Variants of uncertain significance in breast cancer-related genes: real-world implications for a clinical conundrum. Part one: clinical genetics recommendations

How patients deal with an ambiguous medical test: Decision-making after genetic testing

OBJECTIVE

We know little about how patients make decisions when they receive a variant of uncertain significance result (VUS) from genetic testing. The purpose of this study was to elucidate a model of patient-informed decision-making after receiving a VUS result.

METHODS

Using an adapted Mental Models Approach, we conducted semi-structured interviews with women who received a VUS result from genetic testing for hereditary breast cancer (N = 20) to explore factors they believed were relevant to their decision-making. Two coders used a coding scheme informed by experts in hereditary breast cancer to conduct analysis. Inter-coder reliability was α = .86.

RESULTS

Three overarching decision themes emerged from the interviews: managing ambiguity, medical risk management, and sharing results with others. While participants noted some difficulty understanding their result, genetic counselors' interpretations, psychosocial factors (e.g., risk perceptions), and competing extrinsic demands influenced their decisions.

CONCLUSION

Complex influences affect patient decision-making after a VUS result from genetic testing and may encourage health protective behavior.

PRACTICE IMPLICATIONS

Even patients who understand their test result could use support managing the ambiguity of their test result and sharing it with others.

A Modern Dilemma: How Experts Grapple with Ambiguous Genetic Test Results

Objective. Clinicians regularly use panel genetic testing to identify hereditary breast cancer risk, but this practice increases the rate of receiving an ambiguous test result, the variant of uncertain significance (VUS). VUS results are a growing and long-term challenge for providers and have caused negative patient outcomes. The objective of this study was to elicit expert opinions about patients' decision making after receiving a VUS result to provide future guidance for VUS disclosure. Methods. Using an adapted mental models approach, experts (N = 25) completed an online survey and in-depth interview eliciting qualitative judgments of the factors relevant to informed patient decision making after receiving a VUS result. Content analysis of interview transcripts clarified the basis for these judgments. Results. Participants identified 11 decisions facing patients after receiving VUS results grouped into ambiguity management or risk management. The experts also identified 24 factors relevant to each decision, which reflected 2 themes: objective factors (e.g., clinical information, guidelines) and psychosocial factors (e.g., understanding or risk perception). Conclusion. This study presents an adaptation of the mental models approach for communication under conditions of ambiguity. Findings suggest providers who present VUS results from genetic testing for hereditary breast cancer should discuss decisions related to ambiguity management that focus on hope for future reclassification, and be directive when discussing risk management decisions. Objective and psychosocial factors should influence both ambiguity and risk management decisions, but especially risk management decisions.

A meta-analysis of zinc levels in breast cancer

BACKGROUND

Breast cancer is the most commonly occurring neoplasm in females, comprising 16% of all female cancers worldwide. Various studies indicate some discrepancies regarding zinc (Zn) levels in various samples of breast cancer patients.

OBJECTIVE

The present study evaluated by meta-analysed the published data for Zn levels analyzed in breast tissue, plasma, serum, and hair samples and its relationship with breast cancer.

METHODS

The present meta-analysis included 36 studies, all of which were published in the years between 1984 to 2017 and selected by searching the databases MEDLINE, EMBASE, Cochrane Library, PubMed, Scopus, and the ISI Web of Knowledge. The articles were analyzed, and I² statistics were used to examine heterogeneity. The objective analysis was performed on data from the 36 studies, with total 1699 study subjects and 2009 controls.

RESULTS

Significant statistical differences overall were observed, based on a random effects model (SMD (95 % CI), -0.78[-1.40, -0.16], P = 0.014). Data from 19 of these studies indicated significant statistical differences between cancerous patients and controls with regard to serum and plasma Zn concentration (SMD [(95 %CI): -1.61(-2.43, -0.79)]. There was a significant statistical difference between the breast tissue and hair as regards Zn status (SMD (95%CI): 2.32(1.42, 3.21)) and (SMD (95v%CI): -1.80(-3.41, -0.20), respectively. Zn concentration levels typically decreased in blood and hair samples of patients with breast cancer, whereas it was elevated in tumor tissues.

CONCLUSIONS

There is a significant relationship between lowered serum Zn concentrations and risk of breast cancer onset or recurrences in women, but because of high heterogeneity, we recommend other primary studies.

Prevalence of BRCA1/BRCA2 mutations in a Brazilian population sample at-risk for hereditary breast cancer and characterization of its genetic ancestry

Background

There are very few data about the mutational profile of families at-risk for hereditary breast and ovarian cancer (HBOC) from Latin America (LA) and especially from Brazil, the largest and most populated country in LA.

Results

Of the 349 probands analyzed, 21.5% were BRCA1/BRCA2 mutated, 65.3% at BRCA1 and 34.7% at BRCA2 gene. The mutation c.5266dupC (former 5382insC) was the most frequent alteration, representing 36.7% of the BRCA1 mutations and 24.0% of all mutations identified. Together with the BRCA1 c.3331_3334delCAAG mutation, these mutations constitutes about 35% of the identified mutations and more than 50% of the BRCA1 pathogenic mutations. Interestingly, six new mutations were identified. Additionally, 39 out of the 44 pathogenic mutations identified were not previously reported in the Brazilian population. Besides, 36 different variants of unknown significance (VUS) were identified. Regarding ancestry, average ancestry proportions were 70.6% European, 14.5% African, 8.0% Native American and 6.8% East Asian.

Materials and methods

This study characterized 349 Brazilian families at-risk for HBOC regarding their germline BRCA1/BRCA2 status and genetic ancestry.

Conclusions

This is the largest report of BRCA1/BRCA2 assessment in an at-risk HBOC Brazilian population. We identified 21.5% of patients harboring BRCA1/BRCA2 mutations and characterized the genetic ancestry of a sample group at-risk for hereditary breast cancer showing once again how admixed is the Brazilian population. No association was found between genetic ancestry and mutational status. The knowledge of the mutational profile in a population can contribute to the definition of more cost-effective strategies for the identification of HBOC families.

BRCA1 homozygous unclassified variant in a patient with non-Fanconi anemia: A case report

The present case report discusses a woman affected by chronic lymphatic leukemia and breast cancer with a familial history of breast cancer; suspected to be hereditary breast and ovarian cancer (HBOC) syndrome. The patient underwent BRCA1 and BRCA2 genetic testing. Sequencing of BRCA1 revealed the presence of the variant of unknown significance (VUS) c.3082C>T (p.Arg1028Cys) at homozygous state, whereas no mutations were detected in BRCA2. Multiplex ligation-dependent probe amplification confirmed the presence of two alleles. Although consanguineity between her parents was reported, which therefore supported the molecular data, her clinical phenotype was not suggestive of typical Fanconi anemia (FA), particularly of a BRCA1-linked FA. In the two cases reported in the literature, carriers of biallelic BRCA1 mutation present a severe and quite typical phenotype. For this reason, the patient was offered a diepoxybutane test, where neither complex rearrangements nor multiradial formation were detected. We were therefore inclined to consider that BRCA1 VUS as of little clinical significance.

Evaluation of laboratory perspectives on hereditary cancer panels

Genetic counseling and testing for hereditary cancer susceptibility is a rapidly evolving field and partly a result of next-generation sequencing (NGS) allowing analysis of multiple cancer susceptibility genes simultaneously. This qualitative study explored laboratory perspectives on hereditary cancer panels. Semi-structured interviews were conducted with representatives of clinical laboratories offering hereditary cancer panels via NGS. Several themes emerged from the responses pertaining to hereditary cancer panel development, the importance of communication of panel properties with patients, variant reporting policies, and the future of hereditary cancer gene testing. Clinical utility was discussed as primary consideration during panel development. In addition, while participants indicated gene and syndrome overlap prompted panel development in general, laboratories differed in their opinions of whether phenotypic overlap warrants offering pan-cancer panels only versus cancer specific panels. Participants stressed the importance of patients understanding implications of panel testing, including what is tested for and limitations of testing. While all laboratories discussed the limitations of a variant of uncertain significance result, they differed significantly in their reporting methods. This study provides healthcare providers information on the laboratory approach to panel testing, highlighting both commonalities and differences in laboratory approaches, and may allow providers to make more informed decisions when ordering hereditary cancer panels.

A preliminary investigation of genetic counselors' information needs when receiving a variant of uncertain significance result: a mixed methods study

PURPOSE

The aim of this study was to explore genetic counselors' information preferences on reports of variant of uncertain significance (VUS) results from cancer genetic testing.

METHODS

This mixed methods report (quantitative and qualitative approaches) utilized a survey of genetic counselors containing closed- and open-ended questions to explore genetic counselors' information needs and perceptions of the industry's current information sharing practices. Descriptive statistics were calculated for responses to the closed-ended questions, and thematic analysis guided the interpretation of the open-ended questions.

RESULTS

Of the 267 participants (28.6% response rate), the majority indicated a perceived lack of information on VUS laboratory reports, were concerned about the perceived practice of withholding information, and stated the information they wanted to see. Although most did not indicate how additional information would be used, some reported they would provide information directly to patients, and others reported that the information would be used to contextualize the VUS result when counseling patients.

CONCLUSION

This analysis identified information that genetic counselors believe is needed in VUS reports, indicating what they believe are best practices in lieu of guidelines for laboratories currently providing genetic testing services. Future studies should explore how genetic counselors use additional information contained in VUS reports.Genet Med 17 9, 739-746.

Genetic counselors' practices and confidence regarding variant of uncertain significance results and reclassification from BRCA testing

Studies indicate variant of uncertain significance (VUS) results are challenging for genetic counselors and patients, often resulting in negative patient outcomes. Genetic counselors' current practices regarding VUS are unknown. This study utilized a national survey of genetic counselors (n = 932) to examine current practices and confidence related to disclosing BRCA VUS results and reclassification information. For participants (n = 398), descriptive statistics were calculated regarding patient demographic characteristics, practices and confidence, and cross tabulation was used to identify participant's actions when receiving a reclassified VUS. Upon receiving a BRCA VUS report, the majority reported providing patients with information about the frequency with which their VUS was seen and patient ancestry, but a minority discussed DNA banking. Most were confident in their understanding of, and ability to explain, VUS results to patients, but felt less confident about achieving high levels of patient understanding. Upon reclassification, the majority reported calling the patient and mailing the results, but when the reclassification was deleterious, the majority also met with the patient face-to-face. Given the lack of standard professional guidelines about informing patients of initial and reclassified VUS results, this overview provides important insight into genetic counselors' current practices and confidence.

Variants of uncertain significance in BRCA: a harbinger of ethical and policy issues to come?

After two decades of genetic testing and research, the BRCA1 and BRCA2 genes are two of the most well-characterized genes in the human genome. As a result, variants of uncertain significance (VUS; also called variants of unknown significance) are reported less frequently than for genes that have been less thoroughly studied. However, VUS continue to be uncovered, even for BRCA1/2. The increasing use of multi-gene panels and whole-genome and whole-exome sequencing will lead to higher rates of VUS detection because more genes are being tested, and most genomic loci have been far less intensively characterized than BRCA1/2. In this article, we draw attention to ethical and policy-related issues that will emerge. Experience garnered from BRCA1/2 testing is a useful introduction to the challenges of detecting VUS in other genetic testing contexts, while features unique to BRCA1/2 suggest key differences between the BRCA experience and the current challenges of multi-gene panels in clinical care. We propose lines of research and policy development, emphasizing the importance of pooling data into a centralized open-access database for the storage of gene variants to improve VUS interpretation. In addition, establishing ethical norms and regulated practices for sharing and curating data, analytical algorithms, interpretive frameworks and patient re-contact are important policy areas.

Large numbers of individuals are required to classify and define risk for rare variants in known cancer risk genes

PURPOSE

Up to half of unique genetic variants in genomic evaluations of familial cancer risk will be rare variants of uncertain significance. Classification of rare variants will be an ongoing issue as genomic testing becomes more common.

METHODS

We modified standard power calculations to explore sample sizes necessary to classify and estimate relative disease risk for rare variant frequencies (0.001-0.00001) and varying relative risk (20-1.5), using population-based and family-based designs focusing on breast and colon cancer. We required 80% power and tolerated a 10% false-positive rate because variants tested will be in known genes with high pretest probability.

RESULTS

Using population-based strategies, hundreds to millions of cases are necessary to classify rare cancer variants. Larger samples are necessary for less frequent and less penetrant variants. Family-based strategies are robust to changes in variant frequency and require between 8 and 1,175 individuals, depending on risk.

CONCLUSION

It is unlikely that most rare missense variants will be classifiable in the near future, and accurate relative risk estimates may never be available for very rare variants. This knowledge may alter strategies for communicating information about variants of uncertain significance to patients.

Performance of BOADICEA and BRCAPRO genetic models and of empirical criteria based on cancer family history for predicting BRCA mutation carrier probabilities: a retrospective study in a sample of Italian cancer genetics clinics

PURPOSE

To evaluate in current practice the performance of BOADICEA and BRCAPRO risk models and empirical criteria based on cancer family history for the selection of individuals for BRCA genetic testing.

PATIENTS AND METHODS

The probability of BRCA mutation according to the three tools was retrospectively estimated in 918 index cases consecutively undergone BRCA testing at 15 Italian cancer genetics clinics between 2006 and 2008.

RESULTS

179 of 918 cases (19.5%) carried BRCA mutations. With the strict use of the criteria based on cancer family history 173 BRCA (21.9%) mutations would have been detected in 789 individuals. At the commonly used 10% threshold of BRCA mutation carrier probability, the genetic models showed a similar performance [PPV (38% and 37%), sensitivity (76% and 77%) and specificity (70% and 69%)]. Their strict use would have avoided around 60% of the tests but would have missed approximately 1 every 4 carriers.

CONCLUSION

Our data highlight the complexity of BRCA testing referral in routine practice and question the strict use of genetic models for BRCA risk assessment.