Genetic Testing Utilization: Discrepancies Between Somatic and Germline Results in Patients With Cancer Reviewed at the UW Health Precision Medicine Molecular Tumor Board.

PURPOSE: Somatic and germline testing are increasingly used to estimate risks for patients with cancer. Although both germline testing and somatic testing can identify genetic variants that could change a patient's care and eligible treatments, the aims of these tests and their technologies are fundamentally different and cannot be used interchangeably. This study examines the timing and results of somatic and germline genetic testing for patients with cancer at UW Health. METHODS: Eight hundred and seventy-seven participants underwent somatic genetic testing, which was reviewed by the Precision Medicine Molecular Tumor Board (PMMTB). Patients were diagnosed with cancers, including breast, colorectal, endometrial, pancreatic, or ovarian cancer, and met National Comprehensive Cancer Network criteria for germline genetic testing. Germline testing details were collected by medical record review. RESULTS: The results of this study found that only 310 patients (35%) had germline evaluation before PMMTB review. The percent of germline pathogenic/likely pathogenic variants identified in actionable genes was 28%. Most germline variants were identified in the BRCA1 (26%) and BRCA2 (28%) genes. In total, 65% (54/83) of germline variants were detected with both germline testing and somatic testing; however, 35% (29/83) of germline variants were not identified on somatic results. These results demonstrate the importance of combination germline and somatic testing. CONCLUSION: This study highlights the differences in genetic testing types and demonstrates that conducting germline testing at earlier stages of diagnoses is necessary to identify potentially actionable and treatment-specific variants in patients with cancer.

Breast cancers in monoallelic MUTYH germline mutation carriers have clinicopathological features overlapping with those in BRCA1 germline mutation carriers.

PURPOSE: Breast cancer patients referred to genetic counseling often undergo genetic testing with broad panels that include both breast cancer susceptibility genes as well as genes more specific for extramammary sites. As a result, patients are often incidentally found to have germline mutations in genes that are not necessarily related to breast cancer risk. One such gene is MUTYH. To understand the role MUTYH may play in breast cancer, the clinicopathological features of patients with monoallelic MUTYH germline mutation and breast cancer were examined. METHODS: The clinicopathological characteristics of the breast cancers from patients with monoallelic MUTYH mutation were compared to breast cancer patients with other germline mutations in known breast cancer susceptibility genes, including ATM, BRCA1/2, CHEK2, and PALB2. The breast cancer patients who received genetic counseling but tested negative for the aforementioned gene mutations were used as a control group. RESULTS: Histologic characteristics of the breast cancers arising in monoallelic MUTYH mutation carriers had significantly larger tumor size, higher tumor grade, and more high-risk biomarker profiles (i.e., Her2-positive and triple-negative) than breast cancer patients with susceptibility genes, except for BRCA1. MUTYH mutation carriers also showed a trend of more frequent intratumoral divergency in terms of tumor grade and biomarker profiles. CONCLUSION: Although germline monoallelic MUTYH mutation is not thought to confer a meaningfully increased risk of breast cancer development, it may contribute to pathological aggressiveness and diversity of breast cancers when they sporadically arise in MUTYH carriers.

Factors Affecting Genetic Consultation in Adolescent and Young Adult Patients With Sarcoma.

BACKGROUND: Given a link between sarcomas and hereditary cancer predisposition syndromes, including Li-Fraumeni syndrome, the consideration for genetic counseling is recommended for all adolescent and young adult (AYA) patients diagnosed with sarcoma. The aim of this study was to evaluate factors influencing genetic consultations in AYA patients with sarcoma at the University of Wisconsin (UW). METHODS: A retrospective chart review was performed on AYA patients diagnosed with sarcoma between the ages of 15 and 39 years who were seen at least once between 2015 to 2019 at UW. Our chart review identified discussions regarding genetics, referrals to genetics, genetic consultations, and results of genetic testing. Variables hypothesized to affect patient referrals for genetic consultation were identified a priori. Descriptive statistical methods and a univariate analysis were used to identify patient characteristics associated with genetic counseling referral. RESULTS: We identified 87 AYA patients with sarcoma. Only 19 (22%) of these patients had documentation of a discussion about genetics, 15 (17%) of whom were subsequently referred for genetic consultation. Of these 15 patients, 9 (60%) were seen in consultation. All 9 patients seen by genetics underwent genetic testing, with 4 (44%) of these patients having identified heritable cancer predisposition syndromes. Likelihood for genetics referral was linked most strongly to documented genetics discussion with an oncology provider (P<.001). CONCLUSIONS: Despite the recommendation for consideration for genetic counseling in AYA patients with sarcoma, <25% of such patients in our study had a documented discussion about genetics. Supporting this need, all referred patients met criteria for genetic testing, and 44% of tested patients were found to have a heritable cancer predisposition syndrome. These data support the initial conversation by a provider as critical to genetic referral and suggest the need for more specific national recommendations for the genetic evaluation of all AYA patients with sarcoma.

Disparities Between Provider Assessment and Documentation of Care Needs in the Care of Adolescent and Young Adult Patients With Sarcoma.

PURPOSE: Given the occurrence of cancer during a complex developmental time, adolescent and young adult (AYA) patients have unique psychosocial needs that necessitate supportive care, which is optimally provided using National Comprehensive Cancer Network (NCCN) AYA guidelines. We sought to explore compliance with NCCN AYA guidelines and compare with oncology providers' perceptions of AYA care needs. METHODS: Retrospective chart reviews of AYA patients (15-39 years at time of cancer diagnosis) with sarcoma seen at least once in 2019 at the University of Wisconsin identified documentation of discussions deemed critical per NCCN AYA guidelines. As per the ASCO Quality Oncology Practice Initiative certification, we considered a threshold of these factors being discussed 75% of the time or higher to be compliant. Compliance was compared with an electronic survey of University of Wisconsin oncology providers regarding AYA patient needs, with items determined to have adequate resources if noted sufficient by at least 75% of providers. RESULTS: We identified 43 AYA patients with sarcoma. Less than 75% of patients had documentation of discussion of contraception, sexual health, fertility, finances, genetics, social work referral, and clinical trials indicating noncompliance with NCCN guidelines. Surveys, completed by 38 oncology providers, showed significant discordance between providers' perceptions of AYAs' access to resources and providers' documented discussions of supportive care resources. CONCLUSION: Disparities between oncology provider assessment of AYA care needs and documentation of critical components of AYA patient care demonstrate the need for novel tools to evaluate AYA care needs beyond provider assessments.

The impact of genetic counseling on patient engagement in a specialty cancer clinic.

The identification of patient outcomes unique to the field of genetic counseling has become a recent priority of the profession. Current health-care efforts have targeted patient engagement as an outcome capable of improving population health and reducing health-care costs. This study analyzed patient engagement levels among 182 participants who underwent genetic counseling for gastrointestinal (GI) cancer risk assessment in an outpatient specialty clinic. Patients seen at the UPMC Hereditary GI Tumor Program completed a validated patient engagement measure, the Altarum Consumer Engagement (ACE), prior to undergoing genetic counseling and again three months after enrollment. Paired t test analysis was conducted to assess the changes in Total ACE scores, and within the following three domains: Navigation, Informed Choice, and Commitment. In the sample of 182 participants, Total ACE scores increased after genetic counseling (by 5.7%; p < .0001), as did all three domains (Commitment p = .0008; Navigation p = .0008; and Informed Choice p = .0016). This study is the first known report of patient engagement levels in individuals undergoing genetic counseling in a specialty cancer clinic and suggests that genetic counseling improves patient engagement levels.

Genome-wide depletion of replication initiation events in highly transcribed regions.

This report investigates the mechanisms by which mammalian cells coordinate DNA replication with transcription and chromatin assembly. In yeast, DNA replication initiates within nucleosome-free regions, but studies in mammalian cells have not revealed a similar relationship. Here, we have used genome-wide massively parallel sequencing to map replication initiation events, thereby creating a database of all replication initiation sites within nonrepetitive DNA in two human cell lines. Mining this database revealed that genomic regions transcribed at moderate levels were generally associated with high replication initiation frequency. In genomic regions with high rates of transcription, very few replication initiation events were detected. High-resolution mapping of replication initiation sites showed that replication initiation events were absent from transcription start sites but were highly enriched in adjacent, downstream sequences. Methylation of CpG sequences strongly affected the location of replication initiation events, whereas histone modifications had minimal effects. These observations suggest that high levels of transcription interfere with formation of pre-replication protein complexes. Data presented here identify replication initiation sites throughout the genome, providing a foundation for further analyses of DNA-replication dynamics and cell-cycle progression.