15 European countries participating in the European Reference Network for Genetic Tumour Risk Syndromes (ERN GENTURIS). Respondents reported considerable heterogeneity in SF management and reporting, even within countries. While 31% of responding HCP return findings from all 81 genes on the American College of Medical Genetics and Genomics (ACMG) recommended SF list version 3.2, 41% restrict SF disclosure, often excluding genes associated with cardiological or metabolic disorders or with limited clinical actionability. A further 26% do not report ACMG-listed SF at all. Notably, 70% of HCP also assess additional cancer-predisposition genes beyond the ACMG list, using in-house gene lists or national guidelines. Most HCP restrict reporting to (likely) pathogenic variants (90%) and find SF in less than 5% of genetic analyses (59%). Consent procedures and patient information practices varied, with most HCP employing opt-in consent models and genetic counselling primarily delivered by medical geneticists and genetic counsellors. Major institutional challenges raised by participants, include lack of harmonised guidelines, concerns about patient anxiety, and insufficient resources for follow-up care. The findings of this study highlight the need for robust, evidence-based European guidelines to ensure clinically relevant and patient-centred SF management.

Homologous recombination deficiency (HRD) drives oncogenesis and therapeutic vulnerability in high-grade ovarian cancer (HGOC). While HRD testing is widely used to guide platinum- and especially poly(ADP-ribose) polymerase (PARP)-inhibitor-based therapies, its potential to provide evidence for BRCA1 and BRCA2 variant classification under the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP) framework has not been assessed. In this Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) consortium project, a literature review identified four independent HGOC cohorts reporting details on both BRCA1 and BRCA2 pathogenic variant (BRCA^pv) status and HRD-related genomic instability scores (HRD-GISs), all determined by the Myriad MyChoice HRD+ CDx assay. Likelihood ratios (LRs) were calculated to assess the probability that a BRCA1 or BRCA2 variant is pathogenic with a given HRD-GIS^high (≥42) or HRD-GIS^low (<42) tumor status, and these LRs were mapped to ACMG/AMP evidence strength categories defined by Bayesian modeling. Across the pooled dataset of 4,943 tumors (765 BRCA^pv and 4,178 BRCA1 or BRCA2 wild type [BRCA^wt]), 91.0% of BRCA^pv and 30.0% of BRCA^wt tumors were HRD-GIS^high. The LR for a BRCA1 or BRCA2 variant being pathogenic in an HRD-GIS^high HGOC was 3.03 (95% confidence interval [CI]: 2.88-3.19), corresponding to supporting pathogenic evidence. Conversely, the pooled LR for a variant being pathogenic in an HRD-GIS^low HGOC was 0.13 (95% CI: 0.10-0.16), corresponding to moderate benign evidence. The HGOC HRD-GIS determined by the MyChoice HRD+ CDx assay provides statistically robust evidence for BRCA1 and BRCA2 variant interpretation. This approach may refine variant classification, particularly for variants of uncertain significance, and enhance clinical decision-making in hereditary and tumor-based cancer risk assessment.

Background/Objectives: The implementation of polygenic scores (PGSs) and multifactorial risk assessments (MFRAs) has the potential to enhance breast cancer risk stratification, particularly in carriers of moderate-penetrance pathogenic variants (PVs), whose risk profiles often remain unclear if testing is limited to monogenic risk factors. Methods: To enhance breast cancer risk stratification, we included the BCAC313 polygenic score, together with MFRA, for carriers of moderate-penetrance pathogenic variants (PVs) during routine diagnostics and assessed its effect on the classification of patients’ risk categories in a real-world cohort at our center in its first year of implementation. Seventeen carriers with PVs in moderate-risk breast cancer genes were included in this study. Thirteen of them qualified for analysis for a full MFRA, including PGS, according to ancestry estimation and clinical criteria. The MFRA was performed using the CanRisk tool, which incorporates clinical, lifestyle, familial, and genetic data, including the BCAC313 score. Results: PGS z-scores were significantly higher in breast cancer patients compared to the unaffected control cohort (p = 0.016). The MFRA, including PGS, increased risk estimates for contralateral breast cancer in seven of eight patients with breast cancer and for primary breast cancer in three of five healthy carriers, compared to the risk conferred by the MFRA and moderate-penetrance pathogenic variant alone. Risk estimates varied widely, demonstrating the value of MFRA in personalized care. In five cases, one with a CHEK2-PV and four with an ATM-PV, the modified risk assessment contributed to the surgical decision for a prophylactic mastectomy. Conclusions: The MFRA, including PGS, provides the clinically meaningful refinement of breast cancer risk estimates in individuals with moderate-risk PVs. Personalized risk predictions can inform clinical management and support decision-making, which highlights the utility of this approach in clinical practice.

Background Homologous recombination deficiency (HRD) evolved into a major diagnostic marker in high grade ovarian cancer (HGOC) predicting the response to poly (Adenosine diphosphate-ribose) polymerase inhibitors (PARPi) and also platinum-based therapy. In addition to HRD, the type of peritoneal tumor spread influences treatment response and patient survival; miliary type tumor spread has poorer predicted outcome than non-miliary type tumor spread. Methods Known methods for HRD assessment were adapted for our technical requirements and the Predictive-value Integrated Genomic Instability Score (PIGIS) for HRD assessment evolved as an outcome. PIGIS was validated in HGOC samples from 122 patients. We used PIGIS to analyze whether the type of tumor spread correlated with HRD status and whether this had an impact on survival. Results We demonstrated that PIGIS can discriminate HRD positive from HRD negative samples. Tumors with miliary tumor spread are HRD negative and have a very bad prognosis with a progression free survival (PFS) of 15.6 months and an overall survival (OS) of 3.9 years. However, HRD negative non-miliary spreading tumors in our cohort had a much better prognosis (PFS 35.4 months, OS 8.9 years), similar to HRD positive tumors (PFS 34.7 months, OS 8.9 years). Conclusions Our results indicate that in a predominantly PARPi naïve cohort the type of tumor spread might be a better predictor of response to platinum sensitivity than HRD. It remains to be determined, whether this also applies for sensitivity to PARPi.