Multi-gene Panel Testing in Breast Cancer Management

Multigenic panels in breast cancer: Clinical utility and management of patients with pathogenic variants other than BRCA1/2

Multigene panels can analyze high and moderate/intermediate penetrance genes that predispose to breast cancer (BC), providing an opportunity to identify at-risk individuals within affected families. However, considering the complexity of different pathogenic variants and correlated clinical manifestations, a multidisciplinary team is needed to effectively manage BC. A classification of pathogenic variants included in multigene panels was presented in this narrative review to evaluate their clinical utility in BC. Clinical management was discussed for each category and focused on BC, including available evidence regarding the multidisciplinary and integrated management of patients with BC. The integration of both genetic testing and counseling is required for customized decisions in therapeutic strategies and preventative initiatives, as well as for a defined multidisciplinary approach, considering the continuous evolution of guidelines and research in the field.

Economic evaluation of germline genetic testing for breast cancer in low- and middle-income countries: a systematic review

BACKGROUND

Breast cancer (BC) is the most common cancer affecting women globally. Genetic testing serves as a prevention and treatment strategy for managing BC. This study aims to systematically review economic evaluations and the quality of selected studies involving genetic screening strategies for BC in low and middle-income countries (LMICs).

METHODS

A search was performed to identify related articles that were published up to April 2023 on PubMed, Embase, CINAHL, Web of Science, and the Centre for Reviews and Dissemination. Only English-language LMIC studies were included. Synthesis of studies characteristics, methodological and data input variations, incremental cost-effectiveness ratios (ICERs), and reporting quality (Consolidated Health Economic Evaluation Reporting Standards (CHEERS) 2022 checklist) were performed.

RESULTS

This review found five pertinent studies, mainly focusing on economic evaluations of germline genetic testing in upper-middle-income countries (Upper MICs) like Malaysia, China, and Brazil. Only one study covered multiple countries with varying incomes, including lower-middle-income nations (Lower MICs) like India. The ICERs values in various screening scenarios for early-stage BC, HER2 negative BC patients, and healthy women with clinical or family history criteria were ranging from USD 2214/QALY to USD 36,342/QALY. Multigene testing for all breast cancer patients with cascade testing was at USD 7729/QALY compared to BRCA alone. Most studies adhered to the CHEERS 2022 criteria, signifying high methodological quality.

CONCLUSIONS

Germline testing could be considered as cost-effective compared to no testing in Upper MICs (e.g., Malaysia, China, Brazil) but not in Lower MICs (e.g., India) based on the willingness-to-pay (WTP) threshold set by each respective study. Limitations prevent a definite conclusion about cost-effectiveness across LMICs. More high-quality studies are crucial for informed decision-making and improved healthcare practices in these regions.

Novel immune-related gene signature for risk stratification and prognosis prediction in ovarian cancer

BACKGROUND

The immune system played a multifaceted role in ovarian cancer (OC) and was a significant mediator of ovarian carcinogenesis. Various immune cells and immune gene products played an integrated role in ovarian cancer (OC) progression, proved the significance of the immune microenvironment in prognosis. Therefore, we aimed to establish and validate an immune gene prognostic signature for OC patients' prognosis prediction.

METHODS

Differently expressed Immune-related genes (DEIRGs) were identified in 428 OC and 77 normal ovary tissue specimens from 9 independent GEO datasets. The Cancer Genome Atlas (TCGA) cohort was used as a training cohort, Univariate Cox analysis was used to identify prognostic DEIRGs in TCGA cohort. Then, an immune gene-based risk model for prognosis prediction was constructed using the LASSO regression analysis, and validated the accuracy and stability of the model in 374 and 93 OC patients in TCGA training cohort and International Cancer Genome Consortium (ICGC) validation cohort respectively. Finally, the correlation among risk score model, clinicopathological parameters, and immune cell infiltration were analyzed.

RESULTS

Five DEIRGs were identified to establish the immune gene signature and divided OC patients into the low- and high-risk groups. In TCGA and ICGC datasets, patients in the low-risk group showed a substantially higher survival rate than high-risk group. Receiver operating characteristic (ROC) curves, t-distributed stochastic neighbor embedding (t-SNE) analysis and principal component analysis (PCA) showed the good performance of the risk model. Clinicopathological correlation analysis proved the risk score model could serve as an independent prognostic factor in 2 independent datasets.

CONCLUSIONS

The prognostic model based on immune-related genes can function as a superior prognostic indicator for OC patients, which could provide evidence for individualized treatment and clinical decision making.

Impact of High-to-Moderate Penetrance Genes on Genetic Testing: Looking over Breast Cancer

Breast cancer (BC) is the most common cancer and the leading cause of cancer death in women worldwide. Since the discovery of the highly penetrant susceptibility genes BRCA1 and BRCA2, many other predisposition genes that confer a moderate risk of BC have been identified. Advances in multigene panel testing have allowed the simultaneous sequencing of BRCA1/2 with these genes in a cost-effective way. Germline DNA from 521 cases with BC fulfilling diagnostic criteria for hereditary BC were screened with multigene NGS testing. Pathogenic (PVs) and likely pathogenic (LPVs) variants in moderate penetrance genes were identified in 15 out of 521 patients (2.9%), including 2 missense, 7 non-sense, 1 indel, and 3 splice variants, as well as two different exon deletions, as follows: ATM (n = 4), CHEK2 (n = 5), PALB2 (n = 2), RAD51C (n = 1), and RAD51D (n = 3). Moreover, the segregation analysis of PVs and LPVs into first-degree relatives allowed the detection of CHEK2 variant carriers diagnosed with in situ melanoma and clear cell renal cell carcinoma (ccRCC), respectively. Extended testing beyond BRCA1/2 identified PVs and LPVs in a further 2.9% of BC patients. In conclusion, panel testing yields more accurate genetic information for appropriate counselling, risk management, and preventive options than assessing BRCA1/2 alone.

Clinical usefulness of NGS multi-gene panel testing in hereditary cancer analysis

Introduction: A considerable number of families with pedigrees suggestive of a Mendelian form of Breast Cancer (BC), Ovarian Cancer (OC), or Pancreatic Cancer (PC) do not show detectable BRCA1/2 mutations after genetic testing. The use of multi-gene hereditary cancer panels increases the possibility to identify individuals with cancer predisposing gene variants. Our study was aimed to evaluate the increase in the detection rate of pathogenic mutations in BC, OC, and PC patients when using a multi-gene panel.

Methods: 546 patients affected by BC (423), PC (64), or OC (59) entered the study from January 2020 to December 2021. For BC patients, inclusion criteria were i) positive cancer family background, ii) early onset, and iii) triple negative BC. PC patients were enrolled when affected by metastatic cancer, while OC patients were all submitted to genetic testing without selection. The patients were tested using a Next-Generation Sequencing (NGS) panel containing 25 genes in addition to BRCA1/2.

Results: Forty-four out of 546 patients (8%) carried germline pathogenic/likely pathogenic variants (PV/LPV) on BRCA1/2 genes, and 46 (8%) presented PV or LPV in other susceptibility genes.

Discussion: Our findings demonstrate the utility of expanded panel testing in patients with suspected hereditary cancer syndromes, since this approach increased the mutation detection rate of 15% in PC, 8% in BC and 5% in OC cases. In absence of multi-gene panel analysis, a considerable percentage of mutations would have been lost.

Barriers to genetic testing in clinical psychiatry and ways to overcome them: from clinicians' attitudes to sociocultural differences between patients across the globe

Genetic testing has evolved rapidly over recent years and new developments have the potential to provide insights that could improve the ability to diagnose, treat, and prevent diseases. Information obtained through genetic testing has proven useful in other specialties, such as cardiology and oncology. Nonetheless, a range of barriers impedes techniques, such as whole-exome or whole-genome sequencing, pharmacogenomics, and polygenic risk scoring, from being implemented in psychiatric practice. These barriers may be procedural (e.g., limitations in extrapolating results to the individual level), economic (e.g., perceived relatively elevated costs precluding insurance coverage), or related to clinicians' knowledge, attitudes, and practices (e.g., perceived unfavorable cost-effectiveness, insufficient understanding of probability statistics, and concerns regarding genetic counseling). Additionally, several ethical concerns may arise (e.g., increased stigma and discrimination through exclusion from health insurance). Here, we provide an overview of potential barriers for the implementation of genetic testing in psychiatry, as well as an in-depth discussion of strategies to address these challenges.

Multi-gene panel testing increases germline predisposing mutations’ detection in a cohort of breast/ovarian cancer patients from Southern Italy

Breast cancer is the most common neoplasia in females worldwide, about 10% being hereditary/familial and due to DNA variants in cancer-predisposing genes, such as the highly penetrant BRCA1/BRCA2 genes. However, their variants explain up to 25% of the suspected hereditary/familial cases. The availability of NGS methodologies has prompted research in this field. With the aim to improve the diagnostic sensitivity of molecular testing, a custom designed panel of 44 genes, including also non-coding regions and 5’ and 3’ UTR regions, was set up. Here, are reported the results obtained in a cohort of 64 patients, including also few males, from Southern Italy. All patients had a positive personal and/or familial history for breast and other cancers, but tested negative to routine BRCA analysis. After obtaining their written informed consent, a genomic DNA sample/patient was used to obtain an enriched DNA library, then analyzed by NGS. Sequencing data analysis allowed the identification of pathogenic variants in 12 of tested patients (19%). Interestingly, MUTYH was the most frequently altered gene, followed by RNASEL, ATM, MSH6, MRE11A, and PALB2 genes. The reported resultsreinforce the need for enlarged molecular testing beyond BRCA genes, at least in patients with a personal and familial history, strongly suggestive for a hereditary/familial form. This gives also a hint to pursue more specific precision oncology therapy.

Germline Variants in Cancer Genes from Young Breast Cancer Mexican Patients

Breast cancer (BC) is one of the most frequent cancer types in women worldwide. About 7% is diagnosed in young women (YBC) less than 40 years old. In Mexico, however, YBC reaches 15% suggesting a higher genetic susceptibility. There have been some reports of germline variants in YBC across the world. However, there is only one report from a Mexican population, which is not restricted by age and limited to a panel of 143 genes resulting in 15% of patients carrying putatively pathogenic variants. Nevertheless, expanding the analysis to whole exome involves using more complex tools to determine which genes and variants could be pathogenic. We used germline whole exome sequencing combined with the PeCanPie tool to analyze exome variants in 115 YBC patients. Our results showed that we were able to identify 49 high likely pathogenic variants involving 40 genes on 34% of patients. We noted many genes already reported in BC and YBC worldwide, such as BRCA1, BRCA2, ATM, CHEK2, PALB2, and POLQ, but also others not commonly reported in YBC in Latin America, such as CLTCL1, DDX3X, ERCC6, FANCE, and NFKBIE. We show further supporting and controversial evidence for some of these genes. We conclude that exome sequencing combined with robust annotation tools and further analysis, can identify more genes and more patients affected by germline mutations in cancer.

Préoccupations et besoins d’aide psychologiques chez les femmes à risque génétique de cancer du sein ou de l’ovaire : une étude prospective observationnelle en Allemagne, Espagne et France

Objectifs et contexte : L’arrivée des tests de panel de gènes a augmenté la complexité de la communication en consultation d’oncogénétique. Une attention quant à l’impact de cette communication sur les préoccupations et les besoins d’aide psychologique s’avère d’autant plus indispensable. Cette étude vise à en quantifier le type et l’ampleur, avant et après la communication du résultat de test génétique, chez des femmes s’adressant à la consultation d’oncogénétique pour réaliser un test de susceptibilité au cancer du sein ou de l’ovaire en Allemagne, Espagne et France.

Participants et mesures : Parmi les 752 personnes invitées consécutivement à participer à cette étude, 646 (86 %) ― dont 510 (68 %) atteintes d’un cancer du sein―ont répondu à un questionnaire (PAHC (Psychosocial Aspects of Hereditary Cancer)) portant d’une part sur les préoccupations spécifiques à la démarche en oncogénétique et d’autre part sur leurs besoins d’aide psychologique ; questionnaire proposé après la consultation initiale d’oncogénétique initiale (T1) et, pour 460 (61 %) d’entre elles, deux mois après la communication du résultat du test (T2).

Résultats : Soixante-dix-neuf (17,2 %), 19 (4,1 %), 259 (56,3 %), 44 (9,6 %), 59 (12,8 %) femmes ont reçu respectivement les résultats suivants : un variant pathogène sur BRCA1/2 ou sur autre gène à risque élevé ou modéré, un résultat négatif non informatif, un résultat négatif vrai, ou la présence d’un variant dont la signification clinique est incertaine (VUS). Le type de préoccupations et les besoins d’aide psychologique se sont révélés variables selon les pays. Cependant, globalement, les préoccupations les plus fréquentes (> 70 %) étaient relatives à la perte d’un proche familial par cancer, et les moins fréquentes (< 5 %) relatives au soutien des proches. La plupart de ces préoccupations persistent deux mois plus tard, à la suite du résultat de test génétique. En revanche, le besoin d’aide psychologique a globalement diminué sur le plan statistique, excepté, selon le pays, pour les préoccupations familiales/sociales, les difficultés émotionnelles ou les aspects pratiques.

Conclusions : Dans notre étude portant sur des femmes issues de trois pays européens s’adressant à la consultation oncogénétique en vue de réaliser un test de susceptibilité au cancer du sein ou de l’ovaire, la plupart des préoccupations liées à la situation génétique persistent deux mois après la communication du résultat de test, et les besoins d’aide psychologique se manifestent surtout dans le champ des relations et des émotions.

Multi-Gene Panel Testing in Gastroenterology: Are We Ready for the Results?

Genetic testing aims to identify patients at risk for inherited cancer susceptibility. In the last decade, there was a significant increase in the request of broader panels of genes as multi-gene panel testing became widely available. However, physicians may be faced with genetic findings for which there is lack of management evidence, despite some progress in understanding their clinical relevance. In this short review, we discuss the advantages and the drawbacks related to multi-gene panel testing in the setting of a Gastrointestinal Familial Cancer Risk clinic. We also summarize the available recommendations on management of pathogenic variant carriers.

Impact of deleterious variants in other genes beyond BRCA1/2 detected in breast/ovarian and pancreatic cancer patients by NGS-based multi-gene panel testing: looking over the hedge

BACKGROUND

Hereditary breast cancer (BC), ovarian cancer (OC), and pancreatic cancer (PC) are the major BRCA-associated tumours. However, some BRCA1/2-wild-type (wt) patients with a strong personal and/or family history of cancer need a further genetic testing through a multi-gene panel containing other high- and moderate-risk susceptibility genes.

PATIENTS AND METHODS

Our study was aimed to assess if some BC, OC, or PC patients should be offered multi-gene panel testing, based on well-defined criteria concerning their personal and/or family history of cancer, such as earliness of cancer onset, occurrence of multiple tumours, or presence of at least two or more affected first-degree relatives. For this purpose, 205 out of 915 BC, OC, or PC patients, resulted negative for BRCA1/2 and with significant personal and/or family history of cancer, were genetically tested for germline pathogenic or likely pathogenic variants (PVs/LPVs) in genes different from BRCA1/2.

RESULTS

Our investigation revealed that 31 (15.1%) out of 205 patients harboured germline PVs/LPVs in no-BRCA genes, including PALB2, CHEK2, ATM, MUTYH, MSH2, and RAD51C. Interestingly, in the absence of an analysis conducted through multi-gene panel, a considerable percentage (15.1%) of PVs/LPVs would have been lost.

CONCLUSIONS

Providing a multi-gene panel testing to BRCA1/2-wt BC/OC/PC patients with a strong personal and/or family history of cancer could significantly increase the detection rates of germline PVs/LPVs in other cancer predisposition genes beyond BRCA1/2. The use of a multi-gene panel testing could improve the inherited cancer risk estimation and clinical management of patients and unaffected family members.

Success Factors and Barriers in Combining Personalized Medicine and Patient Centered Care in Breast Cancer. Results from a Systematic Review and Proposal of Conceptual Framework

Breast Cancer (BC) is the leading cause of death due to cancer in women. Ensuring equitable, quality-assured and effective care has increased the complexity of BC management. This systematic review reports on the state-of-the art of available literature investigating the enactment of personalized treatment and patient-centered care models in BC clinical practice, building a framework for the delivery of personalized BC care within a Patient-Centered model. Databases were searched for articles (from the inception to December 2020) reporting on Patient-Centered or Personalized Medicine BC management models, assessing success factors or limits. Out of 1885 records, 25 studies were included in our analysis. The main success factors include clearly defined roles and responsibilities within a multi-professional collaboration, appropriate training programs and adequate communication strategies and adopting a universal genomic language to improve patients' involvement in the decision-making process. Among detected barriers, delays in the use of genetic testing were linked to the lack of public reimbursement schemes and of clear indications in timing and appropriateness. Overall, both care approaches are complementary and necessary to effectively improve BC patient management. Our framework attempts to bridge the gap in assigning a central role played by shared decision-making, still scarcely investigated in literature.

Exploration and validation of a novel prognostic signature based on comprehensive bioinformatics analysis in hepatocellular carcinoma

The present study aimed to construct a novel signature for indicating the prognostic outcomes of hepatocellular carcinoma (HCC). Gene expression profiles were downloaded from Gene Expression Omnibus (GEO), The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC) databases. The prognosis-related genes with differential expression were identified with weighted gene co-expression network analysis (WGCNA), univariate analysis, the least absolute shrinkage and selection operator (LASSO). With the stepwise regression analysis, a risk score was constructed based on the expression levels of five genes: Risk score = (−0.7736* CCNB2) + (1.0083* DYNC1LI1) + (−0.6755* KIF11) + (0.9588* SPC25) + (1.5237* KIF18A), which can be applied as a signature for predicting the prognosis of HCC patients. The prediction capacity of the risk score for overall survival was validated with both TCGA and ICGC cohorts. The 1-, 3- and 5-year ROC curves were plotted, in which the AUC was 0.842, 0.726 and 0.699 in TCGA cohort and 0.734, 0.691 and 0.700 in ICGC cohort, respectively. Moreover, the expression levels of the five genes were determined in clinical tumor and normal specimens with immunohistochemistry. The novel signature has exhibited good prediction efficacy for the overall survival of HCC patients.

Germline molecular data in hereditary breast cancer in Brazil: Lessons from a large single-center analysis

Brazil is the largest country in South America and the most genetically heterogeneous. The aim of the present study was to determine the prevalence of germline pathogenic variants (PVs) in Brazilian patients with breast cancer (BC) who underwent genetic counseling and genetic testing at a tertiary Oncology Center. We performed a retrospective analysis of the medical records of Brazilian patients with BC referred to genetic counseling and genetic testing between August 2017 and August 2019. A total of 224 unrelated patients were included in this study. Premenopausal women represented 68.7% of the cohort. The median age at BC diagnosis was 45 years. Multigene panel testing was performed in 219 patients, five patients performed single gene analysis or family variant testing. Forty-eight germline PVs distributed among 13 genes were detected in 20.5% of the patients (46/224). Eighty-five percent of the patients (91/224) fulfilled NCCN hereditary BC testing criteria. Among these patients, 23.5% harbored PVs (45/191). In the group of patients that did not meet NCCN criteria, PV detection rate was 3% (1/33). A total of 61% of the patients (28/46) harbored a PV in a high-penetrance BC gene: 19 (8.5%) BRCA1/2, 8 (3.5%) TP53, 1 (0.5%) PALB2. Moderate penetrance genes (ATM, CHEK2) represented 15.2% (7/46) of the positive results. PVs detection was statistically associated (p<0.05) with BC diagnosis before age 45, high-grade tumors, bilateral BC, history of multiple primary cancers, and family history of pancreatic cancer. According to the current hereditary cancer guidelines, 17.4% (39/224) of the patients had actionable variants. Nine percent of the patients (20/224) had actionable variants in non-BRCA genes, it represented 43.5% of the positive results and 51.2% of the actionable variants. Considering the observed prevalence of PVs in actionable genes beyond BRCA1/2 (9%, 20/224), multigene panel testing may offer an effective first-tier diagnostic approach in this population.

Update on multi-gene panel testing and communication of genetic test results

With technological advances, multi-gene panel testing has become increasingly used to identify patients at risk for hereditary breast cancer (HBC). There are currently evidence-based interventions and breast cancer screening strategies that exist for cancer prevention and early detection among patients with HBC. Moreover, in addition to the personal impact of identifying HBC, this information may be shared with at-risk family members to amplify the benefits of testing and subsequent care among those at high risk. Opportunities and challenges with the utilization of updated multi-gene panel testing for HBC, including: (a) tumor sequencing with germline consequences; (b) genetic counseling implications; and (c) strategies to improve the communication of genetic test results to family members will be reviewed. With the advances and expansion of genetic testing, all health care providers need to be updated on both the importance and complexities of HBC counseling and testing, in order to optimize patient care.

Psychosocial problems in women attending French, German and Spanish genetics clinics before and after targeted or multigene testing results: an observational prospective study

OBJECTIVES AND SETTING

Advances in multigene panel testing for cancer susceptibility has increased the complexity of counselling, requiring particular attention to counselees' psychosocial needs. Changes in psychosocial problems before and after genetic testing were prospectively compared between genetic test results in women tested for breast or ovarian cancer genetic susceptibility in French, German and Spanish clinics.

PARTICIPANTS AND MEASURES

Among 752 counselees consecutively approached, 646 (86%) were assessed after the initial genetic consultation (T1), including 510 (68%) affected with breast cancer, of which 460 (61%) were assessed again after receiving the test result (T2), using questionnaires addressing genetic-specific psychosocial problems (Psychosocial Aspects of Hereditary Cancer (PAHC)-six scales). Sociodemographic and clinical data were also collected.

RESULTS

Seventy-nine (17.2%), 19 (4.1%), 259 (56.3%), 44 (9.6%) and 59 (12.8%) women received a BRCA1/2, another high/moderate-risk pathogenic variant (PV), negative uninformative, true negative (TN) or variant of uncertain significance result (VUS), respectively. On multiple regression analyses, compared with women receiving another result, those with a VUS decreased more in psychosocial problems related to hereditary predisposition (eg, coping with the test result) (ß=-0.11, p<0.05) and familial/social issues (eg, risk communication) (ß=-0.13, p<0.05), almost independently from their problems before testing. Women with a PV presented no change in hereditary predisposition problems and, so as women with a TN result, a non-significant increase in familial/social issues. Other PAHC scales (ie, emotions, familial cancer, personal cancer and children-related issues) were not affected by genetic testing.

CONCLUSIONS

In women tested for breast or ovarian cancer genetic risk in European genetics clinics, psychosocial problems were mostly unaffected by genetic testing. Apart from women receiving a VUS result, those with another test result presented unchanged needs in counselling in particular about hereditary predisposition and familial/social issues.

Familial Cancer: How to Successfully Recruit Families for Germline Mutations Studies? Multiple Myeloma as an Example

INTRODUCTION

Identification of germline mutations related to an increased cancer risk enables diagnostic, preventive, and therapeutic measures for individuals carrying the disease variant. However, recruitment of families for studies on these mutations can be challenging. Herein we present some of the obstacles that can arise during such studies. We suggest solutions for overcoming or avoiding these difficulties, enabling an efficient and ethically correct family recruitment.

PATIENTS AND METHODS

We describe a study on germline mutations associated with familial risk of multiple myeloma using next-generation sequencing of the whole genome. To date, the study has recruited 54 participants/16 families from different centers in Germany. It was performed at the University Hospital of Heidelberg and German Cancer Research Center.

RESULTS

We were confronted with ethical/psychological concerns of patients and family members, a large number of ineligible families, a profound time investment by the participants and the study team, incidental findings, and participants' death. We present solutions to these difficulties such as: knowledge of and adherence to the laws protecting participants' rights, an exact clarification of the inclusion and exclusion criteria, a clear division of tasks within members of the study team, a collaboration with general practitioners/oncologists and patients' support groups, a detailed and understandable informed consent including information about incidental findings, and a choice of a representative in case of participant's death.

CONCLUSION

A successful recruitment for studies on familial cancer is challenging, yet possible. It can be facilitated by applying the previously mentioned strategies.