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Rodgers-Fouche L, Arora S, Ricker C, Li D, Farooqi M, Balaguer F, Dominguez-Valentin M, Guillem JG, Kanth P, Liska D, Melson J, Mraz KA, Shirts BH, Vilar E, Katona BW, Hodan R. Exploring Stakeholders' Perspectives on Implementing Universal Germline Testing for Colorectal Cancer: Findings From a Clinical Practice Survey. JCO Precis Oncol 2023; 7:e2300440. [PMID: 37897815 PMCID: PMC10860957 DOI: 10.1200/po.23.00440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 08/24/2023] [Accepted: 09/13/2023] [Indexed: 10/30/2023] Open
Abstract
PURPOSE New guidelines recommend considering germline genetic testing for all patients with colorectal cancer (CRC). However, there is a lack of data on stakeholders' perspectives on the advantages and barriers of implementing universal germline testing (UGT). This study assessed the perspectives of members of the Collaborative Group of the Americas on Inherited Gastrointestinal Cancer (CGA-IGC) regarding the implementation of UGT for patients with CRC, including readiness, logistics, and barriers. METHODS A cross-sectional survey was sent to 317 active members of CGA-IGC. The survey included sections on demographics, clinical practice specialty, established institutional practices for testing, and questions pertaining to support of and barriers to implementing UGT for patients with CRC. RESULTS Eighty CGA-IGC members (25%) participated, including 42 genetic counselors (53%) and 14 gastroenterologists (18%). Forty-seven (59%) reported an academic medical center as their primary work setting, and most participants (56%) had more than 10 years of clinical practice. Although most participants (73%) supported UGT, 54% indicated that changes in practice would be required before adopting UGT, and 39% indicated that these changes would be challenging to implement. There was support for both genetics and nongenetics providers to order genetic testing, and a majority (57%) supported a standardized multigene panel rather than a customized gene panel. Key barriers to UGT implementation included limited genetics knowledge among nongenetics providers, time-consuming processes for obtaining consent, ordering tests, disclosing results, and lack of insurance coverage. CONCLUSION This study demonstrates wide support among hereditary GI cancer experts for implementation of UGT for patients with CRC. However, alternative service delivery models using nongenetics providers should be considered to address the logistical barriers to UGT implementation, particularly the growing demand for genetic testing.
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Affiliation(s)
| | - Sanjeevani Arora
- Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA
| | - Charité Ricker
- Division of Medical Oncology, Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA
| | - Dan Li
- Department of Gastroenterology, Kaiser Permanente Medical Center, Santa Clara, CA
| | - Maheen Farooqi
- Division of Medical Oncology, University of Southern California, Norris Comprehensive Cancer Center, Los Angeles, CA
| | - Francesc Balaguer
- Department of Gastroenterology, Hospital Clínic de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Spain
| | - Mev Dominguez-Valentin
- Department of Tumor Biology, Institute of Cancer Research, The Norwegian Radium Hospital, Oslo, Norway
| | - Jose G. Guillem
- Department of Surgery, University of North Carolina, Chapel Hill, NC
| | - Priyanka Kanth
- Department of Gastroenterology, MedStar Georgetown University Hospital, Washington, DC
| | - David Liska
- Department of Colorectal Surgery, Digestive Disease Institute, Cleveland Clinic, Cleveland, OH
| | - Joshua Melson
- Division of Gastroenterology, University of Arizona Cancer Center, Tucson, AZ
| | | | - Brian H. Shirts
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Eduardo Vilar
- Department of Clinical Cancer Prevention, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Bryson W. Katona
- Division of Gastroenterology and Hepatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Rachel Hodan
- Cancer Genetics, Stanford Health Care, Palo Alto, CA
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Adedokun B, Ademola A, Makumbi T, Odedina S, Agwai I, Ndom P, Gakwaya A, Ogundiran T, Ojengbede O, Huo D, Olopade OI. Unawareness of breast cancer family history among African women. Pan Afr Med J 2023; 45:188. [PMID: 38020349 PMCID: PMC10656588 DOI: 10.11604/pamj.2023.45.188.21616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 02/04/2020] [Indexed: 12/01/2023] Open
Abstract
Introduction comprehensive cancer risk assessment services are lacking in most sub-Saharan African countries and the use of accurate family history (FH) information could serve as a cheap strategy for risk evaluation. The aim of this study is to determine the proportion of women unaware of family history of cancer among female relatives and associated socio-demographic characteristics. Methods using case-control data on breast cancer among 4294 women in Nigeria, Uganda and Cameroon, we investigated the proportion of women unaware of family history of cancer among their female relatives. The association between participants' response to their awareness of female relatives' cancer history and socio-demographic characteristics was analysed according to case-control status, family side and distance of relation. Results: the proportion of women unaware if any relative had cancer was 33%, and was significantly higher among controls (43.2%) compared to 23.9% among cases (p<0.001) (Adjusted Odds Ratio (OR) = 2.51, 95% CI = 2.14 - 2.95). Age, education and marital status remained significantly associated with being unaware of FH among controls on multiple regression. Conclusion about a third of women interviewed did not know about cancer history in at least one of their female relatives. Efforts aimed at improving cancer awareness in sub-Saharan Africa (SSA) are needed. Our findings could be useful for future studies of cancer risk assessment in SSA.
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Affiliation(s)
- Babatunde Adedokun
- Center for Clinical Cancer Genetics and Global Health, University of Chicago, Chicago, United States of America
| | | | | | - Stella Odedina
- Center for Population and Reproductive Health, University of Ibadan, Ibadan, Nigeria
| | - Imaria Agwai
- Center for Population and Reproductive Health, University of Ibadan, Ibadan, Nigeria
| | - Paul Ndom
- Hôpital Général Yaoundé, Yaoundé, Cameroon
| | - Antony Gakwaya
- School of Medicine, St. Augustine International University, Kampala, Uganda
| | | | - Oladosu Ojengbede
- Center for Population and Reproductive Health, University of Ibadan, Ibadan, Nigeria
| | - Dezheng Huo
- Center for Clinical Cancer Genetics and Global Health, University of Chicago, Chicago, United States of America
| | - Olufunmilayo I. Olopade
- Center for Clinical Cancer Genetics and Global Health, University of Chicago, Chicago, United States of America
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Lučić I, Kurtović M, Mlinarić M, Piteša N, Čipak Gašparović A, Sabol M, Milković L. Deciphering Common Traits of Breast and Ovarian Cancer Stem Cells and Possible Therapeutic Approaches. Int J Mol Sci 2023; 24:10683. [PMID: 37445860 DOI: 10.3390/ijms241310683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 06/21/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023] Open
Abstract
Breast cancer (BC) and ovarian cancer (OC) are among the most common and deadly cancers affecting women worldwide. Both are complex diseases with marked heterogeneity. Despite the induction of screening programs that increase the frequency of earlier diagnosis of BC, at a stage when the cancer is more likely to respond to therapy, which does not exist for OC, more than 50% of both cancers are diagnosed at an advanced stage. Initial therapy can put the cancer into remission. However, recurrences occur frequently in both BC and OC, which are highly cancer-subtype dependent. Therapy resistance is mainly attributed to a rare subpopulation of cells, named cancer stem cells (CSC) or tumor-initiating cells, as they are capable of self-renewal, tumor initiation, and regrowth of tumor bulk. In this review, we will discuss the distinctive markers and signaling pathways that characterize CSC, their interactions with the tumor microenvironment, and the strategies they employ to evade immune surveillance. Our focus will be on identifying the common features of breast cancer stem cells (BCSC) and ovarian cancer stem cells (OCSC) and suggesting potential therapeutic approaches.
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Affiliation(s)
- Ivan Lučić
- Laboratory for Oxidative Stress, Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Matea Kurtović
- Laboratory for Hereditary Cancer, Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Monika Mlinarić
- Laboratory for Oxidative Stress, Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Nikolina Piteša
- Laboratory for Hereditary Cancer, Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Ana Čipak Gašparović
- Laboratory for Oxidative Stress, Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Maja Sabol
- Laboratory for Hereditary Cancer, Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Lidija Milković
- Laboratory for Oxidative Stress, Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia
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Ni M, Wang F, Yang A, Shao Q, Xue C, Xia W, Xu F, Lin X, Huang J, Bi X, Hong R, Chen M, Zheng Q, Jiang K, Xie X, Tang J, Wang X, Yuan Z, Wang S, Shi Y, An X. What is the appropriate genetic testing criteria for breast cancer in the Chinese population?-Analysis of genetic and clinical features from a single cancer center database. Cancer Med 2023. [PMID: 37096751 DOI: 10.1002/cam4.5976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 04/02/2023] [Accepted: 04/09/2023] [Indexed: 04/26/2023] Open
Abstract
BACKGROUND Genetic testing plays an important role in guiding screening, diagnosis, and precision treatment of breast cancer (BC). However, the appropriate genetic testing criteria remain controversial. The current study aims to facilitate the development of suitable strategies by analyzing the germline mutational profiles and clinicopathological features of large-scale Chinese BC patients. METHODS BC patients who had undergone genetic testing at the Sun Yat-sen University Cancer Center (SYSUCC) from September 2014 to March 2022 were retrospectively reviewed. Different screening criteria were applied and compared in the population cohort. RESULTS A total of 1035 BC patients were enrolled, 237 pathogenic or likely pathogenic variants (P/LPV) were identified in 235 patients, including 41 out of 203 (19.6%) patients tested only for BRCA1/2 genes, and 194 out of 832 (23.3%) received 21 genes panel testing. Among the 235 P/LPV carriers, 222 (94.5%) met the NCCN high-risk criteria, and 13 (5.5%) did not. While using Desai's criteria of testing, all females diagnosed with BC by 60 years and NCCN criteria for older patients, 234 (99.6%) met the high-risk standard, and only one did not. The 21 genes panel testing identified 4.9% of non-BRCA P/LPVs and a significantly high rate of variants of uncertain significance (VUSs) (33.9%). The most common non-BRCA P/LPVs were PALB2 (11, 1.3%), TP53 (10, 1.2%), PTEN (3, 0.4%), CHEK2 (3, 0.4%), ATM (3, 0.4%), BARD1 (3, 0.4%), and RAD51C (2, 0.2%). Compared with BRCA1/2 P/LPVs, non-BRCA P/LPVs showed a significantly low incidence of NCCN criteria listed family history, second primary cancer, and different molecular subtypes. CONCLUSIONS Desai's criteria might be a more appropriate genetic testing strategy for Chinese BC patients. Panel testing could identify more non-BRCA P/LPVs than BRCA1/2 testing alone. Compared with BRCA1/2 P/LPVs, non-BRCA P/LPVs exhibited different personal and family histories of cancer and molecular subtype distributions. The optimal genetic testing strategy for BC still needs to be investigated with larger continuous population studies.
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Affiliation(s)
- Mengqian Ni
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Fang Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Molecular Diagnostics, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Anli Yang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Breast Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Qiong Shao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Molecular Diagnostics, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Cong Xue
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Wen Xia
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Fei Xu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xi Lin
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Ultrasound, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jiajia Huang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xiwen Bi
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Ruoxi Hong
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Meiting Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Qiufan Zheng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Kuikui Jiang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xinhua Xie
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Breast Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Jun Tang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Breast Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xi Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Breast Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Zhongyu Yuan
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Shusen Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yanxia Shi
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xin An
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, Guangzhou, China
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Rodríguez-Salgado LE, Silva-Aldana CT, Medina-Méndez E, Bareño-Silva J, Arcos-Burgos M, Silgado-Guzmán DF, Restrepo CM. Frequency of actionable Exomic secondary findings in 160 Colombian patients: Impact in the healthcare system. Gene 2022; 838:146699. [PMID: 35803546 DOI: 10.1016/j.gene.2022.146699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 06/11/2022] [Accepted: 06/24/2022] [Indexed: 11/25/2022]
Abstract
INTRODUCTION By 2021, the American College of Medical Genetics and Genomics (ACMG) published the last version of their secondary findings (SF) reporting recommendations for cases in which a person receives a genetic test. OBJECTIVE To determine in a sample of the Colombian population the prevalence of SF for the 59 genes on the ACMG SF v2.0 list associated with 27 genetic diseases. MATERIALS AND METHODS An analytical cross-sectional study was developed by examining the sequences of 160 exomes. Based on the ACMG guidelines, a variant classification algorithm was designed to filter and select reportable SF. RESULTS Eleven pathogenic variants were identified in 13/160 (8.13%) patients in genes APOB, BRCA2, CACNA1S, COL3A1, LDLR, MYBPC3, PCSK9, PKP2, PMS2 and RYR2. No association was found between the sociodemographic variables and the SF to report (P > 0,05). CONCLUSION We reported the first approach of actionable pathogenic variants spectrum in the Colombian population. Given the frequency found in this study and the clinical impact of genomic variants on health, it is essential to actively search for SF having the opportunity to receive genetic counselling, prevention and clinical management.
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Affiliation(s)
| | | | | | - José Bareño-Silva
- School of Medicine, Mental Health Research Group, CES University, Medellin, Colombia
| | - Mauricio Arcos-Burgos
- Research Group on Psychiatric Disorders (GIPSI), Department of Psychiatry, Institute of Medical Research, School of Medicine, University of Antioquia, Medellín, Colombia
| | | | - Carlos M Restrepo
- Center for Research in Genetics and Genomics (CIGGUR), GeniURos Research Group, School of Medicine and Health Sciences, University of Rosario, Bogotá, Colombia.
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Ajaz S, Zaidi SEZ, Ali S, Siddiqa A, Memon MA. Germline Mutation Analysis in Sporadic Breast Cancer Cases With Clinical Correlations. Front Genet 2022; 13:820610. [PMID: 35356428 PMCID: PMC8959921 DOI: 10.3389/fgene.2022.820610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 02/08/2022] [Indexed: 11/15/2022] Open
Abstract
Demographics for breast cancers vary widely among nations. The frequency of germline mutations in breast cancers, which reflects the hereditary cases, has not been investigated adequately and accurately in highly-consanguineous Pakistani population. In the present discovery case series, germ-line mutations in twenty-seven breast cancer candidate genes were investigated in eighty-four sporadic breast cancer patients along with the clinical correlations. The germ-line variants were also assessed in two healthy gender-matched controls. The clinico-pathological features were evaluated by descriptive analysis and Pearson χ2 test (with significant p-value <0.05). The most frequent parameters associated with hereditary cancer cases are age and ethnicity. Therefore, the analyses were stratified on the basis of age (≤40 years vs. >40 years) and ethnicity. The breast cancer gene panel assay was carried out by BROCA, which is a genomic capture, massively parallel next generation sequencing assay on Illumina Hiseq2000 with 100bp read lengths. Copy number variations were determined by partially-mapped read algorithm. Once the mutation was identified, it was validated by Sanger sequencing. The ethnic analysis stratified on the basis of age showed that the frequency of breast cancer at young age (≤40 years) was higher in Sindhis (n = 12/19; 64%) in contrast to patients in other ethnic groups. Majority of the patients had stage III (38.1%), grade III (50%), tumor size 2–5 cm (54.8%), and invasive ductal carcinoma (81%). Overall, the analysis revealed germ-line mutations in 11.9% of the patients, which was not significantly associated with younger age or any particular ethnicity. The mutational spectrum was restricted to three genes: BRCA1, BRCA2, and TP53. The identified mutations consist of seven novel germ-line mutations, while three mutations have been reported previously. All the mutations are predicted to result in protein truncation. No mutations were identified in the remaining twenty-four candidate breast cancer genes. The present study provides the framework for the development of hereditary-based preventive and treatment strategies against breast cancers in Pakistani population.
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Affiliation(s)
- Sadia Ajaz
- Dr. Panjwani Center for Molecular Medicine and Drug Research (PCMD), International Center for Chemical and Biological Sciences (ICCBS), University of Karachi, Karachi, Pakistan
- Department of Human Genetics and Molecular Biology, University of Health Sciences, Lahore, Pakistan
- *Correspondence: Sadia Ajaz, ,
| | - Sani-e-Zehra Zaidi
- Dr. Panjwani Center for Molecular Medicine and Drug Research (PCMD), International Center for Chemical and Biological Sciences (ICCBS), University of Karachi, Karachi, Pakistan
| | - Saleema Ali
- Dr. Panjwani Center for Molecular Medicine and Drug Research (PCMD), International Center for Chemical and Biological Sciences (ICCBS), University of Karachi, Karachi, Pakistan
| | - Aisha Siddiqa
- Atomic Energy Medical Centre (AEMC), Jinnah Postgraduate Medical Centre (JPMC), Karachi, Pakistan
| | - Muhammad Ali Memon
- Atomic Energy Medical Centre (AEMC), Jinnah Postgraduate Medical Centre (JPMC), Karachi, Pakistan
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Next step in molecular genetics of hereditary breast/ovarian cancer: Multigene panel testing in clinical actionably genes and prioritization algorithms in the study of variants of uncertain significance. Eur J Med Genet 2022; 65:104468. [PMID: 35245693 DOI: 10.1016/j.ejmg.2022.104468] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 01/15/2022] [Accepted: 02/25/2022] [Indexed: 02/06/2023]
Abstract
INTRODUCTION BRCA1 and BRCA2 are the two main genes causing hereditary breast and ovarian cancer (HBOC). However, thanks to the development of Next Generation Sequencing (NGS), other genes linked to this syndrome (CHEK2, BRIP1, ATM and PALB2 among others) can be analysed. MATERIAL AND METHODS an analysis by multigene panel testing was performed in 138 index cases (ICs) from HBOC Spanish families with a previous non-informative result for BRCA1/2. The BRCA Hereditary Cancer Master™ Plus kit, including 26 actionable and candidate genes related to HBOC was employed. Once classified, an algorithm was employed to prioritized those variants of unknown significance with a higher risk of having a deleterious effect. Moreover, a mRNA splicing assay was performed for the prioritized VUS c.3402+3A > C in ATM, located at intron 23. RESULTS A total of 82 variants were found: 70 VUS and 12 pathogenic or probably pathogenic variants. The diagnostic yield in actionable genes non-BRCA was 7.97% of the total tested ICs. Overall, 19 VUS were prioritized, which meant 27% of the 70 total VUS. RNA analysis of the variant 3402+3A > C confirmed a deleterious impact on splicing. DISCUSSION The implementation of a multigene panel in HBOC studied families improved the diagnostic yield, concordant with results obtained in previous publications. Due to the important number of VUS obtained in NGS, the application of a prioritization algorithm is needed in order to select those variants in which it is necessary to conduct further studies.
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Horton C, Blanco K, Lo MT, Speare V, LaDuca H, Dolinsky J, Kurian AW. Clinician-Reported Impact of Germline Multigene Panel Testing on Cancer Risk Management Recommendations. JNCI Cancer Spectr 2022; 6:6510947. [PMID: 35603838 PMCID: PMC8904928 DOI: 10.1093/jncics/pkac002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 10/14/2021] [Accepted: 11/11/2021] [Indexed: 11/26/2022] Open
Abstract
Background With increased adoption of multi-gene panel testing (MGPT) for hereditary cancer, management guidelines now include a wider range of predisposition genes. Yet little is known about whether MGPT results prompt changes to clinicians’ risk management recommendations and whether those recommendations adhere to guidelines. Methods We assessed cancer risk management recommendations made by clinicians ordering MGPT for hereditary cancer at a diagnostic laboratory using an internet-based survey. We received paired pre- and posttest responses for 2172 patients (response rate = 14.3%). Unpaired posttest responses were received in 168 additional patients with positive results. All tests were 2-sided. Results Clinicians reported a change in risk management recommendations for 76.6% of patients who tested positive for a pathogenic or likely pathogenic variant, with changes to surveillance being most common (71.1%), followed by surgical (33.6%), chemoprevention (15.1%), and clinical trial (9.4%) recommendations. Clinicians recommended risk-reducing interventions more often for patients with pathogenic variants in high-risk than moderate-risk genes (P < .001), whereas surveillance recommendations were similar for high-risk and moderate-risk genes. Guideline adherence was high for surveillance (86.3%) and surgical (79.6%) recommendations. Changes to risk management recommendations occurred in 8.8% and 7.6% of patients with uncertain and negative results, respectively. Conclusions Clinicians report frequent changes to cancer risk management recommendations based on positive results in both high-risk and moderate-risk genes. Reported introduction of interventions in patients with inconclusive and negative results is rare and adherence to practice guidelines is high in patients with positive results, suggesting a low probability of harm resulting from MGPT.
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Affiliation(s)
- Carolyn Horton
- Ambry Genetics, 1 Enterprise, Aliso Viejo, 92656, CA, USA
| | - Kirsten Blanco
- Ambry Genetics, 1 Enterprise, Aliso Viejo, 92656, CA, USA
| | - Min-Tzu Lo
- Ambry Genetics, 1 Enterprise, Aliso Viejo, 92656, CA, USA
| | | | - Holly LaDuca
- Ambry Genetics, 1 Enterprise, Aliso Viejo, 92656, CA, USA
| | - Jill Dolinsky
- Ambry Genetics, 1 Enterprise, Aliso Viejo, 92656, CA, USA
| | - Allison W Kurian
- Departments of Medicine and of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, 94305, CA, USA
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Germline sequence variants contributing to cancer susceptibility in South African breast cancer patients of African ancestry. Sci Rep 2022; 12:802. [PMID: 35039564 PMCID: PMC8763903 DOI: 10.1038/s41598-022-04791-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 12/23/2021] [Indexed: 11/08/2022] Open
Abstract
Since the discovery of the breast cancer susceptibility genes, BRCA1 and BRCA2, various other genes conferring an increased risk for breast cancer have been identified. Studies to evaluate sequence variants in cancer predisposition genes among women of African ancestry are limited and mostly focused on BRCA1 and BRCA2. To characterize germline sequence variants in cancer susceptibility genes, we analysed a cohort of 165 South African women of self-identified African ancestry diagnosed with breast cancer, who were unselected for family history of cancer. With the exception of four cases, all others were previously investigated for BRCA1 and BRCA2 deleterious variants, and were negative for pathogenic variants. We utilized the Illumina TruSight cancer panel for targeted sequencing of 94 cancer susceptibility genes. A total of 3.6% of patients carried a pathogenic/likely pathogenic variant in a known breast cancer susceptibility gene: 1.2% in BRCA1, 0.6% in each of BRCA2, ATM, CHEK2 and PALB, none of whom had any family history of breast cancer. The mean age of patients who carried deleterious variant in BRCA1/BRCA2 was 39 years and 8 months compared to 47 years and 3 months among women who carried a deleterious variant in other breast cancer susceptibility genes.
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Czekalski MA, Huziak RC, Durst AL, Taylor S, Mai PL. Mainstreaming Genetic Testing for Epithelial Ovarian Cancer by Oncology Providers: A Survey of Current Practice. JCO Precis Oncol 2022; 6:e2100409. [PMID: 35025618 DOI: 10.1200/po.21.00409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
PURPOSE With limitations in early detection and poor treatment response, ovarian cancer is associated with significant morbidity and mortality. Up to 25% of epithelial ovarian cancer (EOC) is related to a hereditary predisposition. Current National Comprehensive Cancer Network guidelines recommend that all individuals diagnosed with EOC be offered germline genetic testing. Although this would ideally be performed by genetics professionals, a shortage of genetic counselors can affect timely access to these services. This study sought to investigate the current genetic testing practices of oncology providers to determine the feasibility of oncologist-led genetic testing for patients with EOC. METHODS A survey was distributed to members of the Society of Gynecologic Oncologists with questions regarding timing, frequency, and type of cancer genetic testing, referrals to genetics professionals, confidence with aspects of genetic testing, and any barriers to these processes. RESULTS We received 170 evaluable responses. Eighty-five percent of providers always ordered genetic testing for patients with EOC. Most providers ordered germline multigene panel testing (95.8%), generally at diagnosis (64.5%). Provider confidence with the genetic testing process was generally high and significantly differed by providers' testing practices, namely, respondents who reported always ordering genetic testing tended to be more confident in ordering testing (P = .008), interpreting results (P = .005), and counseling a patient (P = .002). Patient disinterest and concerns for insurance coverage were commonly cited as barriers to testing and referrals. CONCLUSION The findings from this study suggest that oncologist-led genetic testing for patients with EOC, with referrals to genetics professionals when appropriate, has the potential to be a viable alternative service delivery model to increase access to genetic testing for patients diagnosed with EOC.
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Affiliation(s)
- Megan A Czekalski
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA. Megan A. Czekalski is currently at Department of Pediatric Genetics, University of Maryland Baltimore, Baltimore, MD
| | | | - Andrea L Durst
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA. Megan A. Czekalski is currently at Department of Pediatric Genetics, University of Maryland Baltimore, Baltimore, MD
| | - Sarah Taylor
- Department of Obstetrics, Gynecology and Reproductive Sciences, School of Medicine, University of Pittsburgh, Pittsburgh, PA
| | - Phuong L Mai
- Center for Clinical Genetics and Genomics, Department of Obstetrics, Gynecology, and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA
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11
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Increased incidence of pathogenic variants in ATM in the context of testing for breast and ovarian cancer predisposition. J Hum Genet 2022; 67:339-345. [PMID: 35017683 DOI: 10.1038/s10038-022-01014-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 12/21/2021] [Accepted: 01/04/2022] [Indexed: 11/09/2022]
Abstract
Pathogenic Variants (PV) in major cancer predisposition genes are only identified in approximately 10% of patients with Hereditary Breast and Ovarian Cancer (HBOC) syndrome. Next Generation Sequencing (NGS) leads to the characterization of incidental variants in genes other than those known to be associated with HBOC syndrome. The aim of this study was to determine if such incidental PV were specific to a phenotype. The detection rates of HBOC-associated and incidental PV in 1812 patients who underwent genetic testing were compared with rates in control groups FLOSSIES and ExAC. The rates of incidental PV in the PALB2, ATM and CHEK2 genes were significantly increased in the HBOC group compared to controls with, respective odds ratios of 15.2 (95% CI = 5.6-47.6), 9.6 (95% CI = 4.8-19.6) and 2.7 (95% CI = 1.3-5.5). Unsupervised Hierarchical Clustering on Principle Components characterized 3 clusters: by HBOC (P = 0.01); by ExAC and FLOSSIES (P = 0.01 and 0.02 respectively); and by HBOC, ExAC and FLOSSIES (P = 0.01, 0.04 and 0.04 respectively). Interestingly, PALB2 and ATM were grouped in the same statistical cluster defined by the HBOC group, whereas CHEK2 was in a different cluster. We identified co-occurrences of PV in ATM and BRCA genes and confirmed the Manchester Scoring System as a reliable PV predictor tool for BRCA genes but not for ATM or PALB2. This study demonstrates that ATM PV, and to a lesser extent CHEK2 PV, are associated with HBOC syndrome. The co-occurrence of ATM PV with BRCA PV suggests that such ATM variants are not sufficient alone to induce cancer, supporting a multigenism hypothesis.
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12
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Zimmermann BM, Shaw DM, Elger B, Koné I. The use of heuristics in genetic testing decision-making: A qualitative interview study. PLoS One 2021; 16:e0260597. [PMID: 34847204 PMCID: PMC8631642 DOI: 10.1371/journal.pone.0260597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 11/14/2021] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Decision-making concerning predictive genetic testing for hereditary cancer syndromes is inherently complex. This study aims to investigate what kind of complexities adults undergoing genetic counseling in Switzerland experience, how they deal with them, and what heuristics they use during the decision-making process. METHODS Semi-structured qualitative interviews with eighteen Swiss adults seeking genetic counseling for hereditary cancer syndrome genetic testing and two counseling physicians were conducted and analyzed using a grounded theory approach. RESULTS Counselees stated that once they were aware of their eligibility for genetic testing they perceived an inevitable necessity to make a decision in a context of uncertainties. Some counselees perceived this decision as simple, others as very complex. High emotional involvement increased perceived complexity. We observed six heuristics that counselees used to facilitate their decision: Anticipating the test result; Focusing on consequences; Dealing with information; Interpreting disease risk; Using external guidance; and (Re-)Considering the general uncertainty of life. LIMITATIONS Our findings are limited to the context of predictive genetic testing for hereditary cancer syndromes. This qualitative study does not allow extrapolation of the relative frequency of which heuristics occur. CONCLUSIONS The use of heuristics is an inherent part of decision-making, particularly in the complex context of genetic testing for inherited cancer predisposition. However, some heuristics increase the risk of misinterpretation or exaggerated external influences. This may negatively impact informed decision-making. Thus, this study illustrates the importance of genetic counselors and medical professionals being aware of these heuristics and the individual manner in which they might be applied in the context of genetic testing decision-making. Findings may offer practical support to achieve this, as they inductively focus on the counselees' perspective.
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Affiliation(s)
- Bettina Maria Zimmermann
- Institute for Biomedical Ethics, University of Basel, Basel, Switzerland
- Institute of History and Ethics in Medicine, School of Medicine, Technical University of Munich, Munich, Germany
| | - David Martin Shaw
- Institute for Biomedical Ethics, University of Basel, Basel, Switzerland
- Care and Public Health Research Institute, Maastricht University, Maastricht, The Netherlands
| | - Bernice Elger
- Institute for Biomedical Ethics, University of Basel, Basel, Switzerland
- Center for Legal Medicine, University of Geneva, Geneva, Switzerland
| | - Insa Koné
- Institute for Biomedical Ethics, University of Basel, Basel, Switzerland
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Fonfria M, de Juan Jiménez I, Tena I, Chirivella I, Richart-Aznar P, Segura A, Sánchez-Heras AB, Martinez-Dueñas E. Prevalence and Clinicopathological Characteristics of Moderate and High-Penetrance Genes in Non-BRCA1/2 Breast Cancer High-Risk Spanish Families. J Pers Med 2021; 11:jpm11060548. [PMID: 34204722 PMCID: PMC8231620 DOI: 10.3390/jpm11060548] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 06/09/2021] [Accepted: 06/10/2021] [Indexed: 01/10/2023] Open
Abstract
(1) Background: Over the last decade, genetic counseling clinics have moved from single-gene sequencing to multigene panel sequencing. Multiple genes related to a moderate risk of breast cancer (BC) have emerged, although many questions remain regarding the risks and clinical features associated with these genes. (2) Methods: Ninety-six BC index cases (ICs) with high-risk features for hereditary breast and ovarian cancer (HBOC) and with a previous uninformative result for BRCA1/2 were tested with a panel of 41 genes associated with BC risk. The frequency of pathogenic variants (PVs) was related to the clinical characteristics of BC. (3) Results: We detected a PV rate of 13.5% (excluding two cases each of BRCA1 and MUTYH). Among the 95 assessed cases, 17 PVs were identified in 16 ICs, as follows: BRCA1 (n = 2), CHEK2 (n = 3), ATM (n = 5), MUTYH (n = 2), TP53 (n = 2), BRIP1 (n = 1), CASP8 (n = 1), and MSH2 (n = 1). We also identified a novel loss-of-function variant in CASP8, a candidate gene for increased BC risk. There was no evidence that the clinical characteristics of BC might be related to a higher chance of identifying a PV. (4) Conclusions: In our cohort, which was enriched with families with a high number of BC cases, a high proportion of mutations in ATM and CHEK2 were identified. The clinical characteristics of BC associated with moderate-risk genes were different from those related to BRCA1/2 genes.
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Affiliation(s)
- Maria Fonfria
- Cancer Genetic Counseling Unit, Medical Oncology Department, Castellon Provincial Hospital, 12002 Castellon, Spain; (M.F.); (I.T.); (E.M.-D.)
| | - Inmaculada de Juan Jiménez
- Molecular Biology Unit, Service of Clinical Analysis, La Fe University Hospital, 46026 Valencia, Spain
- Correspondence: ; Tel.: +34-961244587
| | - Isabel Tena
- Cancer Genetic Counseling Unit, Medical Oncology Department, Castellon Provincial Hospital, 12002 Castellon, Spain; (M.F.); (I.T.); (E.M.-D.)
| | - Isabel Chirivella
- Medical Oncology Department, INCLIVA Biomedical Research Institute, University of Valencia, 46001 Valencia, Spain;
| | - Paula Richart-Aznar
- Cancer Genetic Counseling Unit, Medical Oncology Department, La Fe University Hospital, 46026 Valencia, Spain; (P.R.-A.); (A.S.)
| | - Angel Segura
- Cancer Genetic Counseling Unit, Medical Oncology Department, La Fe University Hospital, 46026 Valencia, Spain; (P.R.-A.); (A.S.)
| | - Ana Beatriz Sánchez-Heras
- Cancer Genetic Counseling Unit, Medical Oncology Department, Elche University Hospital, 03203 Elche, Spain;
| | - Eduardo Martinez-Dueñas
- Cancer Genetic Counseling Unit, Medical Oncology Department, Castellon Provincial Hospital, 12002 Castellon, Spain; (M.F.); (I.T.); (E.M.-D.)
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14
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Clinicopathologic Profile of Breast Cancer in Germline ATM and CHEK2 Mutation Carriers. Genes (Basel) 2021; 12:genes12050616. [PMID: 33919281 PMCID: PMC8143279 DOI: 10.3390/genes12050616] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 04/15/2021] [Accepted: 04/20/2021] [Indexed: 01/07/2023] Open
Abstract
The most common breast cancer (BC) susceptibility genes beyond BRCA1/2 are ATM and CHEK2. For the purpose of exploring the clinicopathologic characteristics of BC developed by ATM or CHEK2 mutation carriers, we reviewed the archive of our Family Cancer Clinic. Since 2018, 1185 multi-gene panel tests have been performed. Nineteen ATM and 17 CHEK2 mutation carriers affected by 46 different BCs were identified. A high rate of bilateral tumors was observed in ATM (26.3%) and CHEK2 mutation carriers (41.2%). While 64.3% of CHEK2 tumors were luminal A-like, 56.2% of ATM tumors were luminal B-like/HER2-negative. Moreover, 21.4% of CHEK2-related invasive tumors showed a lobular histotype. About a quarter of all ATM-related BCs and a third of CHEK2 BCs were in situ carcinomas and more than half of ATM and CHEK2-related BCs were diagnosed at stage I-II. Finally, 63.2% of ATM mutation carriers and 64.7% of CHEK2 mutation carriers presented a positive BC family history. The biological and clinical characteristics of ATM and CHEK2-related tumors may help improve diagnosis, prognostication and targeted therapeutic approaches. Contralateral mastectomy should be considered and discussed with ATM and CHEK2 mutation carriers at the first diagnosis of BC.
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15
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Ece Solmaz A, Yeniay L, Gökmen E, Zekioğlu O, Haydaroğlu A, Bilgen I, Özkınay F, Onay H. Clinical Contribution of Next-Generation Sequencing Multigene Panel Testing for BRCA Negative High-Risk Patients With Breast Cancer. Clin Breast Cancer 2021; 21:e647-e653. [PMID: 33980423 DOI: 10.1016/j.clbc.2021.04.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 02/19/2021] [Accepted: 04/05/2021] [Indexed: 12/22/2022]
Abstract
BACKGROUND Breast cancer is the most common malignancy in women and thought to be hereditary in 10% of patients. Recent next-generation sequencing studies have increased the detection of pathogenic or likely pathogenic (P/LP) variants in genes other than BRCA1/2 in patients with breast cancer. This study evaluated pathogenic variants, likely pathogenic variants, and variants of unknown significance in 18 hereditary cancer susceptibility genes in patients with BRCA1/2-negative breast cancer. PATIENTS AND METHODS This retrospective study included 188 high-risk BRCA1/2-negative patients with breast cancer tested with a multigene cancer panel using next-generation sequencing. RESULTS Among 188 proband cases, 18 variants in 21 patients (11.1%) were classified as P/LP in PALB2 (n = 6), CHEK2 (n = 5), MUTYH (n = 4), ATM (n = 3), TP53 (n = 2), BRIP1 (n = 1), and MSH2 (n = 1). Three novel P/LP variants were identified. An additional 28 variants were classified as variants of unknown significance and detected in 30 different patients (15.9%). CONCLUSION This is one of the largest study from Turkey to investigate the mutation spectrum in non-BRCA hereditary breast cancer susceptibility genes. A multigene panel test increased the likelihood of identifying a molecular diagnosis in patients with BRCA 1/2-negative breast cancer at risk for a hereditary breast cancer syndrome. More studies are needed to enable the clinical interpretation of these P/LP variants in hereditary patients with breast cancer.
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Affiliation(s)
- Aslı Ece Solmaz
- Department of Medical Genetic, Ege University Faculty of Medicine, Izmir, Turkey.
| | - Levent Yeniay
- Department of General Surgery, Ege University Faculty of Medicine, Izmir, Turkey
| | - Erhan Gökmen
- Department of Medical Oncology, Ege University Faculty of Medicine, Izmir, Turkey
| | - Osman Zekioğlu
- Department of Pathology, Ege University Faculty of Medicine, Izmir, Turkey
| | - Ayfer Haydaroğlu
- Department of Radiation Oncology, Ege University Faculty of Medicine, Izmir, Turkey
| | - Işıl Bilgen
- Department of Radiology, Ege University Faculty of Medicine, Izmir, Turkey
| | - Ferda Özkınay
- Department of Medical Genetic, Ege University Faculty of Medicine, Izmir, Turkey
| | - Hüseyin Onay
- Department of Medical Genetic, Ege University Faculty of Medicine, Izmir, Turkey
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16
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Kadri MSN, Patel KM, Bhargava PA, Shah FD, Badgujar NV, Tarapara BV, Patel PS, Shaikh MI, Shah K, Patel A, Pandya S, Vora H, Joshi CG, Joshi MN. Mutational Landscape for Indian Hereditary Breast and Ovarian Cancer Cohort Suggests Need for Identifying Population Specific Genes and Biomarkers for Screening. Front Oncol 2021; 10:568786. [PMID: 33552952 PMCID: PMC7859489 DOI: 10.3389/fonc.2020.568786] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 12/02/2020] [Indexed: 12/29/2022] Open
Abstract
Background Breast and ovarian cancers are the most prevalent cancers and one of the leading causes of death in Indian women. The healthcare burden of breast and ovarian cancers and the rise in mortality rate are worrying and stress the need for early detection and treatment. Methods We performed amplicon sequencing of 144 cases who had breast/ovarian cancer disease (total 137 cases are patients and seven are tested for BRCA1/2 carrier) Using our custom designed gene panel consisting of 14 genes, that are associated with high to moderate risk of breast and ovarian cancers. Variants were called using Torrent Variant Caller and were annotated using ThermoFisher's Ion Reporter software. Classification of variants and their clinical significance were identified by searching the variants against ClinVar database. Results From a total of 144 cases, we were able to detect 42 pathogenic mutations in [40/144] cases. Majority of pathogenic mutations (30/41) were detected in BRCA1 gene, while (7/41) pathogenic mutations were detected in BRCA2 gene, whereas, (2/41) pathogenic mutations were detected in TP53 gene and BRIP1, PALB2, and ATM genes respectively. So, BRCA genes contributed 88.09% of pathogenic mutations, whereas non-BRCA genes contributed 11.91% of pathogenic mutations. We were also able to detect 25 VUS which were predicted to be damaging by in silico prediction tools. Conclusion Early detection of cancers in the Indian population can be done by genetic screening using customized multi-gene panels. Indications of our findings show that in the Indian population, apart from the common BRCA genes, there are other genes that are also responsible for the disease. High frequency mutations detected in the study and variants of uncertain significance predicted to be damaging by in silico pathogenicity prediction tools can be potential biomarkers of hereditary breast and ovarian cancer in Indian HBOC patients.
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Affiliation(s)
- Mohammed Shaad N Kadri
- Gujarat Biotechnology Research Centre, Department of Science and Technology, Government of Gujarat, Gandhinagar, India
| | - Komal M Patel
- Gujarat Biotechnology Research Centre, Department of Science and Technology, Government of Gujarat, Gandhinagar, India
| | - Poonam A Bhargava
- Gujarat Biotechnology Research Centre, Department of Science and Technology, Government of Gujarat, Gandhinagar, India
| | - Franky D Shah
- Gujarat Cancer Research Institute, Civil Hospital, Ahmedabad, India
| | - Nutan V Badgujar
- Gujarat Cancer Research Institute, Civil Hospital, Ahmedabad, India
| | | | | | - Mohammed Inayatullah Shaikh
- Gujarat Biotechnology Research Centre, Department of Science and Technology, Government of Gujarat, Gandhinagar, India
| | - Krati Shah
- Clinical Genetics, ONE-Centre for Rheumatology and Genetics, Vadodara, India
| | - Apurva Patel
- Gujarat Cancer Research Institute, Civil Hospital, Ahmedabad, India
| | - Shashank Pandya
- Gujarat Cancer Research Institute, Civil Hospital, Ahmedabad, India
| | - Hemangini Vora
- Gujarat Cancer Research Institute, Civil Hospital, Ahmedabad, India
| | - Chaitanya G Joshi
- Gujarat Biotechnology Research Centre, Department of Science and Technology, Government of Gujarat, Gandhinagar, India
| | - Madhvi N Joshi
- Gujarat Biotechnology Research Centre, Department of Science and Technology, Government of Gujarat, Gandhinagar, India
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Prevalence of germline variants in consensus moderate-to-high-risk predisposition genes to hereditary breast and ovarian cancer in BRCA1/2-negative Brazilian patients. Breast Cancer Res Treat 2020; 185:851-861. [PMID: 33128190 DOI: 10.1007/s10549-020-05985-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 10/15/2020] [Indexed: 12/23/2022]
Abstract
PURPOSE This study aimed to identify and classify genetic variants in consensus moderate-to-high-risk predisposition genes associated with Hereditary Breast and Ovarian Cancer Syndrome (HBOC), in BRCA1/2-negative patients from Brazil. METHODS The study comprised 126 index patients who met NCCN clinical criteria and tested negative for all coding exons and intronic flanking regions of BRCA1/2 genes. Multiplex PCR-based assays were designed to cover the complete coding regions and flanking splicing sites of six genes implicated in HBOC. Sequencing was performed on HiSeq2500 Genome Analyzer. RESULTS Overall, we identified 488 unique variants. We identified five patients (3.97%) that harbored pathogenic or likely pathogenic variants in four genes: ATM (1), CHEK2 (2), PALB2 (1), and TP53 (1). One hundred and thirty variants were classified as variants of uncertain significance (VUS), 10 of which were predicted to disrupt mRNA splicing (seven non-coding variants and three coding variants), while other six missense VUS were classified as probably damaging by prediction algorithms. CONCLUSION A detailed mutational profile of non-BRCA genes is still being described in Brazil. In this study, we contributed to filling this gap, by providing important data on the diversity of genetic variants in a Brazilian high-risk patient cohort. ATM, CHEK2, PALB2 and TP53 are well established as HBOC predisposition genes, and the identification of deleterious variants in such actionable genes contributes to clinical management of probands and relatives.
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18
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Suszynska M, Kozlowski P. Summary of BARD1 Mutations and Precise Estimation of Breast and Ovarian Cancer Risks Associated with the Mutations. Genes (Basel) 2020; 11:genes11070798. [PMID: 32679805 PMCID: PMC7397132 DOI: 10.3390/genes11070798] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/13/2020] [Accepted: 07/14/2020] [Indexed: 12/12/2022] Open
Abstract
Over the last two decades, numerous BARD1 mutations/pathogenic variants (PVs) have been found in patients with breast cancer (BC) and ovarian cancer (OC). However, their role in BC and OC susceptibility remains controversial, and strong evidence-based guidelines for carriers are not yet available. Herein, we present a comprehensive catalog of BARD1 PVs identified in large cumulative cohorts of ~48,700 BC and ~20,800 OC cases (retrieved from 123 studies examining the whole coding sequence of BARD1). Using these resources, we compared the frequency of BARD1 PVs in the cases and ~134,100 controls from the gnomAD database and estimated the effect of the BARD1 PVs on BC and OC risks. The analysis revealed that BARD1 is a BC moderate-risk gene (odds ratio (OR) = 2.90, 95% CIs:2.25–3.75, p < 0.0001) but not an OC risk gene (OR = 1.36, 95% CIs:0.87–2.11, p = 0.1733). In addition, the BARD1 mutational spectrum outlined in this study allowed us to determine recurrent PVs and evaluate the variant-specific risk for the most frequent PVs. In conclusion, these precise estimates improve the understanding of the role of BARD1 PVs in BC and OC predisposition and support the need for BARD1 diagnostic testing in BC patients.
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Affiliation(s)
| | - Piotr Kozlowski
- Correspondence: ; Tel.: +48-618-528-503 (ext. 261); Fax: +48-618-520-532
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19
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Velázquez C, Lastra E, Avila Cobos F, Abella L, de la Cruz V, Hernando BA, Hernández L, Martínez N, Infante M, Durán M. A comprehensive custom panel evaluation for routine hereditary cancer testing: improving the yield of germline mutation detection. J Transl Med 2020; 18:232. [PMID: 32522261 PMCID: PMC7288470 DOI: 10.1186/s12967-020-02391-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 05/28/2020] [Indexed: 12/12/2022] Open
Abstract
Background In the context of our Regional Program of Hereditary Cancer, individuals fulfilling the criteria are tested for germline mutations to subsequently establish the clinical management. Our standard diagnostic approach focuses on sequencing a few classic high-risk genes, a method that frequently renders uninformative genetic results. This study aims to examine the improved yield offered by an On-Demand panel. Methods We designed an On-Demand panel for the analysis of 35-genes associated with inherited cancer susceptibility in a total of 128 cases of Hereditary Breast and Ovarian Cancer (HBOC) and Hereditary Nonpolyposis Colorectal Cancer (HNPCC). Results Eighteen deleterious mutations were detected, in both routinely (BRCA2, MLH1, MSH2, PMS2) and non-routinely (ATM, BLM, BRIP1, CHEK2, MUTYH) tested genes. The screening extended to 35 genes rendered by patients carrying several- up to 6-Variants of Unknown Significance (VUS). Moreover, we confirmed the splicing disruption at RNA level for a not previously reported BRIP1 splicing mutation. Using an On-Demand panel, we identified 18 pathogenic mutation carriers, seven of which would have gone unnoticed with traditional analysis. Conclusions Our results reinforce the utility of NGS gene panels in the diagnostic routine to increase the performance of genetic testing, especially in individuals from families with overlapping cancer phenotypes.
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Affiliation(s)
- Carolina Velázquez
- Cancer Genetics Group, Institute of Genetics and Molecular Biology (UVa-CSIC), Sanz y Forés 3, 47003, Valladolid, Spain. .,IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Montpellier, France.
| | - Enrique Lastra
- Unit of Genetic Counseling in Cancer, Complejo Hospitalario de Burgos, Burgos, Spain
| | | | - Luis Abella
- Unit of Genetic Counseling in Cancer, Hospital Universitario Rio Hortega, Valladolid, Spain
| | - Virginia de la Cruz
- Unit of Genetic Counseling in Cancer, Hospital Universitario Rio Hortega, Valladolid, Spain
| | | | - Lara Hernández
- Cancer Genetics Group, Institute of Genetics and Molecular Biology (UVa-CSIC), Sanz y Forés 3, 47003, Valladolid, Spain
| | - Noemí Martínez
- Cancer Genetics Group, Institute of Genetics and Molecular Biology (UVa-CSIC), Sanz y Forés 3, 47003, Valladolid, Spain
| | - Mar Infante
- Cancer Genetics Group, Institute of Genetics and Molecular Biology (UVa-CSIC), Sanz y Forés 3, 47003, Valladolid, Spain
| | - Mercedes Durán
- Cancer Genetics Group, Institute of Genetics and Molecular Biology (UVa-CSIC), Sanz y Forés 3, 47003, Valladolid, Spain
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Achatz MI, Caleffi M, Guindalini R, Marques RM, Nogueira-Rodrigues A, Ashton-Prolla P. Recommendations for Advancing the Diagnosis and Management of Hereditary Breast and Ovarian Cancer in Brazil. JCO Glob Oncol 2020; 6:439-452. [PMID: 32155091 PMCID: PMC7113069 DOI: 10.1200/jgo.19.00170] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/21/2020] [Indexed: 12/20/2022] Open
Abstract
PURPOSE The objective of this review was to address the barriers limiting access to genetic cancer risk assessment and genetic testing for individuals with suspected hereditary breast and ovarian cancer (HBOC) through a review of the diagnosis and management steps of HBOC. METHODS A selected panel of Brazilian experts in fields related to HBOC was provided with a series of relevant questions to address before the multiday conference. During this conference, each narrative was discussed and edited by the entire group, through numerous drafts and rounds of discussion, until a consensus was achieved. RESULTS The authors propose specific and realistic recommendations for improving access to early diagnosis, risk management, and cancer care of HBOC specific to Brazil. Moreover, in creating these recommendations, the authors strived to address all the barriers and impediments mentioned in this article. CONCLUSION There is a great need to expand hereditary cancer testing and counseling in Brazil, and changing current policies is essential to accomplishing this goal. Increased knowledge and awareness, together with regulatory actions to increase access to this technology, have the potential to improve patient care and prevention and treatment efforts for patients with cancer across the country.
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Affiliation(s)
| | - Maira Caleffi
- Nucleo Mama Porto Alegre and Associação Hospitalar Moinhos de Vento, Porto Alegre, Brazil
| | - Rodrigo Guindalini
- Oncologia D’or, Rede D’or São Luiz, Brazil
- Centro de Investigação Translacional em Oncologia, Instituto do Cancer do Estado de Sao Paulo, Hospital das Clínicas da Faculdade de Medicina da Universidade de Sao Paulo, São Paulo, Brazil
| | - Renato Moretti Marques
- Programa da Saúde da Mulher, Hospital Israelita Albert Einstein, São Paulo, Brazil
- Centro de Oncologia e Hematologia, Hospital Israelita Albert Einstein, São Paulo, Brazil
| | - Angelica Nogueira-Rodrigues
- Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Grupo Brasileiro de Oncologia Ginecológica, Belo Horizonte, Brazil
- DOM Oncologia, Minas Gerais, Brazil
| | - Patricia Ashton-Prolla
- Departmento de Genética, Universidade Federal do Rio Grande do Sul
- Laboratório de Medicina Genômica, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
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Kwong A, Shin VY, Chen J, Cheuk IWY, Ho CYS, Au CH, Chan KKL, Ngan HYS, Chan TL, Ford JM, Ma ESK. Germline Mutation in 1338 BRCA-Negative Chinese Hereditary Breast and/or Ovarian Cancer Patients: Clinical Testing with a Multigene Test Panel. J Mol Diagn 2020; 22:544-554. [PMID: 32068069 DOI: 10.1016/j.jmoldx.2020.01.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Revised: 12/16/2019] [Accepted: 01/14/2020] [Indexed: 12/23/2022] Open
Abstract
Differences in the mutation spectrum across ethnicities suggest the importance of identifying genes in addition to common high penetrant genes to estimate the associated breast cancer risk in China. A total of 1338 high-risk breast cancer patients who tested negative for germline BRCA1, BRCA2, TP53, and PTEN mutations between 2007 and 2017 were selected from the Hong Kong Hereditary Breast Cancer Family Registry. Patient samples were subjected to next-generation DNA sequencing using a multigene panel (Color Genomics). All detected pathogenic variants were validated by bidirectional DNA sequencing. The sequencing data were coanalyzed by a bioinformatics pipeline developed in-house. Sixty-one pathogenic variants (4.6%) were identified in this cohort in 11 cancer predisposition genes. Most carriers (77.1%) had early onset of breast cancer (age <45 years), 32.8% had family members with breast cancer, and 11.5% had triple-negative breast cancer. The most common mutated genes were PALB2 (1.4%), RAD51D (0.8%), and ATM (0.8%). A total of 612 variants of unknown significance were identified in 494 patients, and 87.4% of the variants of unknown significance were missense mutations. Pathogenic variants in cancer predisposition genes beyond BRCA1, BRCA2, TP53, and PTEN were detected in an additional 4.6% of patients using the multigene panel. PALB2 (1.4%) and RAD51D (0.8%) were the most commonly mutated genes in patients who tested mutation negative by a four-gene panel.
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Affiliation(s)
- Ava Kwong
- Department of Surgery, The University of Hong Kong and The University of Hong Kong-Shenzhen Hospital, Hong Kong Special Administrative Region; Department of Surgery, Hong Kong Sanatorium and Hospital, Hong Kong Special Administrative Region; Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong Sanatorium and Hospital, Hong Kong Special Administrative Region.
| | - Vivian Y Shin
- Department of Surgery, The University of Hong Kong and The University of Hong Kong-Shenzhen Hospital, Hong Kong Special Administrative Region
| | - Jiawei Chen
- Department of Surgery, The University of Hong Kong and The University of Hong Kong-Shenzhen Hospital, Hong Kong Special Administrative Region
| | - Isabella W Y Cheuk
- Department of Surgery, The University of Hong Kong and The University of Hong Kong-Shenzhen Hospital, Hong Kong Special Administrative Region
| | - Cecilia Y S Ho
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong Special Administrative Region
| | - Chun H Au
- Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong Special Administrative Region
| | - Karen K L Chan
- Department of Obstetrics and Gynecology, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Hextan Y S Ngan
- Department of Obstetrics and Gynecology, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Tsun L Chan
- Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong Sanatorium and Hospital, Hong Kong Special Administrative Region; Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong Special Administrative Region
| | - James M Ford
- Department of Medicine (Oncology), Stanford University School of Medicine, Stanford, California
| | - Edmond S K Ma
- Hong Kong Hereditary Breast Cancer Family Registry, Hong Kong Sanatorium and Hospital, Hong Kong Special Administrative Region; Division of Molecular Pathology, Department of Pathology, Hong Kong Sanatorium and Hospital, Hong Kong Special Administrative Region
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Development and Validation of a 34-Gene Inherited Cancer Predisposition Panel Using Next-Generation Sequencing. BIOMED RESEARCH INTERNATIONAL 2020; 2020:3289023. [PMID: 32090079 PMCID: PMC6998746 DOI: 10.1155/2020/3289023] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 08/04/2019] [Indexed: 12/18/2022]
Abstract
The use of genetic testing to identify individuals with hereditary cancer syndromes has been widely adopted by clinicians for management of inherited cancer risk. The objective of this study was to develop and validate a 34-gene inherited cancer predisposition panel using targeted capture-based next-generation sequencing (NGS). The panel incorporates genes underlying well-characterized cancer syndromes, such as BRCA1 and BRCA2 (BRCA1/2), along with more recently discovered genes associated with increased cancer risk. We performed a validation study on 133 unique specimens, including 33 with known variant status; known variants included single nucleotide variants (SNVs) and small insertions and deletions (Indels), as well as copy-number variants (CNVs). The analytical validation study achieved 100% sensitivity and specificity for SNVs and small Indels, with 100% sensitivity and 98.0% specificity for CNVs using in-house developed CNV flagging algorithm. We employed a microarray comparative genomic hybridization (aCGH) method for all specimens that the algorithm flags as CNV-positive for confirmation. In combination with aCGH confirmation, CNV detection specificity improved to 100%. We additionally report results of the first 500 consecutive specimens submitted for clinical testing with the 34-gene panel, identifying 53 deleterious variants in 13 genes in 49 individuals. Half of the detected pathogenic/likely pathogenic variants were found in BRCA1 (23%), BRCA2 (23%), or the Lynch syndrome-associated genes PMS2 (4%) and MLH1 (2%). The other half were detected in 9 other genes: MUTYH (17%), CHEK2 (15%), ATM (4%), PALB2 (4%), BARD1 (2%), CDH1 (2%), CDKN2A (2%), RAD51C (2%), and RET (2%). Our validation studies and initial clinical data demonstrate that a 34-gene inherited cancer predisposition panel can provide clinically significant information for cancer risk assessment.
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Vysotskaia V, Kaseniit KE, Bucheit L, Ready K, Price K, Johansen Taber K. Clinical utility of hereditary cancer panel testing: Impact of PALB2, ATM, CHEK2, NBN, BRIP1, RAD51C, and RAD51D results on patient management and adherence to provider recommendations. Cancer 2019; 126:549-558. [PMID: 31682005 PMCID: PMC7003834 DOI: 10.1002/cncr.32572] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 09/06/2019] [Accepted: 09/16/2019] [Indexed: 12/15/2022]
Abstract
BACKGROUND Although management guidelines exist for several genes associated with a 2-fold to 5-fold increase in the relative risk for certain cancers, the value of testing for them remains controversial. METHODS De-identified personal and family history data for 654 individuals with pathogenic variants (PVs) in PALB2, ATM, CHEK2, NBN, BRIP1, RAD51C, and/or RAD51D were analyzed for pretest and post-test candidacy for guideline-recommended management of cancer risk. These individuals were invited to complete a survey about provider recommendations and their adherence. RESULTS Twenty-four percent of CHEK2, ATM, PALB2, or NBN PV carriers were appropriate for consideration of annual breast magnetic resonance imaging screening before genetic testing, with the remaining 76% appropriate only after testing. No BRIP1, RAD51C, or RAD51D PV carriers were appropriate for consideration of risk-reducing salpingo-oophorectomy before genetic testing; 100% were appropriate only after testing. Seventeen percent of CHEK2 PV carriers were appropriate for earlier and more frequent colonoscopy before genetic testing, with the remaining 83% appropriate only after testing. Provider recommendations for annual breast magnetic resonance imaging, consideration of risk-reducing salpingo-oophorectomy, and earlier and more frequent colonoscopy were reported by 42%, 26%, and 66% of breast, ovarian, and colorectal cancer risk PV carriers, respectively, before genetic testing, versus 82%, 79%, and 81%, respectively, after testing. Nearly all respondents had planned or undertaken provider-recommended management. CONCLUSIONS Testing for PALB2, ATM, CHEK2, NBN, BRIP1, RAD51C, and RAD51D changed management for those carrying PVs. Provider recommendations were aligned with guidelines, and patients adhered to recommendations, both of which are critical for reducing both long-term cancer morbidity and mortality.
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Affiliation(s)
| | | | | | - Kaylene Ready
- Myriad Women's Health, South San Francisco, California
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Catana A, Apostu AP, Antemie RG. Multi gene panel testing for hereditary breast cancer - is it ready to be used? Med Pharm Rep 2019; 92:220-225. [PMID: 31460501 PMCID: PMC6709965 DOI: 10.15386/mpr-1083] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 02/28/2019] [Accepted: 03/27/2019] [Indexed: 02/06/2023] Open
Abstract
Breast cancer is one of the most common malignancies and the leading cause of death among women worldwide. About 20% of breast cancers are hereditary. Approximately 30% of the mutations have remained negative after testing BRCA1/2 even in families with a Mendelian inheritance pattern for breast cancer. Additional non-BRCA genes have been identified as predisposing for breast cancer. Multi gene panel testing tries to cover and explain the BRCA negative inherited breast cancer, improving efficiency, speed and costs of the breast cancer screening. We identified 23 studies reporting results from individuals who have undergone multi gene panel testing for hereditary breast cancer and noticed a prevalence of 1-12% of non-BRCA genes, but also a high level of variants of uncertain significance. A result with a high level of variants of uncertain significance is likely to be more costly than bring benefits, as well as increase the anxiety for patients. Regarding further development of multi gene panel testing, more research is required to establish both the optimal care of patients with cancer (specific treatments like PARP inhibitors) and the management of unaffected individuals (chemoprevention and/or prophylactic surgeries). Early detection in these patients as well as prophylactic measures will significantly increase the chance of survival. Therefore, multi gene panel testing is not yet ready to be used outside clear guidelines. In conclusion, studies on additional cohorts will be needed to better define the real prevalence, penetrance and the variants of these genes, as well as to describe clear evidence-based guidelines for these patients.
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Affiliation(s)
- Andreea Catana
- Genetics Department, Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | | | - Razvan-Geo Antemie
- Iuliu Hatieganu University of Medicine and Pharmacy, Cluj-Napoca, Romania
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BARD1 is A Low/Moderate Breast Cancer Risk Gene: Evidence Based on An Association Study of the Central European p.Q564X Recurrent Mutation. Cancers (Basel) 2019; 11:cancers11060740. [PMID: 31142030 PMCID: PMC6627038 DOI: 10.3390/cancers11060740] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 05/21/2019] [Accepted: 05/24/2019] [Indexed: 12/14/2022] Open
Abstract
In addition to several well-established breast cancer (BC) susceptibility genes, the contribution of other candidate genes to BC risk remains mostly undefined. BARD1 is a potentially predisposing BC gene, however, the rarity of its mutations and an insufficient family/study size have hampered corroboration and estimation of the associated cancer risks. To clarify the role of BARD1 mutations in BC predisposition, a comprehensive case-control association study of a recurring nonsense mutation c.1690C>T (p.Q564X) was performed, comprising ~14,000 unselected BC patients and ~5900 controls from Polish and Belarusian populations. For comparisons, two BARD1 variants of unknown significance were also genotyped. We detected the highest number of BARD1 variants in BC cases in any individual BARD1-specific study, including 38 p.Q564X mutations. The p.Q564X was associated with a moderately increased risk of BC (OR = 2.30, p = 0.04). The estimated risk was even higher for triple-negative BC and bilateral BC. As expected, the two tested variants of unknown significance did not show significant associations with BC risk. Our study provides substantial evidence for the association of a deleterious BARD1 mutation with BC as a low/moderate risk allele. The p.Q564X was shown to be a Central European recurrent mutation with potential relevance for future genetic testing.
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Macedo GS, Alemar B, Ashton-Prolla P. Reviewing the characteristics of BRCA and PALB2-related cancers in the precision medicine era. Genet Mol Biol 2019; 42:215-231. [PMID: 31067289 PMCID: PMC6687356 DOI: 10.1590/1678-4685-gmb-2018-0104] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 10/24/2018] [Indexed: 12/24/2022] Open
Abstract
Germline mutations in BRCA1 and BRCA2 (BRCA) genes confer high risk of developing cancer, especially breast and ovarian tumors. Since the cloning of these tumor suppressor genes over two decades ago, a significant amount of research has been done. Most recently, monoallelic loss-of-function mutations in PALB2 have also been shown to increase the risk of breast cancer. The identification of BRCA1, BRCA2 and PALB2 as proteins involved in DNA double-strand break repair by homologous recombination and of the impact of complete loss of BRCA1 or BRCA2 within tumors have allowed the development of novel therapeutic approaches for patients with germline or somatic mutations in said genes. Despite the advances, especially in the clinical use of PARP inhibitors, key gaps remain. Now, new roles for BRCA1 and BRCA2 are emerging and old concepts, such as the classical two-hit hypothesis for tumor suppression, have been questioned, at least for some BRCA functions. Here aspects regarding cancer predisposition, cellular functions, histological and genomic findings in BRCA and PALB2-related tumors will be presented, in addition to an up-to-date review of the evolution and challenges in the development and clinical use of PARP inhibitors.
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Affiliation(s)
- Gabriel S Macedo
- Post-Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.,Precision Medicine Program, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
| | - Barbara Alemar
- Post-Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Patricia Ashton-Prolla
- Post-Graduate Program in Genetics and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil.,Precision Medicine Program, Hospital de Clínicas de Porto Alegre, Porto Alegre, RS, Brazil
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27
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Cline MS, Liao RG, Parsons MT, Paten B, Alquaddoomi F, Antoniou A, Baxter S, Brody L, Cook-Deegan R, Coffin A, Couch FJ, Craft B, Currie R, Dlott CC, Dolman L, den Dunnen JT, Dyke SOM, Domchek SM, Easton D, Fischmann Z, Foulkes WD, Garber J, Goldgar D, Goldman MJ, Goodhand P, Harrison S, Haussler D, Kato K, Knoppers B, Markello C, Nussbaum R, Offit K, Plon SE, Rashbass J, Rehm HL, Robson M, Rubinstein WS, Stoppa-Lyonnet D, Tavtigian S, Thorogood A, Zhang C, Zimmermann M, Burn J, Chanock S, Rätsch G, Spurdle AB. BRCA Challenge: BRCA Exchange as a global resource for variants in BRCA1 and BRCA2. PLoS Genet 2018; 14:e1007752. [PMID: 30586411 PMCID: PMC6324924 DOI: 10.1371/journal.pgen.1007752] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Revised: 01/08/2019] [Indexed: 12/20/2022] Open
Abstract
The BRCA Challenge is a long-term data-sharing project initiated within the Global Alliance for Genomics and Health (GA4GH) to aggregate BRCA1 and BRCA2 data to support highly collaborative research activities. Its goal is to generate an informed and current understanding of the impact of genetic variation on cancer risk across the iconic cancer predisposition genes, BRCA1 and BRCA2. Initially, reported variants in BRCA1 and BRCA2 available from public databases were integrated into a single, newly created site, www.brcaexchange.org. The purpose of the BRCA Exchange is to provide the community with a reliable and easily accessible record of variants interpreted for a high-penetrance phenotype. More than 20,000 variants have been aggregated, three times the number found in the next-largest public database at the project’s outset, of which approximately 7,250 have expert classifications. The data set is based on shared information from existing clinical databases—Breast Cancer Information Core (BIC), ClinVar, and the Leiden Open Variation Database (LOVD)—as well as population databases, all linked to a single point of access. The BRCA Challenge has brought together the existing international Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) consortium expert panel, along with expert clinicians, diagnosticians, researchers, and database providers, all with a common goal of advancing our understanding of BRCA1 and BRCA2 variation. Ongoing work includes direct contact with national centers with access to BRCA1 and BRCA2 diagnostic data to encourage data sharing, development of methods suitable for extraction of genetic variation at the level of individual laboratory reports, and engagement with participant communities to enable a more comprehensive understanding of the clinical significance of genetic variation in BRCA1 and BRCA2. The goal of this study and paper has been to develop an international resource to generate an informed and current understanding of the impact of genetic variation on cancer risk across the cancer predisposition genes, BRCA1 and BRCA2. Reported variants in BRCA1 and BRCA2 available from public databases were integrated into a single, newly created site, www.brcaexchange.org, to provide a reliable and easily accessible record of variants interpreted for a high-penetrance phenotype.
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Affiliation(s)
- Melissa S. Cline
- University of California Santa Cruz Genomics Institute, University of California, Santa Cruz, California, United States of America
| | - Rachel G. Liao
- Broad Institute, Cambridge, Massachusetts, United States of America
| | - Michael T. Parsons
- Genetics and Computational Biology Division, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Benedict Paten
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Faisal Alquaddoomi
- Department of Computer Science, Biomedical Informatics Group Universitätsstrasse, Zürich, Switzerland
- Biomedical Informatics, University Hospital Zurich, Zurich, Switzerland
- Biocybernetics Laboratory, Computer Science Department, University of California, Los Angeles, California, United States of America
| | - Antonis Antoniou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Samantha Baxter
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Larry Brody
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, Bethesda, Maryland, United States of America
| | - Robert Cook-Deegan
- School for the Future of Innovation in Society, and Consortium for Science, Policy & Outcomes, Arizona State University, Tempe, Arizona, United States of America
| | - Amy Coffin
- University of California Santa Cruz Genomics Institute, University of California, Santa Cruz, California, United States of America
| | - Fergus J. Couch
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Brian Craft
- University of California Santa Cruz Genomics Institute, University of California, Santa Cruz, California, United States of America
| | - Robert Currie
- University of California Santa Cruz Genomics Institute, University of California, Santa Cruz, California, United States of America
| | - Chloe C. Dlott
- University of California Santa Cruz Genomics Institute, University of California, Santa Cruz, California, United States of America
| | - Lena Dolman
- The Global Alliance for Genomics and Health, Toronto, Ontario, Canada
| | - Johan T. den Dunnen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Stephanie O. M. Dyke
- Centre of Genomics and Policy, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Susan M. Domchek
- Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Douglas Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kingdom
| | - Zachary Fischmann
- University of California Santa Cruz Genomics Institute, University of California, Santa Cruz, California, United States of America
| | - William D. Foulkes
- Program in Cancer Genetics, Department of Oncology and Human Genetics, McGill University, Montréal, Quebec, Canada
| | - Judy Garber
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - David Goldgar
- Huntsman Cancer Institute and Department of Dermatology, University of Utah, Salt Lake City, Utah, United States of America
| | - Mary J. Goldman
- University of California Santa Cruz Genomics Institute, University of California, Santa Cruz, California, United States of America
| | - Peter Goodhand
- The Global Alliance for Genomics and Health, Toronto, Ontario, Canada
| | - Steven Harrison
- Partners HealthCare Laboratory for Molecular Medicine and Harvard Medical School, Boston, Massachusetts, United States of America
| | - David Haussler
- University of California Santa Cruz Genomics Institute, University of California, Santa Cruz, California, United States of America
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
| | - Kazuto Kato
- Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Bartha Knoppers
- Centre of Genomics and Policy, Faculty of Medicine, Human Genetics, McGill University, Montreal, Québec, Canada
| | - Charles Markello
- University of California Santa Cruz Genomics Institute, University of California, Santa Cruz, California, United States of America
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America
- Center for Biomolecular Science & Engineering, University of California, Santa Cruz, California, United States of America
| | - Robert Nussbaum
- Invitae, San Francisco, California, United States of America
| | - Kenneth Offit
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Sharon E. Plon
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Jem Rashbass
- National Disease Registration, National Cancer Registration and Analysis Service, Public Health England, London, United Kingdom
| | - Heidi L. Rehm
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, Massachusetts, United States of America
- Department of Pathology, Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
| | - Mark Robson
- Clinical Genetics Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
| | - Wendy S. Rubinstein
- CancerLinQ at American Society of Clinical Oncology (ASCO), Alexandria, Virginia, United States of America
| | | | - Sean Tavtigian
- Partners HealthCare Laboratory for Molecular Medicine and Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Oncological Sciences, The University of Utah, Salt Lake City, Utah, United States of America
| | - Adrian Thorogood
- The Global Alliance for Genomics and Health, Toronto, Ontario, Canada
- Centre of Genomics and Policy, McGill University, Montreal, Canada
| | - Can Zhang
- Department of Computer Science, University of California, Santa Cruz, Santa Cruz, California, United States of America
| | - Marc Zimmermann
- Department of Computer Science, Biomedical Informatics Group Universitätsstrasse, Zürich, Switzerland
- Biomedical Informatics, University Hospital Zurich, Zurich, Switzerland
| | | | - John Burn
- Institute of Genetic Medicine, Newcastle University, Centre for Life, Newcastle upon Tyne, United Kingdom
| | - Stephen Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, United States of America
| | - Gunnar Rätsch
- Department of Computer Science, Biomedical Informatics Group Universitätsstrasse, Zürich, Switzerland
- Biomedical Informatics, University Hospital Zurich, Zurich, Switzerland
- Computational Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America
- Swiss Institute for Bioinformatics, Lausanne, Switzerland
- * E-mail: (GR); (ABS)
| | - Amanda B. Spurdle
- Genetics and Computational Biology Division, QIMR Berghofer Medical Research Institute, Herston, Brisbane, Australia
- * E-mail: (GR); (ABS)
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Bonache S, Esteban I, Moles-Fernández A, Tenés A, Duran-Lozano L, Montalban G, Bach V, Carrasco E, Gadea N, López-Fernández A, Torres-Esquius S, Mancuso F, Caratú G, Vivancos A, Tuset N, Balmaña J, Gutiérrez-Enríquez S, Diez O. Multigene panel testing beyond BRCA1/2 in breast/ovarian cancer Spanish families and clinical actionability of findings. J Cancer Res Clin Oncol 2018; 144:2495-2513. [PMID: 30306255 DOI: 10.1007/s00432-018-2763-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 10/01/2018] [Indexed: 12/15/2022]
Abstract
PURPOSE Few and small studies have been reported about multigene testing usage by massively parallel sequencing in European cancer families. There is an open debate about what genes should be tested, and the actionability of some included genes is under research. METHODS We investigated a panel of 34 known high/moderate-risk cancer genes, including 16 related to breast or ovarian cancer (BC/OC) genes, and 63 candidate genes to BC/OC in 192 clinically suspicious of hereditary breast/ovarian cancer (HBOC) Spanish families without pathogenic variants in BRCA1 or BRCA2 (BRCA1/2). RESULTS We identified 16 patients who carried a high- or moderate-risk pathogenic variant in eight genes: 4 PALB2, 3 ATM, 2 RAD51D, 2 TP53, 2 APC, 1 BRIP1, 1 PTEN and 1 PMS2. These findings led to increased surveillance or prevention options in 12 patients and predictive testing in their family members. We detected 383 unique variants of uncertain significance in known cancer genes, of which 35 were prioritized in silico. Eighteen loss-of-function variants were detected in candidate BC/OC genes in 17 patients (1 BARD1, 1 ERCC3, 1 ERCC5, 2 FANCE, 1 FANCI, 2 FANCL, 1 FANCM, 1 MCPH1, 1 PPM1D, 2 RBBP8, 3 RECQL4 and 1 with SLX4 and XRCC2), three of which also carry pathogenic variants in known cancer genes. CONCLUSIONS Eight percent of the BRCA1/2 negative patients carry pathogenic variants in other actionable genes. The multigene panel usage improves the diagnostic yield in HBOC testing and it is an effective tool to identify potentially new candidate genes.
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Affiliation(s)
- Sandra Bonache
- Oncogenetics Group, Vall d'Hebron Institute of Oncology-VHIO, Lab 2.02A, CELLEX CENTER, c/Natzaret, 115-117, 08035, Barcelona, Catalonia, Spain
| | - Irene Esteban
- High Risk and Cancer Prevention Group, VHIO, Barcelona, Spain
- Genetics and Microbiology Department, Universitat Autònoma de Barcelona, Campus UAB, Bellaterra, Spain
| | - Alejandro Moles-Fernández
- Oncogenetics Group, Vall d'Hebron Institute of Oncology-VHIO, Lab 2.02A, CELLEX CENTER, c/Natzaret, 115-117, 08035, Barcelona, Catalonia, Spain
| | - Anna Tenés
- Area of Clinical and Molecular Genetics, University Hospital of Vall d'Hebron, Barcelona, Spain
| | - Laura Duran-Lozano
- Oncogenetics Group, Vall d'Hebron Institute of Oncology-VHIO, Lab 2.02A, CELLEX CENTER, c/Natzaret, 115-117, 08035, Barcelona, Catalonia, Spain
| | - Gemma Montalban
- Oncogenetics Group, Vall d'Hebron Institute of Oncology-VHIO, Lab 2.02A, CELLEX CENTER, c/Natzaret, 115-117, 08035, Barcelona, Catalonia, Spain
| | - Vanessa Bach
- Oncogenetics Group, Vall d'Hebron Institute of Oncology-VHIO, Lab 2.02A, CELLEX CENTER, c/Natzaret, 115-117, 08035, Barcelona, Catalonia, Spain
| | - Estela Carrasco
- High Risk and Cancer Prevention Group, VHIO, Barcelona, Spain
| | - Neus Gadea
- High Risk and Cancer Prevention Group, VHIO, Barcelona, Spain
- Medical Oncology Department, University Hospital of Vall d'Hebron, Barcelona, Spain
| | | | | | - Francesco Mancuso
- Cancer Genomics Group, Vall d'Hebron Institute of Oncology, VHIO, Barcelona, Spain
| | - Ginevra Caratú
- Cancer Genomics Group, Vall d'Hebron Institute of Oncology, VHIO, Barcelona, Spain
| | - Ana Vivancos
- Cancer Genomics Group, Vall d'Hebron Institute of Oncology, VHIO, Barcelona, Spain
| | - Noemí Tuset
- Medical Oncology Department, Hospital Universitari Arnau de Vilanova, Lleida, Spain
| | - Judith Balmaña
- High Risk and Cancer Prevention Group, VHIO, Barcelona, Spain
- Medical Oncology Department, University Hospital of Vall d'Hebron, Barcelona, Spain
| | - Sara Gutiérrez-Enríquez
- Oncogenetics Group, Vall d'Hebron Institute of Oncology-VHIO, Lab 2.02A, CELLEX CENTER, c/Natzaret, 115-117, 08035, Barcelona, Catalonia, Spain.
| | - Orland Diez
- Oncogenetics Group, Vall d'Hebron Institute of Oncology-VHIO, Lab 2.02A, CELLEX CENTER, c/Natzaret, 115-117, 08035, Barcelona, Catalonia, Spain.
- Area of Clinical and Molecular Genetics, University Hospital of Vall d'Hebron, Barcelona, Spain.
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Fortuno C, James PA, Spurdle AB. Current review of TP53 pathogenic germline variants in breast cancer patients outside Li-Fraumeni syndrome. Hum Mutat 2018; 39:1764-1773. [PMID: 30240537 DOI: 10.1002/humu.23656] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 08/31/2018] [Accepted: 09/19/2018] [Indexed: 12/16/2022]
Abstract
Pathogenic germline variants in TP53 predispose carriers to the multi-cancer Li-Fraumeni syndrome (LFS). Widespread multigene panel testing is identifying TP53 pathogenic variants in breast cancer patients outside the strict clinical criteria recommended for LFS testing. We aimed to assess frequency and clinical implications of TP53 pathogenic variants in breast cancer cohorts ascertained outside LFS. Classification of TP53 germline variants reported in 59 breast cancer studies, and publicly available population control sets was reviewed and identified evidence for misclassification of variants. TP53 pathogenic variant frequency was determined for: breast cancer studies grouped by ascertainment characteristics; breast cancer cohorts undergoing panel testing; and population controls. Early age of breast cancer onset, regardless of family history or BRCA1/BRCA2 previous testing, had the highest pick-up rate for TP53 carriers. Patients at risk of hereditary breast cancer unselected for features of LFS carried TP53 pathogenic variants at a frequency comparable to that of other non-BRCA1/2 breast cancer predisposing genes, and ∼threefold more than reported in population controls. These results have implications for the implementation of TP53 testing in broader clinical settings, and suggest urgent need to investigate cancer risks associated with TP53 pathogenic variants in individuals outside the LFS spectrum.
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Affiliation(s)
- Cristina Fortuno
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Australia
| | - Paul A James
- Peter MacCallum Cancer Centre and Royal Melbourne Hospital Familial Cancer Centre, Melbourne, Australia
| | - Amanda B Spurdle
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, Australia
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Abstract
OBJECTIVE To evaluate the role of screening patients at increased risk for hereditary cancer syndromes with an extended panel of cancer predisposition genes to identify actionable genetic mutations. METHODS A retrospective chart review was conducted of all patients presenting to a multidisciplinary cancer program for genetic counseling and testing from January 2015 to December 2016. Individuals presenting to the program were identified as at-risk by a personal or family history of cancer, by their health care provider, or by self-referral. All participants met current National Comprehensive Cancer Network criteria for genetic risk evaluation for hereditary cancer. The results of testing and its implications for management, based on National Comprehensive Cancer Network guidelines, were recorded. RESULTS Of 670 at-risk patients who underwent genetic testing, 66 (9.9%) had BRCA-limited testing; of these, 26 of 670 (3.9%) had a deleterious or likely pathogenic mutation. Expanded panel testing was done for 560 of the 670 patients (83.4%), and abnormal results were found in 65 of 670 (9.7%); non-BRCA mutations (predominantly CHEK2) were found in 49 of the 65 (75%). Abnormal genetic testing was associated with increased surveillance in 96% of those with deleterious mutations, whereas negative testing for a known familial mutation in 45 patients was associated with a downgrade of their risk and reduction of subsequent surveillance and management. CONCLUSION Guideline-based management is frequently altered by genetic testing, including panel testing, in patients at risk for cancer. We recommend that obstetrics and gynecology providers routinely refer at-risk patients for genetic counseling and testing when clinically appropriate.
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Predictors of next-generation sequencing panel selection using a shared decision-making approach. NPJ Genom Med 2018; 3:11. [PMID: 29736259 PMCID: PMC5923203 DOI: 10.1038/s41525-018-0050-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 04/02/2018] [Accepted: 04/05/2018] [Indexed: 01/05/2023] Open
Abstract
The introduction of next-generation sequencing panels has transformed the approach for genetic testing in cancer patients, however, established guidelines for their use are lacking. A shared decision-making approach has been adopted by our service, where patients play an active role in panel selection and we sought to identify factors associated with panel selection and report testing outcomes. Demographic and clinical data were gathered for female breast and/or ovarian cancer patients aged 21 and over who underwent panel testing. Panel type was classified as ‘breast cancer panel’ (BCP) or ‘multi-cancer panel’ (MCP). Stepwise multiple logistic regression analysis was used to identify clinical factors most predictive of panel selection. Of the 265 included subjects, the vast majority selected a broader MCP (81.5%). Subjects who chose MCPs were significantly more likely to be ≥50 years of age (49 vs. 31%; p < 0.05), Chinese (76 vs. 47%; p < 0.001) and have a personal history of ovarian cancer (41 vs. 8%; p < 0.001) with the latter two identified as the best predictors of panel selection. Family history of cancer was not significantly associated with panel selection. There were no statistically significant differences in result outcomes between the two groups. In summary, our findings demonstrate that the majority of patients have a preference for interrogating a larger number of genes beyond those with established testing guidelines, despite the additional likelihood of uncertainty. Individual factors, including cancer history and ethnicity, are the best predictors of panel selection. Thanks to next-generation sequencing (NGS) it is possible to test multiple genes for cancer susceptibility quickly and cheaply. At the National Cancer Centre Singapore, shared decision-making is used to actively encourage the involvement of patients in the selection of either a ‘breast cancer panel’ (BCP) or a broader ‘multi-cancer panel’ (MCP) test. Joanne Ngeow at the Centre’s Cancer Genetics Service and colleagues examined the choices made by 265 patients with breast and/or ovarian cancer following detailed pre-test counselling by the genetics team. The majority of patients selected the MCP, potentially highlighting a willingness to accept the additional uncertainty that comes with broader NGS panels. Interestingly, a personal history of ovarian cancer and Chinese ethnicity, but not a family history of cancer, were significantly associated with panel selection.
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Screening of over 1000 Indian patients with breast and/or ovarian cancer with a multi-gene panel: prevalence of BRCA1/2 and non-BRCA mutations. Breast Cancer Res Treat 2018; 170:189-196. [PMID: 29470806 DOI: 10.1007/s10549-018-4726-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 02/19/2018] [Indexed: 12/15/2022]
Abstract
PURPOSE Breast and/or ovarian cancers are among the most common cancers in women across the world. In the Indian population, the healthcare burden of breast and/or ovarian cancers has been steadily rising, thus stressing the need for early detection, surveillance, and disease management measures. However, the burden attributable to inherited mutations is not well characterized. METHODS We sequenced 1010 unrelated patients and families from across India with an indication of breast and/or ovarian cancers, using the TruSight Cancer panel which includes 14 genes, strongly associated with risk of hereditary breast and/or ovarian cancers. Genetic variations were identified using the StrandNGS software and interpreted using the StrandOmics platform. RESULTS We were able to detect mutations in 304 (30.1%) cases, of which, 56 mutations were novel. A majority (84.9%) of the mutations were detected in the BRCA1/2 genes as compared to non-BRCA genes (15.1%). When the cases were stratified on the basis of age at diagnosis and family history of cancer, the high rate of 75% of detection of hereditary variants was observed in patients whose age at diagnosis was below 40 years and had first-degree family member(s) affected by breast and/or ovarian cancers. Our findings indicate that in the Indian population, there is a high prevalence of mutations in the high-risk breast cancer genes: BRCA1, BRCA2, TP53, and PALB2. CONCLUSION In India, socioeconomic inequality limiting access to treatment is a major factor towards increased cancer burden; therefore, incorporation of a cost-effective and comprehensive multi-gene test will be helpful in ensuring widespread implementation of genetic screening in the clinical practice for hereditary breast and/or ovarian cancers.
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Oda K, Tanikawa M, Sone K, Mori-Uchino M, Osuga Y, Fujii T. Recent advances in targeting DNA repair pathways for the treatment of ovarian cancer and their clinical relevance. Int J Clin Oncol 2017; 22:611-618. [DOI: 10.1007/s10147-017-1137-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 04/28/2017] [Indexed: 11/24/2022]
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