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Guo Q, Ji S, Takeuchi K, Urasaki W, Suzuki A, Iwasaki Y, Saito H, Xu Z, Arai M, Nakamura S, Momozawa Y, Chiba N, Miki Y, Matsuura M, Sunada S. Functional evaluation of BRCA1/2 variants of unknown significance with homologous recombination assay and integrative in silico prediction model. J Hum Genet 2023; 68:849-857. [PMID: 37731132 DOI: 10.1038/s10038-023-01194-6] [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: 12/25/2022] [Revised: 08/01/2023] [Accepted: 08/29/2023] [Indexed: 09/22/2023]
Abstract
Numerous variants of unknown significance (VUSs) exist in hereditary breast and ovarian cancers. Although multiple methods have been developed to assess the significance of BRCA1/2 variants, functional discrepancies among these approaches remain. Therefore, a comprehensive functional evaluation system for these variants should be established. We performed conventional homologous recombination (HR) assays for 50 BRCA1 and 108 BRCA2 VUSs and complementarily predicted VUSs using a statistical logistic regression prediction model that integrated six in silico functional prediction tools. BRCA1/2 VUSs were classified according to the results of the integrative in vitro and in silico analyses. Using HR assays, we identified 10 BRCA1 and 4 BRCA2 VUSs as low-functional pathogenic variants. For in silico prediction, the statistical prediction model showed high accuracy for both BRCA1 and BRCA2 compared with each in silico prediction tool individually and predicted nine BRCA1 and seven BRCA2 variants to be pathogenic. Integrative functional evaluation in this study and the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP) guidelines strongly suggested that seven BRCA1 variants (p.Glu272Gly, p.Lys1095Glu, p.Val1653Leu, p.Thr1681Pro, p.Phe1761Val, p.Thr1773Ile, and p.Gly1803Ser) and four BRCA2 variants (p.Trp31Gly, p.Ser2616Phe, p.Tyr2660Cys, and p.Leu2792Arg) were pathogenic. This study demonstrates that integrative evaluation using conventional HR assays and optimized in silico prediction comprehensively classified the significance of BRCA VUSs for future clinical applications.
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Affiliation(s)
- Qianqian Guo
- Department of Molecular Genetics, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Shuting Ji
- Department of Molecular Genetics, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Kazuma Takeuchi
- Graduate School of Public Health, Teikyo University, 2-11-1 Kaga, Itabashi-ku, Tokyo, 173-8605, Japan
| | - Wataru Urasaki
- Department of Information Sciences, Tokyo University of Science, 2641 Yamazaki, Noda City, Chiba, 278-8510, Japan
| | - Asuka Suzuki
- Graduate School of Public Health, Teikyo University, 2-11-1 Kaga, Itabashi-ku, Tokyo, 173-8605, Japan
| | - Yusuke Iwasaki
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Hiroko Saito
- Department of Genetic Diagnosis, The Cancer Institute, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan
| | - Zeyu Xu
- Department of Molecular Genetics, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Masami Arai
- Department of Clinical Genetics, Juntendo University, Graduate School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Seigo Nakamura
- Division of Breast Surgical Oncology, Department of Surgery, Showa University School of Medicine, 1-5-8 Hatanodai, Shinagawa-ku, Tokyo, 142-8555, Japan
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Natsuko Chiba
- Department of Cancer Biology; Institute of Development, Aging and Cancer, Tohoku University, 4-1 Seiryomachi, Aoba-ku, Sendai, 980-8575, Japan
| | - Yoshio Miki
- Department of Molecular Genetics, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan.
- Department of Genetic Diagnosis, The Cancer Institute, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan.
| | - Masaaki Matsuura
- Graduate School of Public Health, Teikyo University, 2-11-1 Kaga, Itabashi-ku, Tokyo, 173-8605, Japan.
| | - Shigeaki Sunada
- Department of Molecular Genetics, Medical Research Institute, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan.
- Juntendo Advanced Research Institute for Health Science, Juntendo University, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan.
- Department of Oncology, School of Medicine, Juntendo University School of Medicine, 2-1-1 Hongo, Bunkyo-ku, Tokyo, 113-8421, Japan.
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2
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Identification of Germline Variants in Patients with Hereditary Cancer Syndromes in Northeast Mexico. Genes (Basel) 2023; 14:genes14020341. [PMID: 36833268 PMCID: PMC9957276 DOI: 10.3390/genes14020341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/12/2023] [Accepted: 01/24/2023] [Indexed: 01/31/2023] Open
Abstract
Hereditary cancer syndromes (HCS) are genetic diseases with an increased risk of developing cancer. This research describes the implementation of a cancer prevention model, genetic counseling, and germline variants testing in an oncologic center in Mexico. A total of 315 patients received genetic counseling, genetic testing was offered, and 205 individuals were tested for HCS. In 6 years, 131 (63.90%) probands and 74 (36.09%) relatives were tested. Among the probands, we found that 85 (63.9%) had at least one germline variant. We identified founder mutations in BRCA1 and a novel variant in APC that led to the creation of an in-house detection process for the whole family. The most frequent syndrome was hereditary breast and ovarian cancer syndrome (HBOC) (41 cases with BRCA1 germline variants in most of the cases), followed by eight cases of hereditary non-polyposic cancer syndrome (HNPCC or Lynch syndrome) (with MLH1 as the primarily responsible gene), and other high cancer risk syndromes. Genetic counseling in HCS is still a global challenge. Multigene panels are an essential tool to detect the variants frequency. Our program has a high detection rate of probands with HCS and pathogenic variants (40%), compared with other reports that detect 10% in other populations.
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Salvati A, Carnevali I, Alexandrova E, Facchi S, Ronchi S, Libera L, Sahnane N, Memoli D, Lamberti J, Amabile S, Pepe S, Tarallo R, Sessa F, Weisz A, Tibiletti MG, Rizzo F. Targeted molecular profiling of epithelial ovarian cancer from Italian BRCA wild-type patients with a BRCA and PARP pathways gene panel. Exp Mol Pathol 2022; 128:104833. [PMID: 36165864 DOI: 10.1016/j.yexmp.2022.104833] [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: 03/21/2022] [Revised: 09/01/2022] [Accepted: 09/15/2022] [Indexed: 12/15/2022]
Abstract
Ovarian cancer (OC) is the fifth most common type of cancer in women and the fourth most common cause of cancer death in women. Identification of pathogenic variants in OC tissues has an important clinical significance for therapeutic and prevention purposes. This study aims to evaluate the mutational profile of a patient cohort, negative for BRCA1/2 germinal variants and Mismatch Repair defects, using next-generation sequencing (NGS) approach on DNA from formalin-fixed paraffin-embedded samples. We used a custom NGS panel, targeting 34 cancer-related genes, mainly of the BRCA and PARP pathways, and analyzed NGS data to identify somatic and germline variants in Italian patients affected by primary epithelial ovarian cancer. We analyzed 75 epithelial ovarian cancer tissues and identified 54 pathogenic variants and 56 variants of unknown significance. TP53 was characterized by the highest mutational rate, occurring in 55% of tested epithelial ovarian cancers (EOCs). Interestingly, a subset of 8 EOCs showed pathogenic variants of homologous recombination pathway, which could be sensitive to PARP-inhibitor therapies. Germline analysis of actionable genes revealed 4 patients carrier of pathogenic germline variants respectively of RAD51C (2 patients), RAD51D, and PALB2. Molecular profiling of EOCs using our custom NGS panel has enabled the detection of both somatic and germline variants, allowing the selection of patients suitable for targeted therapies, and the identification of high-risk OC families that can benefit from genetic counseling and testing.
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Affiliation(s)
- Annamaria Salvati
- Medical Genomics Program and Division of Oncology, AOU'S. Giovanni di Dio e Ruggi d'Aragona' Università di Salerno, 84131 Salerno, Rete Oncologica Campana, Italy; Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, 84081 Baronissi, Italy
| | - Ileana Carnevali
- Department of Pathology, Ospedale di Circolo - ASST Settelaghi and Research Center for the Study of Hereditary and Familial Tumors, Department of Medicine and Surgery of the University of Insubria, 21100 Varese, Italy
| | - Elena Alexandrova
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, 84081 Baronissi, Italy
| | - Sofia Facchi
- Department of Pathology, Ospedale di Circolo - ASST Settelaghi and Research Center for the Study of Hereditary and Familial Tumors, Department of Medicine and Surgery of the University of Insubria, 21100 Varese, Italy
| | - Susanna Ronchi
- Department of Pathology, Ospedale di Circolo - ASST Settelaghi and Research Center for the Study of Hereditary and Familial Tumors, Department of Medicine and Surgery of the University of Insubria, 21100 Varese, Italy
| | - Laura Libera
- Department of Pathology, Ospedale di Circolo - ASST Settelaghi and Research Center for the Study of Hereditary and Familial Tumors, Department of Medicine and Surgery of the University of Insubria, 21100 Varese, Italy
| | - Nora Sahnane
- Department of Pathology, Ospedale di Circolo - ASST Settelaghi and Research Center for the Study of Hereditary and Familial Tumors, Department of Medicine and Surgery of the University of Insubria, 21100 Varese, Italy
| | - Domenico Memoli
- Medical Genomics Program and Division of Oncology, AOU'S. Giovanni di Dio e Ruggi d'Aragona' Università di Salerno, 84131 Salerno, Rete Oncologica Campana, Italy; Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, 84081 Baronissi, Italy
| | - Jessica Lamberti
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, 84081 Baronissi, Italy
| | - Sonia Amabile
- Medical Genomics Program and Division of Oncology, AOU'S. Giovanni di Dio e Ruggi d'Aragona' Università di Salerno, 84131 Salerno, Rete Oncologica Campana, Italy
| | - Stefano Pepe
- Medical Genomics Program and Division of Oncology, AOU'S. Giovanni di Dio e Ruggi d'Aragona' Università di Salerno, 84131 Salerno, Rete Oncologica Campana, Italy
| | - Roberta Tarallo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, 84081 Baronissi, Italy; Genome Research Center for Health - CRGS, Campus of Medicine of the University of Salerno, 84081 Baronissi, SA, Italy
| | - Fausto Sessa
- Department of Pathology, Ospedale di Circolo - ASST Settelaghi and Research Center for the Study of Hereditary and Familial Tumors, Department of Medicine and Surgery of the University of Insubria, 21100 Varese, Italy
| | - Alessandro Weisz
- Medical Genomics Program and Division of Oncology, AOU'S. Giovanni di Dio e Ruggi d'Aragona' Università di Salerno, 84131 Salerno, Rete Oncologica Campana, Italy; Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, 84081 Baronissi, Italy; Genome Research Center for Health - CRGS, Campus of Medicine of the University of Salerno, 84081 Baronissi, SA, Italy.
| | - Maria Grazia Tibiletti
- Department of Pathology, Ospedale di Circolo - ASST Settelaghi and Research Center for the Study of Hereditary and Familial Tumors, Department of Medicine and Surgery of the University of Insubria, 21100 Varese, Italy.
| | - Francesca Rizzo
- Laboratory of Molecular Medicine and Genomics, Department of Medicine, Surgery and Dentistry 'Scuola Medica Salernitana', University of Salerno, 84081 Baronissi, Italy; Genome Research Center for Health - CRGS, Campus of Medicine of the University of Salerno, 84081 Baronissi, SA, Italy.
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4
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Sokolenko AP, Sultanova LV, Stepanov IA, Romanko AA, Venina AR, Sokolova TN, Musayeva HS, Tovgereeva MY, Magomedova MK, Akhmatkhanov KU, Vagapova EI, Suleymanov E, Vasilyeva EV, Bakaeva EK, Bizin IV, Aleksakhina SN, Imyanitov EN. Strong founder effect for BRCA1 c.3629_3630delAG pathogenic variant in Chechen patients with breast or ovarian cancer. Cancer Med 2022; 12:3167-3171. [PMID: 36000185 PMCID: PMC9939208 DOI: 10.1002/cam4.5159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 07/21/2022] [Accepted: 08/03/2022] [Indexed: 11/08/2022] Open
Abstract
Coding sequences of BRCA1, BRCA2, ATM, TP53, and PALB2 genes were analyzed in 68 consecutive Chechen patients with high-grade serous ovarian cancer (HGSOC). Pathogenic BRCA1/2 variants were identified in 15 (22%) out of 68 HGSOC cases. Nine out of ten patients with BRCA1 pathogenic alleles carried the same deletion (c.3629_3630delAG), and three out of five BRCA2 heterozygotes had Q3299X allele. The analysis of 49 consecutive patients with triple-negative breast cancer (TNBC) revealed 3 (6%) additional BRCA1 heterozygotes. All women with BRCA1 c.3629_3630delAG allele also carried linked c.1067G>A (Q356R) single nucleotide polymorphism, indicating that this is a genuine founder variant but not a mutational hotspot. An ATM truncating allele was detected in one HGSOC patient. There were no women with TP53 or PALB2 germline alterations. Genetic analysis of non-selected HGSOC patients is an efficient tool for the identification of ethnicity-specific BRCA1/2 pathogenic variants.
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Affiliation(s)
- Anna P. Sokolenko
- Department of Tumor Growth BiologyN.N. Petrov Institute of OncologySaint‐PetersburgRussia,Department of Medical GeneticsSt.‐Petersburg Pediatric Medical UniversitySaint‐PetersburgRussia
| | | | - Ilya A. Stepanov
- Department of Tumor Growth BiologyN.N. Petrov Institute of OncologySaint‐PetersburgRussia
| | - Alexandr A. Romanko
- Department of Tumor Growth BiologyN.N. Petrov Institute of OncologySaint‐PetersburgRussia,Department of Medical GeneticsSt.‐Petersburg Pediatric Medical UniversitySaint‐PetersburgRussia
| | - Aigul R. Venina
- Department of Tumor Growth BiologyN.N. Petrov Institute of OncologySaint‐PetersburgRussia
| | - Tatiana N. Sokolova
- Department of Tumor Growth BiologyN.N. Petrov Institute of OncologySaint‐PetersburgRussia
| | | | | | | | | | | | | | - Elena V. Vasilyeva
- Department of Tumor Growth BiologyN.N. Petrov Institute of OncologySaint‐PetersburgRussia
| | - Elvina Kh. Bakaeva
- Department of Tumor Growth BiologyN.N. Petrov Institute of OncologySaint‐PetersburgRussia
| | - Ilya V. Bizin
- Department of Tumor Growth BiologyN.N. Petrov Institute of OncologySaint‐PetersburgRussia
| | | | - Evgeny N. Imyanitov
- Department of Tumor Growth BiologyN.N. Petrov Institute of OncologySaint‐PetersburgRussia,Department of Medical GeneticsSt.‐Petersburg Pediatric Medical UniversitySaint‐PetersburgRussia,Department of OncologyI.I. Mechnikov North‐Western Medical UniversitySaint‐PetersburgRussia
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5
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Rweyemamu LP, Gültaşlar BK, Akan G, Dharsee N, Namkinga LA, Lyantagaye SL, Yazıcı H, Atalar F. Breast cancer in East Africa: Prevalence and spectrum of germline SNV/indel and CNVs in BRCA1 and BRCA2 genes among breast cancer patients in Tanzania. Cancer Med 2022; 12:3395-3409. [PMID: 35908255 PMCID: PMC9939169 DOI: 10.1002/cam4.5091] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 07/08/2022] [Accepted: 07/19/2022] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND Growing prevalence and aggressiveness of breast cancer (BC) among East African women strongly indicate that the genetic risk factor implicated in the etiology of the disease may have a key role. Germline pathogenic variants in BRCA1 and BRCA2 (BRCA1/2) are known to increase the lifetime risk of BC. This study investigated the prevalence and spectrum of germline single nucleotide variant/insertion and deletion (SNV/indel), and copy number variations (CNVs) in BRCA1/2 among Tanzanian BC patients, and evaluated the associations of identified variants with patient's socio-demographic and histopathological characteristics. METHODS One hundred BC patients were examined for BRCA1/2 variants using next-generation sequencing (NGS). Sanger sequencing and multiplex ligation-dependent probe amplification (MLPA) assay were performed for the confirmation of SNV/indel and CNVs, respectively. RESULTS Six germline SNV/indel pathogenic variants were detected from six unrelated patients. Five of these variants were identified in BRCA1, and one in BRCA2. We also identified, in one patient, one variant of uncertain clinical significance (VUS). CNV was not detected in any of the BC patients. Furthermore, we found that in our cohort, BRCA1/2 variant carriers were triple-negative BC patients (p = 0.019). CONCLUSIONS Our study provides first insight into BC genetic landscape by the use of NGS in the under-represented East African Tanzanian populations. Our findings support the importance of genetic risk factors in BC etiology in Tanzania and showed a relatively high overall prevalence (6%) of germline BRCA1/2 pathogenic variants in BC patients. Therefore, our results indicate that BRCA1/2 pathogenic variants may well contribute to BC incidence in Tanzania. Thus, the identification of frequent variants in BRCA1/2 genes will enable implementation of rapid, inexpensive population-specific BRCA1/2 genetic testing, particularly for triple-negative BC patients known for their high prevalence in Tanzania. This will, in turn, greatly contributes to provide effective therapeutic strategies.
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Affiliation(s)
- Linus P. Rweyemamu
- Department of Molecular Biology and BiotechnologyUniversity of Dar es SalaamDar es SalaamTanzania,Mbeya College of Health and Allied SciencesUniversity of Dar es SalaamMbeyaTanzania
| | - Büşra K. Gültaşlar
- Division of Cancer Genetics, Department of Basic Oncology, Institute of OncologyIstanbul UniversityIstanbulTurkiye
| | - Gokce Akan
- DESAM Research InstituteNear East UniversityNicosiaCyprus,MUHAS Genetic Laboratory, Department of BiochemistryMuhimbili University of Health and Allied SciencesDar es SalaamTanzania
| | - Nazima Dharsee
- Academic, Research and Consultancy UnitOcean Road Cancer InstituteDar es SalaamTanzania
| | - Lucy A. Namkinga
- Department of Molecular Biology and BiotechnologyUniversity of Dar es SalaamDar es SalaamTanzania
| | - Sylvester L. Lyantagaye
- Department of Molecular Biology and BiotechnologyUniversity of Dar es SalaamDar es SalaamTanzania,Mbeya College of Health and Allied SciencesUniversity of Dar es SalaamMbeyaTanzania
| | - Hülya Yazıcı
- Division of Cancer Genetics, Department of Basic Oncology, Institute of OncologyIstanbul UniversityIstanbulTurkiye,Department of Medical Biology and Genetics, Faculty of MedicineIstanbul Arel UniversityIstanbulTurkiye
| | - Fatmahan Atalar
- MUHAS Genetic Laboratory, Department of BiochemistryMuhimbili University of Health and Allied SciencesDar es SalaamTanzania,Department of Rare Diseases, Child Health InstituteIstanbul UniversityIstanbulTurkiye
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6
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Aljarf R, Shen M, Pires DEV, Ascher DB. Understanding and predicting the functional consequences of missense mutations in BRCA1 and BRCA2. Sci Rep 2022; 12:10458. [PMID: 35729312 PMCID: PMC9213547 DOI: 10.1038/s41598-022-13508-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 05/25/2022] [Indexed: 11/21/2022] Open
Abstract
BRCA1 and BRCA2 are tumour suppressor genes that play a critical role in maintaining genomic stability via the DNA repair mechanism. DNA repair defects caused by BRCA1 and BRCA2 missense variants increase the risk of developing breast and ovarian cancers. Accurate identification of these variants becomes clinically relevant, as means to guide personalized patient management and early detection. Next-generation sequencing efforts have significantly increased data availability but also the discovery of variants of uncertain significance that need interpretation. Experimental approaches used to measure the molecular consequences of these variants, however, are usually costly and time-consuming. Therefore, computational tools have emerged as faster alternatives for assisting in the interpretation of the clinical significance of newly discovered variants. To better understand and predict variant pathogenicity in BRCA1 and BRCA2, various machine learning algorithms have been proposed, however presented limited performance. Here we present BRCA1 and BRCA2 gene-specific models and a generic model for quantifying the functional impacts of single-point missense variants in these genes. Across tenfold cross-validation, our final models achieved a Matthew's Correlation Coefficient (MCC) of up to 0.98 and comparable performance of up to 0.89 across independent, non-redundant blind tests, outperforming alternative approaches. We believe our predictive tool will be a valuable resource for providing insights into understanding and interpreting the functional consequences of missense variants in these genes and as a tool for guiding the interpretation of newly discovered variants and prioritizing mutations for experimental validation.
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Affiliation(s)
- Raghad Aljarf
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia.,Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, VIC, 3010, Australia.,Systems and Computational Biology, Bio21 Institute, University of Melbourne, 30 Flemington Rd, Parkville, VIC, 3052, Australia
| | - Mengyuan Shen
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia.,Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, VIC, 3010, Australia.,Systems and Computational Biology, Bio21 Institute, University of Melbourne, 30 Flemington Rd, Parkville, VIC, 3052, Australia.,School of Computing and Information Systems, University of Melbourne, Melbourne, VIC, 3053, Australia
| | - Douglas E V Pires
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia. .,Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, VIC, 3010, Australia. .,Systems and Computational Biology, Bio21 Institute, University of Melbourne, 30 Flemington Rd, Parkville, VIC, 3052, Australia. .,School of Computing and Information Systems, University of Melbourne, Melbourne, VIC, 3053, Australia.
| | - David B Ascher
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia. .,Department of Biochemistry and Pharmacology, University of Melbourne, Melbourne, VIC, 3010, Australia. .,Systems and Computational Biology, Bio21 Institute, University of Melbourne, 30 Flemington Rd, Parkville, VIC, 3052, Australia. .,Department of Biochemistry, University of Cambridge, 80 Tennis Ct Rd, Cambridge, CB2 1GA, UK.
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7
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Herzog JS, Chavarri-Guerra Y, Castillo D, Abugattas J, Villarreal-Garza C, Sand S, Clague-Dehart J, Alvarez-Gómez RM, Wegman-Ostrosky T, Mohar A, Mora P, Del Toro-Valero A, Daneri-Navarro A, Rodriguez Y, Cruz-Correa M, Ashton-Prolla P, Alemar B, Mejia R, Gallardo L, Shaw R, Yang K, Cervantes A, Tsang K, Nehoray B, Barrera Saldana H, Neuhausen S, Weitzel JN. Genetic epidemiology of BRCA1- and BRCA2-associated cancer across Latin America. NPJ Breast Cancer 2021; 7:107. [PMID: 34413315 PMCID: PMC8377150 DOI: 10.1038/s41523-021-00317-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 07/26/2021] [Indexed: 12/11/2022] Open
Abstract
The prevalence and contribution of BRCA1/2 (BRCA) pathogenic variants (PVs) to the cancer burden in Latin America are not well understood. This study aims to address this disparity. BRCA analyses were performed on prospectively enrolled Latin American Clinical Cancer Genomics Community Research Network participants via a combination of methods: a Hispanic Mutation Panel (HISPANEL) on MassARRAY; semiconductor sequencing; and copy number variant (CNV) detection. BRCA PV probability was calculated using BRCAPRO. Among 1,627 participants (95.2% with cancer), we detected 236 (14.5%) BRCA PVs; 160 BRCA1 (31% CNVs); 76 BRCA2 PV frequency varied by country: 26% Brazil, 9% Colombia, 13% Peru, and 17% Mexico. Recurrent PVs (seen ≥3 times), some region-specific, represented 42.8% (101/236) of PVs. There was no ClinVar entry for 14% (17/125) of unique PVs, and 57% (111/196) of unique VUS. The area under the ROC curve for BRCAPRO was 0.76. In summary, we implemented a low-cost BRCA testing strategy and documented a significant burden of non-ClinVar reported BRCA PVs among Latin Americans. There are recurrent, population-specific PVs and CNVs, and we note that the BRCAPRO mutation probability model performs adequately. This study helps address the gap in our understanding of BRCA-associated cancer in Latin America.
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Affiliation(s)
| | - Yanin Chavarri-Guerra
- Instituto Nacional de Ciencias Medicas y Nutrición, Salvador Zubiran, Mexico City, Mexico
| | | | | | - Cynthia Villarreal-Garza
- Hospital Zambrano Hellion TecSalud, Tecnologico de Monterrey, Monterrey, Mexico
- Instituto Nacional de Cancerología, México City, México
| | | | - Jessica Clague-Dehart
- City of Hope, Duarte, CA, USA
- School of Community & Global Health, Claremont Graduate University, Claremont, CA, USA
| | | | | | - Alejandro Mohar
- Instituto Nacional de Cancerología, México City, México
- Instituto de Investigaciones Biomédicas, Mexico City, Mexico
| | - Pamela Mora
- Instituto Nacional de Enfermedades Neoplásicas, Lima, Peru
| | - Azucena Del Toro-Valero
- Instituto Jalisciense de Cancerología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, México City, México
| | - Adrian Daneri-Navarro
- Instituto Jalisciense de Cancerología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, México City, México
| | | | - Marcia Cruz-Correa
- University of Puerto Rico Comprehensive Cancer Center, San Juan, Puerto Rico
| | - Patricia Ashton-Prolla
- Hospital de Clínicas de Porto Alegre and Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
| | - Bárbara Alemar
- Hospital de Clínicas de Porto Alegre and Universidade Federal do Rio Grande do Sul, Porto Alegre, Rio Grande do Sul, Brazil
- Roche Pharmaceutical, Basel, Switzerland
| | | | | | - Robin Shaw
- Instituto Nacional de Cancerología, México City, México
| | | | | | | | | | | | | | - Jeffrey N Weitzel
- Latin American School of Oncology (Escuela Latinoamericana de Oncología), Tuxla Gutiérrez, Chiapas, Mexico.
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8
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DiNardo CD, Korde LA, Yurgelun MB. A Case-Based Approach to Understanding Complex Genetic Information in an Evolving Landscape. Am Soc Clin Oncol Educ Book 2021; 41:1-11. [PMID: 34010053 DOI: 10.1200/edbk_321041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The rapid integration of highly sensitive next-generation sequencing technologies into clinical oncology care has led to unparalleled progress, and yet these technological advances have also made genetic information considerably more complex. For instance, accurate interpretation of genetic testing for germline/inherited cancer predisposition syndromes and somatic/acquired pathogenic variants now requires a more nuanced understanding of the presence and incidence of clonal hematopoiesis and circulating tumor cells, with careful evaluation of pathogenic variants occurring at low variant allele frequency required. The interplay between somatic and germline pathogenic variants and awareness of distinct genotype-phenotype manifestations in various inherited cancer syndromes are now increasingly appreciated and can impact patient management. Through a case-based approach, we focus on three areas of particular relevance to the treating clinician oncologist: (1) understanding clonal hematopoiesis and somatic mosaicism, which can be detected on germline sequencing and lead to considerable confusion in clinical interpretation; (2) implications of the detection of a potentially germline pathogenic variant in a high-penetrance cancer susceptibility gene during routine tumor testing; and (3) a review of gene-specific risks and surveillance recommendations in Lynch syndrome. A discussion on the availability and difficulties often associated with direct-to-consumer genetic testing is also provided.
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Affiliation(s)
- Courtney D DiNardo
- Department of Leukemia, The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | - Matthew B Yurgelun
- Dana-Farber Cancer Institute, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA
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Alvarez-Gomez RM, De la Fuente-Hernandez MA, Herrera-Montalvo L, Hidalgo-Miranda A. Challenges of diagnostic genomics in Latin America. Curr Opin Genet Dev 2021; 66:101-109. [PMID: 33517184 DOI: 10.1016/j.gde.2020.12.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/11/2020] [Accepted: 12/16/2020] [Indexed: 12/24/2022]
Abstract
Cancer genome sequencing methods have now become essential for diagnostic purposes, for devising treatment strategies, and for monitoring disease regression and progression. However, access to these benefits has not permeated homogeneously throughout the world; certain regions, such as Latin America, have been slower at adopting these technologies in terms of their routine use, development and patient access. There are also differences among Latin American subregions with respect to their prioritized types of neoplasia and the drugs that are available and approved in them. An overview of the current situation, including the status of genomics for cancer diagnostics and efforts by type of cancer is presented. In addition, we discuss the perspective of initiatives, alliances, and educational/research programs that pledge to make cancer genomics diagnosis a reality for Latin American individuals' health.
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Affiliation(s)
- Rosa Maria Alvarez-Gomez
- National Institute of Genomic Medicine, Periferico Sur 4809, Arenal Tepepan, Tlalpan, 14610, Mexico City, Mexico; National Cancer Institute, San Fernando 22, Seccion XVI, Tlalpan, Mexico City, Mexico
| | - Marcela Angelica De la Fuente-Hernandez
- National Institute of Genomic Medicine, Periferico Sur 4809, Arenal Tepepan, Tlalpan, 14610, Mexico City, Mexico; Doctoral Program in Biological Sciences, National Autonomous University of Mexico, C.U., Coyoacan, 04510, Mexico City, Mexico
| | - Luis Herrera-Montalvo
- National Institute of Genomic Medicine, Periferico Sur 4809, Arenal Tepepan, Tlalpan, 14610, Mexico City, Mexico
| | - Alfredo Hidalgo-Miranda
- National Institute of Genomic Medicine, Periferico Sur 4809, Arenal Tepepan, Tlalpan, 14610, Mexico City, Mexico.
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Fragoso-Ontiveros V, Velázquez-Aragón JA, Nuñez-Martínez PM, de la Luz Mejía-Aguayo M, Vidal-Millán S, Pedroza-Torres A, Sánchez-Contreras Y, Ramírez-Otero MA, Muñiz-Mendoza R, Domínguez-Ortíz J, Wegman-Ostrosky T, Bargalló-Rocha JE, Gallardo-Rincón D, Reynoso-Noveron N, Arriaga-Canon C, Meneses-García A, Herrera-Montalvo LA, Alvarez-Gomez RM. Mexican BRCA1 founder mutation: Shortening the gap in genetic assessment for hereditary breast and ovarian cancer patients. PLoS One 2019; 14:e0222709. [PMID: 31545835 PMCID: PMC6756553 DOI: 10.1371/journal.pone.0222709] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 09/05/2019] [Indexed: 12/19/2022] Open
Abstract
The deletion of exons 9 to 12 of BRCA1 (9-12 del BRCA1) is considered a founder mutation in the Mexican population. We evaluate the usefulness of the target detection of 9-12 del BRCA1 as the first molecular diagnostic strategy in patients with Hereditary Breast and Ovarian Cancer (HBOC). We performed the genetic assessment of 637 patients with suspected HBOC. The region corresponding to the breakpoints for the 9-12 del BRCA1 was amplified by polymerase chain reaction (PCR). An analysis of the clinical data of the carriers and non-carriers was done, searching for characteristics that correlated with the deletion. The 9-12 del BRCA1 was detected in 5% of patients with suspected HBOC (30/637). In patients diagnosed with ovarian cancer, 13 of 30 were 9-12 del BRCA1 carriers, which represents 43%. We found a significant association between the 9-12 del BRCA1 carriers with triple negative breast cancer and high-grade papillary serous ovarian cancer. We concluded that the detection of the 9-12 del BRCA1 is useful as a first molecular diagnostic strategy in the Mexican population. In particular, it shortens the gap in genetic assessment in patients with triple negative breast cancer and ovarian cancer.
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