Great expectations: patients' preferences for clinically significant results from genomic sequencing.

We aimed to describe patient preferences for a broad range of secondary findings (SF) from genomic sequencing (GS) and factors driving preferences. We assessed preference data within a trial of the Genomics ADvISER, (SF decision aid) among adult cancer patients. Participants could choose from five categories of SF: (1) medically actionable; (2) polygenic risks; (3) rare diseases; (4) early-onset neurological diseases; and (5) carrier status. We analyzed preferences using descriptive statistics and drivers of preferences using multivariable logistic regression models. The 133 participants were predominantly European (74%) or East Asian or mixed ancestry (13%), female (90%), and aged > 50 years old (60%). The majority chose to receive SF. 97% (129/133) chose actionable findings with 36% (48/133) choosing all 5 categories. Despite the lack of medical actionability, participants were interested in receiving SF of polygenic risks (74%), carrier status (75%), rare diseases (59%), and early-onset neurologic diseases (53%). Older participants were more likely to be interested in receiving results for early-onset neurological diseases, while those exhibiting lower decisional conflict were more likely to select all categories. Our results highlight a disconnect between cancer patient preferences and professional guidelines on SF, such as ACMG's recommendations to only return medically actionable secondary findings. In addition to clinical evidence, future guidelines should incorporate patient preferences.

Analysis of the reported use of practice-based competencies by North American genetic counselors during the COVID-19 pandemic.

Genetic counseling services changed due to the COVID-19 pandemic. Many genetic counselors (GCs) moved from in-person to telehealth services. Others were redeployed by choice or necessity, using their expertise to provide COVID-19 care and education. For some, their employment status changed due to budgetary constraints or decreasing referrals. This study surveyed North American GCs to assess the relative use of genetic counseling Practice-Based Competencies (PBCs) as a proxy for the skills used during the first wave of the pandemic, whether GCs were in their current role or in new or adjusted roles. A secondary aim was to determine whether GCs believe their training should be refocused in view of the workforce shifts posed by the pandemic. The survey comprised closed- and open-ended questions and was completed in full by 97 respondents. The study population was representative of the general genetic counseling workforce in terms of gender, race/ethnicity, age, and practice area when compared to the National Society of Genetic Counselors 2020 Professional Status Survey. Most participants (97.9%) indicated that the COVID-19 pandemic resulted in a change to their work, and 89.7% used at least one PBC at a different frequency than before the pandemic. The most significant change was the adaptation of genetic counseling skills for varied service delivery models: 83.5% of respondents indicated that their roles and responsibilities moved to a remote setting and/or utilized telehealth. The majority of participants felt competent using the PBCs during the pandemic. Major themes that emerged from the qualitative data were as follows: (a) adaptation of service delivery, (b) translation of genetic counseling skills, and (c) provision of psychosocial support. This study highlights practice changes for GCs due to the COVID-19 pandemic as well as the increased use of, and need for focused training in, varied service delivery models.

Mainstream Model of Genetic Testing for Prostate Cancer at a Large Tertiary Cancer Centre.

BACKGROUND: An estimated 20% to 30% of men with advanced prostate cancer carry a mutation in DNA damage repair genes, of which half are estimated to be germline. Eligibility criteria for germline genetic testing expanded significantly for Ontario patients in May 2021 and many centers adopted a "mainstream" model, defined as oncologist-initiated genetic testing. METHODS: We conducted a retrospective chart review to report on the first-year mainstream experience of a large tertiary oncologic center, the Sunnybrook Odette Cancer Centre. All patients who underwent mainstream at the discretion of their treating physician were included. A subset underwent somatic profiling as part of clinical trial screening. Descriptive statistics were used to report baseline clinicopathologic characteristics and treatments received. RESULTS: Between May 1, 2021, and May 30, 2022, 174 patients with prostate cancer underwent mainstream germline genetic testing with a 19-gene panel. Median age was 75 (IQR 68-80), and 82% of patients were diagnosed with either de novo metastatic or high-risk localized prostate adenocarcinoma. Fourteen patients (8%; 95% CI 4%-12%) were found to have a deleterious germline mutation, including pathogenic or likely pathogenic variants in BRCA1/2, ATM, CHEK2, PMS2, RAD51C, HOXB13, and BRIP1. Forty-nine patients (28%; 95% CI 21%-35%) were found to have a variant of uncertain significance. Thirty-four patients also had next-generation sequencing (NGS) of their somatic tissue. Among this subset, 8 of 34 (23%) had an alteration in homologous recombination repair (HRR) genes. Of the 14 patients with a germline mutation, none had a prior personal history of malignancy and 6 (43%) did not have any first- or second-degree relatives with history of prostate, pancreatic, breast, or ovarian cancer. CONCLUSION: We report on the real-world characteristics of prostate cancer patients who underwent mainstream germline genetic testing. Personal history and family history of cancer cannot reliably stratify patients for the presence of pathogenic germline variants.

Germline TP53 mutations undergo copy number gain years prior to tumor diagnosis.

Li-Fraumeni syndrome (LFS) is a hereditary cancer predisposition syndrome associated with germline TP53 pathogenic variants. Here, we perform whole-genome sequence (WGS) analysis of tumors from 22 patients with TP53 germline pathogenic variants. We observe somatic mutations affecting Wnt, PI3K/AKT signaling, epigenetic modifiers and homologous recombination genes as well as mutational signatures associated with prior chemotherapy. We identify near-ubiquitous early loss of heterozygosity of TP53, with gain of the mutant allele. This occurs earlier in these tumors compared to tumors with somatic TP53 mutations, suggesting the timing of this mark may distinguish germline from somatic TP53 mutations. Phylogenetic trees of tumor evolution, reconstructed from bulk and multi-region WGS, reveal that LFS tumors exhibit comparatively limited heterogeneity. Overall, our study delineates early copy number gains of mutant TP53 as a characteristic mutational process in LFS tumorigenesis, likely arising years prior to tumor diagnosis.

The clinical utility of integrative genomics in childhood cancer extends beyond targetable mutations.

We conducted integrative somatic-germline analyses by deeply sequencing 864 cancer-associated genes, complete genomes and transcriptomes for 300 mostly previously treated children and adolescents/young adults with cancer of poor prognosis or with rare tumors enrolled in the SickKids Cancer Sequencing (KiCS) program. Clinically actionable variants were identified in 56% of patients. Improved diagnostic accuracy led to modified management in a subset. Therapeutically targetable variants (54% of patients) were of unanticipated timing and type, with over 20% derived from the germline. Corroborating mutational signatures (SBS3/BRCAness) in patients with germline homologous recombination defects demonstrates the potential utility of PARP inhibitors. Mutational burden was significantly elevated in 9% of patients. Sequential sampling identified changes in therapeutically targetable drivers in over one-third of patients, suggesting benefit from rebiopsy for genomic analysis at the time of relapse. Comprehensive cancer genomic profiling is useful at multiple points in the care trajectory for children and adolescents/young adults with cancer, supporting its integration into early clinical management.

Perspectives and Experiences of Parents and Adolescents Who Participate in a Pediatric Precision Oncology Program: "When You Feel Helpless, This Kind of Thing Is Very Helpful".

PURPOSE: The SickKids Cancer Sequencing (KiCS) Program, launched in 2016, evaluates the clinical utility of paired tumor/germline Next-Generation Sequencing (NGS) in pediatric oncology patients with hard-to-cure and rare cancers. In anticipation of further widespread adoption of NGS, we aimed to characterize the experiences and perspectives of adolescents and parents of patients who have already undergone NGS evaluation, focusing on the psychosocial impact and personal utility. METHODS: Parents of patients with pediatric cancer and adolescent patients who have participated in KiCS were invited to participate in semistructured interviews. Transcripts were analyzed using an inductive content analytic approach. RESULTS: Of 45 individuals invited, 22 parents and 10 adolescents were interviewed (71% response rate). Prominent psychosocial themes were low distress, relief, and sense of control; some expressed fear of the unknown. In exploring constructs of personal utility, parents highlighted hope for treatment options despite low expectations for results with clinical impact, whereas adolescents articulated altruistic motivations and less hope for personal clinical benefit. Bringing closure and answering the question of why the cancer occurred was a salient theme among both groups. Both parents and adolescents find benefit and clear decisional satisfaction with participation. No participants expressed regret. CONCLUSION: This study suggests that parents and adolescents benefit from NGS evaluation beyond the return of clinically relevant results. Our findings lay the framework for future work evaluating the value of NGS in pediatric precision oncology care through assessment of patient-reported outcomes and experiences. These results also guide provision of pre- and post-test education and support, which will facilitate patient-centered delivery of NGS practices.

Perplexed by PGx? Exploring the impact of pharmacogenomic results on medical management, disclosures and patient behavior.

Pharmacogenomic (PGx) tests represent significant advances in precision medicine. Our aim was to explore perceptions following the return of PGx results, medication management, and disclosure to providers. We surveyed clients who had PGx testing and conducted a chart review of PGx results. Respectively, 84% and 94% of participants found pre- and post-test genetic counseling helpful. There was a significant difference in disclosure, while 6% disclosed results to a pharmacist, 50% disclosed to a physician. Qualitative analysis identified three themes: 1) psychological response; 2) perceived utility; 3) experiences with disclosure. Our study supports the provision of genetic counseling for a non-disease related genetic test. Benefits of PGx testing can be optimized by the collaboration of physicians, pharmacists, genetic counselors and patients.