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Abdel-Razeq H, Tamimi F, Iweir S, Sharaf B, Abdel-Razeq S, Salama O, Edaily S, Bani Hani H, Azzam K, Abaza H. Genetic counseling and genetic testing for pathogenic germline mutations among high-risk patients previously diagnosed with breast cancer: a traceback approach. Sci Rep 2024; 14:12820. [PMID: 38834641 DOI: 10.1038/s41598-024-63300-8] [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: 11/10/2023] [Accepted: 05/27/2024] [Indexed: 06/06/2024] Open
Abstract
Genetic counseling and testing are more accessible than ever due to reduced costs, expanding indications and public awareness. Nonetheless, many patients missed the opportunity of genetic counseling and testing due to barriers that existed at that time of their cancer diagnoses. Given the identified implications of pathogenic mutations on patients' treatment and familial outcomes, an opportunity exists to utilize a 'traceback' approach to retrospectively examine their genetic makeup and provide consequent insights to their disease and treatment. In this study, we identified living patients diagnosed with breast cancer (BC) between July 2007 and January 2022 who would have been eligible for testing, but not tested. Overall, 422 patients met the eligibility criteria, 282 were reached and invited to participate, and germline testing was performed for 238, accounting for 84.4% of those invited. The median age (range) was 39.5 (24-64) years at BC diagnosis and 49 (31-75) years at the date of testing. Genetic testing revealed that 25 (10.5%) patients had pathogenic/likely pathogenic (P/LP) variants; mostly in BRCA2 and BRCA1. We concluded that long overdue genetic referral through a traceback approach is feasible and effective to diagnose P/LP variants in patients with history of BC who had missed the opportunity of genetic testing, with potential clinical implications for patients and their relatives.
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Affiliation(s)
- Hikmat Abdel-Razeq
- Department of Internal Medicine, King Hussein Cancer Center, 202 Queen Rania Al Abdullah Street, P.O. Box: 1269, Amman, 11941, Jordan.
- School of Medicine, The University of Jordan, Amman, Jordan.
| | - Faris Tamimi
- Department of Internal Medicine, King Hussein Cancer Center, 202 Queen Rania Al Abdullah Street, P.O. Box: 1269, Amman, 11941, Jordan
| | - Sereen Iweir
- Department of Internal Medicine, King Hussein Cancer Center, 202 Queen Rania Al Abdullah Street, P.O. Box: 1269, Amman, 11941, Jordan
- CRDF Global, Global Health Mission Area, Amman, Jordan
| | - Baha Sharaf
- Department of Internal Medicine, King Hussein Cancer Center, 202 Queen Rania Al Abdullah Street, P.O. Box: 1269, Amman, 11941, Jordan
| | | | - Osama Salama
- Department of Internal Medicine, King Hussein Cancer Center, 202 Queen Rania Al Abdullah Street, P.O. Box: 1269, Amman, 11941, Jordan
| | - Sarah Edaily
- Department of Internal Medicine, King Hussein Cancer Center, 202 Queen Rania Al Abdullah Street, P.O. Box: 1269, Amman, 11941, Jordan
| | - Hira Bani Hani
- Department of Internal Medicine, King Hussein Cancer Center, 202 Queen Rania Al Abdullah Street, P.O. Box: 1269, Amman, 11941, Jordan
| | - Khansa Azzam
- Department of Internal Medicine, King Hussein Cancer Center, 202 Queen Rania Al Abdullah Street, P.O. Box: 1269, Amman, 11941, Jordan
| | - Haneen Abaza
- Office of Scientific Affairs and Research, King Hussein Cancer Center, Amman, Jordan
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Walsh N, Cooper A, Dockery A, O'Byrne JJ. Variant reclassification and clinical implications. J Med Genet 2024; 61:207-211. [PMID: 38296635 DOI: 10.1136/jmg-2023-109488] [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: 06/30/2023] [Accepted: 12/30/2023] [Indexed: 02/02/2024]
Abstract
Genomic technologies have transformed clinical genetic testing, underlining the importance of accurate molecular genetic diagnoses. Variant classification, ranging from benign to pathogenic, is fundamental to these tests. However, variant reclassification, the process of reassigning the pathogenicity of variants over time, poses challenges to diagnostic legitimacy. This review explores the medical and scientific literature available on variant reclassification, focusing on its clinical implications.Variant reclassification is driven by accruing evidence from diverse sources, leading to variant reclassification frequency ranging from 3.6% to 58.8%. Recent studies have shown that significant changes can occur when reviewing variant classifications within 1 year after initial classification, illustrating the importance of early, accurate variant assignation for clinical care.Variants of uncertain significance (VUS) are particularly problematic. They lack clear categorisation but have influenced patient treatment despite recommendations against it. Addressing VUS reclassification is essential to enhance the credibility of genetic testing and the clinical impact. Factors affecting reclassification include standardised guidelines, clinical phenotype-genotype correlations through deep phenotyping and ancestry studies, large-scale databases and bioinformatics tools. As genomic databases grow and knowledge advances, reclassification rates are expected to change, reducing discordance in future classifications.Variant reclassification affects patient diagnosis, precision therapy and family screening. The exact patient impact is yet unknown. Understanding influencing factors and adopting standardised guidelines are vital for precise molecular genetic diagnoses, ensuring optimal patient care and minimising clinical risk.
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Affiliation(s)
- Nicola Walsh
- Department of Clinical Genetics, Children's Health Ireland, Dublin, Ireland
| | - Aislinn Cooper
- Next Generation Sequencing Lab, Mater Misericordiae University Hospital, Dublin, Ireland
| | - Adrian Dockery
- Next Generation Sequencing Lab, Mater Misericordiae University Hospital, Dublin, Ireland
| | - James J O'Byrne
- National Centre for Inherited Metabolic Disorders, Mater Misericordiae University Hospital, Dublin, Ireland
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Taghizadeh Mortezaei N, Mohammadi S, Abolhassani H, Shokri S, Nabavi M, Fallahpour M, Bemanian MH. From variant of uncertain significance to likely pathogenic in two siblings with atypical RAG2 Deficiency: a case report and review of the literature. BMC Pediatr 2024; 24:116. [PMID: 38350907 PMCID: PMC10863182 DOI: 10.1186/s12887-024-04597-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 01/26/2024] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND Severe combined immunodeficiencies (SCIDs) are hereditary disorders characterized by impaired T and B cell function, resulting in significant immune system dysfunction. Recombination-activating gene (RAG) mutations account for a substantial proportion of SCID cases. Here, we present two sibling cases of SCID caused by a novel RAG2 gene mutation. CASE PRESENTATION The index case was an 8-year-old boy who had a history of recurring infections. After a comprehensive immunological workup, the initial diagnosis of agammaglobulinemia was revised to combined immunodeficiency (CID). The patient underwent hematopoietic stem cell transplantation (HSCT) but succumbed to cytomegalovirus (CMV) infection. His brother, a 4-month-old boy, presented with CMV chorioretinitis. Leaky SCID was diagnosed based on genetic tests and immunological findings. The patient received appropriate treatment and was considered for HSCT. Both siblings had a homozygous RAG2 gene variant, with the first case classified as a variant of uncertain significance (VUS). The presence of the same mutation in the second brother, and the clinical phenotype, supports considering the mutation as likely pathogenic. CONCLUSIONS This case report highlights a novel RAG2 gene mutation associated with CID. The classification of a VUS may evolve with accumulating evidence, and additional studies are warranted to establish its pathogenicity. Proper communication between genetic counselors and immunologists, accurate documentation of patient information, increased public awareness, and precise utilization of genetic techniques are essential for optimal patient management.
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Affiliation(s)
- Nima Taghizadeh Mortezaei
- School of Medicine, Iran University of Medical Sciences (IUMS), Tehran, Iran
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Soha Mohammadi
- School of Medicine, Iran University of Medical Sciences (IUMS), Tehran, Iran
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Hassan Abolhassani
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Sima Shokri
- Department of Allergy and Clinical Immunology, School of Medicine, Iran University of Medical Sciences (IUMS), Rasool-e-Akram Hospital, Mansoori ave, Sattarkhan street, Tehran, 14456 13131, Iran.
| | - Mohammad Nabavi
- Department of Allergy and Clinical Immunology, School of Medicine, Iran University of Medical Sciences (IUMS), Rasool-e-Akram Hospital, Mansoori ave, Sattarkhan street, Tehran, 14456 13131, Iran
| | - Morteza Fallahpour
- Department of Allergy and Clinical Immunology, School of Medicine, Iran University of Medical Sciences (IUMS), Rasool-e-Akram Hospital, Mansoori ave, Sattarkhan street, Tehran, 14456 13131, Iran
| | - Mohammad Hassan Bemanian
- Department of Allergy and Clinical Immunology, School of Medicine, Iran University of Medical Sciences (IUMS), Rasool-e-Akram Hospital, Mansoori ave, Sattarkhan street, Tehran, 14456 13131, Iran
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Gressel GM, Frey MK, Norquist B, Senter L, Blank SV, Urban RR. Germline and somatic testing for ovarian Cancer: An SGO clinical practice statement. Gynecol Oncol 2024; 181:170-178. [PMID: 38215513 DOI: 10.1016/j.ygyno.2023.12.010] [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: 09/29/2023] [Revised: 12/09/2023] [Accepted: 12/13/2023] [Indexed: 01/14/2024]
Abstract
Germline and somatic genetic testing have become critical components of care for people with ovarian cancer. The identification of germline and somatic pathogenic variants as well as homologous recombination deficiency can contribute to the prediction of treatment response, prognostic outcome, and suitability for targeted agents (e.g. poly (ADP-ribose) polymerase (PARP) inhibitors). Furthermore, identifying germline pathogenic variants can prompt cascade genetic testing for at-risk relatives. Despite the clinical benefits and consensus recommendations from several organizations calling for universal genetic testing in ovarian cancer, only about one third of patients complete germline or somatic genetic testing. The members of the Society of Gynecologic Oncology (SGO) Clinical Practice Committee have composed this statement to provide an overview of germline and somatic genetic testing for patients with epithelial ovarian cancer, focusing on available testing modalities and options for care delivery.
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Affiliation(s)
- G M Gressel
- Corewell Health Cancer Center, Division of Gynecologic Oncology, Michigan State University- College of Human Medicine, United States.
| | - M K Frey
- Weill Cornell Medicine, Division of Gynecologic Oncology, United States
| | - B Norquist
- University of Washington School of Medicine, Division of Gynecologic Oncology, United States
| | - L Senter
- The Ohio State University, Comprehensive Cancer Center,United States
| | - S V Blank
- Icahn School of Medicine at Mount Sinai, United States
| | - R R Urban
- University of Washington School of Medicine, Division of Gynecologic Oncology, United States
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Cheung C, Berger SM, Ross M, Kramer T, Li Y, Andrews C, Dergham KR, Spitz E, Florido ME, Ahimaz P. Assessing management practices for variants of uncertain significance among genetic counselors in pediatrics. J Genet Couns 2024. [PMID: 38217320 DOI: 10.1002/jgc4.1860] [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: 02/14/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 01/15/2024]
Abstract
Increased utilization of genomic sequencing in pediatric medicine has increased the detection of variants of uncertain significance (VUS). Periodic VUS reinterpretation can clarify clinical significance and increase diagnostic yield, highlighting the importance of systematic VUS tracking and reinterpretation. There are currently no standardized guidelines or established best practices for VUS management, and our understanding of how genetic counselors (GCs) track and manage VUS results for pediatric patients is limited. In this exploratory study, GCs in pediatric clinics in North America were surveyed about their VUS management practices. A total of 124 responses were included in the analysis. The majority (n = 115, 92.7%) of GCs reported that VUS management workflows were at the discretion of each individual provider in their workplace. Approximately half (n = 65, 52%) kept track of patient VUS results over time, and GCs with lower patient volumes were more likely to do so (p = 0.04). While 95% (n = 114) of GCs had requested VUS reinterpretation at least once, only 5% (n = 6) requested it routinely. Most (n = 80, 86%) GCs notified patients when a VUS was reclassified, although methods of recontact differed when the reclassification was an upgrade versus a downgrade. GCs who asked patients to stay in touch through periodic recontact or follow-up appointments were more likely to request VUS reinterpretation (p = 0.01). The most frequently reported barriers to requesting reinterpretation regularly were patients being lost to follow-up (n = 39, 33.1%), insufficient bandwidth (n = 27, 22.9%), and lack of standardized guidelines (n = 25, 21.2%). GCs had consistent overall practices around VUS management around investigation, disclosure, reinterpretation, and recontact, but specific methods used differed and were at the discretion of each provider. These results showcase the current landscape of VUS management workflows in pediatrics and the challenges associated with adopting more uniform practices. The study findings can help inform future strategies to develop standardized guidelines surrounding VUS management.
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Affiliation(s)
- Chloe Cheung
- Genetic Counseling Graduate Program, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
- Clinical Trials Office, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Sara M Berger
- Department of Pediatrics, Division of Clinical Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Meredith Ross
- Department of Pediatrics, Division of Clinical Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Tamar Kramer
- Department of Pediatrics, Division of Clinical Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Yuhuan Li
- Department of Biostatistics, Columbia University, New York, New York, USA
| | - Carli Andrews
- Department of Pediatrics, Division of Clinical Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Katia R Dergham
- Department of Pediatrics, Division of Clinical Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
- School of Pharmacy and Health Sciences, Keck Graduate Insititute, Claremont, California, USA
| | - Elana Spitz
- Department of Pediatrics, Division of Clinical Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
- Department of Hematology Oncology, University of Carlifornia, Los Angeles Health, Los Angeles, California, USA
| | - Michelle E Florido
- Genetic Counseling Graduate Program, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
- Department of Genetics and Development, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
| | - Priyanka Ahimaz
- Genetic Counseling Graduate Program, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
- Department of Pediatrics, Division of Clinical Genetics, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
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6
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Yoon E, Lee JK, Park TK, Chang SA, Huh J, Kim JW, Kim DK, Jang JH. Experience of reassessing FBN1 variants of uncertain significance by gene-specific guidelines. J Med Genet 2023; 61:57-60. [PMID: 37558401 DOI: 10.1136/jmg-2023-109433] [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: 05/30/2023] [Accepted: 07/22/2023] [Indexed: 08/11/2023]
Abstract
BACKGROUND Despite the 2015 American College of Medical Genetics and Genomics (ACMG) and Association of Molecular Pathology (AMP) guideline, many variants of FBN1 gene remain inconclusive. In line with publication of the FBN1-specific variant interpretation guideline by ClinGen in 2022, we reassessed variants of uncertain significance (VUS) in FBN1 gene found in our institution. METHODS VUS found in the course of FBN1 sequencing between December 2015 and April 2022 were reassessed based on FBN1-specific variant interpretation guideline, review of updated literatures and additional genetic tests including family study and/or RNA study if available. RESULTS Out of 695 patients who underwent FBN1 sequencing, 61 VUS were found in 69 patients. Among them, 38 VUS in 43 patients (62.3%) were reclassified as pathogenic and likely pathogenic variant ((L)PV), including 20 novel (L)PV. Major causes of reclassification were: (1) gene-specific modification of ACMG/AMP criteria, (2) updated literatures and (3) additional genetic tests. The most important evidence for reclassification was clarification of critical amino acid residues. CONCLUSIONS After reassessing FBN1 variants according to FBN1-specific guideline and up-to-date database, a significant number of VUS was reclassified. Clinical laboratories are encouraged to perform variant reassessment at regular intervals or when there is a major change in the principle of variant interpretation.
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Affiliation(s)
- Eungjun Yoon
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Jong Kwon Lee
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Taek Kyu Park
- Division of Cardiology, Department of Medicine, Heart Vascular Stroke Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Sung-A Chang
- Division of Cardiology, Department of Medicine, Heart Vascular Stroke Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - June Huh
- Division of Cardiology, Department of Pediatrics, Adult Congenital Heart Disease Clinic, Heart Vascular Stroke Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Jong-Won Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Duk-Kyung Kim
- Division of Cardiology, Department of Medicine, Heart Vascular Stroke Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- Division of Cardiology, Department of Medicine, Samsung Changwon Hospital, Sungkyunkwan University School of Medicine, Changwon, Republic of Korea
| | - Ja-Hyun Jang
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
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Lazareva TE, Barbitoff YA, Nasykhova YA, Pavlova NS, Bogaychuk PM, Glotov AS. Statistical Dissection of the Genetic Determinants of Phenotypic Heterogeneity in Genes with Multiple Associated Rare Diseases. Genes (Basel) 2023; 14:2100. [PMID: 38003043 PMCID: PMC10671084 DOI: 10.3390/genes14112100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/13/2023] [Accepted: 11/15/2023] [Indexed: 11/26/2023] Open
Abstract
Phenotypicheterogeneity is a phenomenon in which distinct phenotypes can develop in individuals bearing pathogenic variants in the same gene. Genetic factors, gene interactions, and environmental factors are usually considered the key mechanisms of this phenomenon. Phenotypic heterogeneity may impact the prognosis of the disease severity and symptoms. In our work, we used publicly available data on the association between genetic variants and Mendelian disease to investigate the genetic factors (such as the intragenic localization and type of a variant) driving the heterogeneity of gene-disease relationships. First, we showed that genes linked to multiple rare diseases (GMDs) are more constrained and tend to encode more transcripts with high levels of expression across tissues. Next, we assessed the role of variant localization and variant types in specifying the exact phenotype for GMD variants. We discovered that none of these factors is sufficient to explain the phenomenon of such heterogeneous gene-disease relationships. In total, we identified only 38 genes with a weak trend towards significant differences in variant localization and 30 genes with nominal significant differences in variant type for the two associated disorders. Remarkably, four of these genes showed significant differences in both tests. At the same time, our analysis suggests that variant localization and type are more important for genes linked to autosomal dominant disease. Taken together, our results emphasize the gene-level factors dissecting distinct Mendelian diseases linked to one common gene based on open-access genetic data and highlight the importance of exploring other factors that contributed to phenotypic heterogeneity.
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Affiliation(s)
- Tatyana E. Lazareva
- Department of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia; (T.E.L.); (Y.A.N.)
| | - Yury A. Barbitoff
- Department of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia; (T.E.L.); (Y.A.N.)
- Bioinformatics Institute, Kantemirovskaya St. 2A, 197342 St. Petersburg, Russia; (N.S.P.); (P.M.B.)
| | - Yulia A. Nasykhova
- Department of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia; (T.E.L.); (Y.A.N.)
| | - Nadezhda S. Pavlova
- Bioinformatics Institute, Kantemirovskaya St. 2A, 197342 St. Petersburg, Russia; (N.S.P.); (P.M.B.)
| | - Polina M. Bogaychuk
- Bioinformatics Institute, Kantemirovskaya St. 2A, 197342 St. Petersburg, Russia; (N.S.P.); (P.M.B.)
| | - Andrey S. Glotov
- Department of Genomic Medicine, D.O. Ott Research Institute of Obstetrics, Gynaecology, and Reproductology, 199034 St. Petersburg, Russia; (T.E.L.); (Y.A.N.)
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Chen D, Pruthi RK. Platelet genetic testing by next-generation sequencing: A practical update. Int J Lab Hematol 2023; 45:630-642. [PMID: 37463678 DOI: 10.1111/ijlh.14136] [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: 03/09/2023] [Accepted: 06/27/2023] [Indexed: 07/20/2023]
Abstract
Inherited platelet disorders (IPDs) are a heterogeneous group of disorders characterized by normal or reduced platelet counts, bleeding diatheses of varying severities, and the presence (syndromic) or absence (non-syndromic) of involvement of other organs. Due to the lack of highly specific platelet function tests and overlapping clinical and laboratory features, diagnosing the underlying cause of IPDs remains challenging. In recent years, genetic testing via next-generation sequencing (NGS) technologies to rapidly analyze multiple genes has gradually emerged as an important part of the laboratory investigation of patients with IPDs. A systemic clinical and laboratory testing approach and thorough phenotype and genotype correlation studies of both patients and their family members are crucial for accurate diagnoses of IPDs.
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Affiliation(s)
- Dong Chen
- Special Coagulation Laboratory, Division of Hematopathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Rajiv K Pruthi
- Special Coagulation Laboratory, Division of Hematopathology, Mayo Clinic, Rochester, Minnesota, USA
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Arranz-Ledo M, Lastra E, Abella L, Ferreira R, Orozco M, Hernández L, Martínez N, Infante M, Durán M. Multigene germline testing usefulness instead of BRCA1/2 single screening in triple negative breast cancer cases. Pathol Res Pract 2023; 247:154514. [PMID: 37201465 DOI: 10.1016/j.prp.2023.154514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 05/06/2023] [Indexed: 05/20/2023]
Abstract
Triple negative breast cancer is considered as the worst aggressive subtype with poor prognosis. Recent studies suggest a hereditary component is involved in TNBC development, especially in young patients. However, genetic spectrum remains unclear. Our purpose was to evaluate the usefulness of multigene panel testing in triple negative patients compared to overall breast cancer cases as well as contributing to elucidate which genes are most implicated in triple negative subtype development. Two breast cancer cohorts, comprising 100 triple negative breast cancer patients and 100 patients with other breast cancer subtypes, were analyzed by Next-Generation Sequencing using an On-Demand panel which included 35 predisposition cancer genes associated with inherited cancer susceptibility. The percentage of germline pathogenic variant carriers was higher in the triple negative cohort. ATM, PALB2, BRIP1 and TP53 were the most non-BRCA mutated genes. Moreover, triple negative breast cancer patients without family history related who were identified as carriers were diagnosed at significantly earlier age. As conclusion, our study reinforces the usefulness of multigene panel testing in breast cancer cases but specifically in those with triple negative subtype regardless family history.
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Affiliation(s)
- M Arranz-Ledo
- Cancer Genetics Group. Instituto de Biología y Genética Molecular (UVa-CSIC), Universidad de Valladolid, C/ Sanz y Forés 3, 47003 Valladolid, Spain
| | - E Lastra
- Unit of Genetic Counselling in Cancer, Complejo Hospitalario de Burgos, Burgos, Spain
| | - L Abella
- Unit of Genetic Counselling in Cancer, Hospital Universitario Rio Hortega, Valladolid, Spain
| | - R Ferreira
- Unit of Genetic Counselling in Cancer, Hospital Universitario Rio Hortega, Valladolid, Spain
| | - M Orozco
- Unit of Genetic Counselling in Cancer, Hospital Universitario Rio Hortega, Valladolid, Spain
| | - L Hernández
- Cancer Genetics Group. Instituto de Biología y Genética Molecular (UVa-CSIC), Universidad de Valladolid, C/ Sanz y Forés 3, 47003 Valladolid, Spain
| | - N Martínez
- Cancer Genetics Group. Instituto de Biología y Genética Molecular (UVa-CSIC), Universidad de Valladolid, C/ Sanz y Forés 3, 47003 Valladolid, Spain
| | - M Infante
- Cancer Genetics Group. Instituto de Biología y Genética Molecular (UVa-CSIC), Universidad de Valladolid, C/ Sanz y Forés 3, 47003 Valladolid, Spain
| | - M Durán
- Cancer Genetics Group. Instituto de Biología y Genética Molecular (UVa-CSIC), Universidad de Valladolid, C/ Sanz y Forés 3, 47003 Valladolid, Spain.
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CHEK2 Alterations in Pediatric Malignancy: A Single-Institution Experience. Cancers (Basel) 2023; 15:cancers15061649. [PMID: 36980535 PMCID: PMC10046043 DOI: 10.3390/cancers15061649] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 03/03/2023] [Indexed: 03/11/2023] Open
Abstract
Background: Approximately 10% of pediatric malignancies are secondary to germline alterations in cancer-predisposing genes. Checkpoint kinase 2 (CHEK2) germline loss-of-function variants have been reported in pediatric cancer patients, but clinical phenotypes and outcomes are poorly described. We present our single-institution experience of pediatric oncology patients with CHEK2 germline alterations, including clinical presentations and outcomes. Methods: Pediatric oncology patients with CHEK2 germline alterations were identified among those assessed by clinical or translational research at the Institute for Genomic Medicine at Nationwide Children’s Hospital. A chart review of disease course was conducted on identified patients. Results: We identified 6 patients with germline CHEK2 variants from a cohort of 300 individuals, including 1 patient with concurrent presentation of Burkitt lymphoma and neuroblastoma, 3 patients with brain tumors, 1 patient with Ewing sarcoma, and 1 patient with myelodysplastic syndrome. Three patients had a family history of malignancies. Four patients were in remission; one was undergoing treatment; one patient had developed treatment-related meningiomas. We review prior data regarding CHEK2 variants in this population, challenges associated with variant interpretation, and genetic counseling for individuals with CHEK2 variants. Conclusions: CHEK2 germline loss-of-function alterations occur in patients with a variety of pediatric tumors. Larger multicenter studies will improve our understanding of the incidence, phenotype, and molecular biology of CHEK2 germline variants in pediatric cancers.
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Makhnoon S, Levin B, Ensinger M, Mattie K, Volk RJ, Zhao Z, Mendoza T, Shete S, Samiian L, Grana G, Grainger A, Arun B, Shirts BH, Peterson SK. A multicenter study of clinical impact of variant of uncertain significance reclassification in breast, ovarian and colorectal cancer susceptibility genes. Cancer Med 2023; 12:2875-2884. [PMID: 36426404 PMCID: PMC9939195 DOI: 10.1002/cam4.5202] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/30/2022] [Accepted: 08/23/2022] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Clinical interpretation of genetic test results is complicated by variants of uncertain significance (VUS) that have an unknown impact on health but can be clarified through reclassification. There is little empirical evidence regarding VUS reclassification in oncology care settings, including the prevalence and outcomes of reclassification, and racial/ethnic differences. METHODS This was a retrospective analysis of persons with and without a personal history of cancer carrying VUS (with or without an accompanying pathogenic or likely pathogenic [P/LP] variant) in breast, ovarian, and colorectal cancer predisposition genes seen at four cancer care settings (in Texas, Florida, Ohio, and New Jersey) between 2013 and 2019. RESULTS In 2715 individuals included in the study, 3261 VUS and 313 P/LP variants were reported; 8.1% of all individuals with VUS experienced reclassifications and rates varied significantly among cancer care settings from 4.81% to 20.19% (overall p < 0.001). Compared to their prevalence in the overall sample, reclassification rates for Black individuals were higher (13.6% vs. 19.0%), whereas the rates for Asian individuals were lower (6.3% vs. 3.5%) and rates for White and Hispanic individuals were proportional. Two-year prevalence of VUS reclassification remained steady between 2014 and 2019. Overall, 11.3% of all reclassified VUS resulted in clinically actionable findings and 4.6% subsequently changed individuals' clinical managements. CONCLUSIONS The findings from this large multisite study suggest that VUS reclassification alters clinical management, has implications for precision cancer prevention, and highlights the need for implementing practices and solutions for efficiently returning reinterpreted genetic test results.
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Affiliation(s)
- Sukh Makhnoon
- Department of Behavioral ScienceUT MD Anderson Cancer CenterHoustonTexasUSA
| | - Brooke Levin
- William G. Rohrer Cancer Genetics Program, Division of Hematology and Medical OncologyMD Anderson Cancer Center at Cooper University Health CareCamdenNew JerseyUSA
| | | | - Kristin Mattie
- William G. Rohrer Cancer Genetics Program, Division of Hematology and Medical OncologyMD Anderson Cancer Center at Cooper University Health CareCamdenNew JerseyUSA
| | - Robert J. Volk
- Department of Health Services ResearchUT MD Anderson Cancer CenterHoustonTexasUSA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical InformaticsThe University of Texas Health Science Center at HoustonHoustonTexasUSA
| | - Tito Mendoza
- Department of Symptoms researchUT MD Anderson Cancer CenterHoustonTexasUSA
| | - Sanjay Shete
- Division of Cancer Prevention and Population SciencesUT MD Anderson Cancer CenterHoustonTexasUSA
| | | | - Generosa Grana
- William G. Rohrer Cancer Genetics Program, Division of Hematology and Medical OncologyMD Anderson Cancer Center at Cooper University Health CareCamdenNew JerseyUSA
| | | | - Banu Arun
- Clinical Cancer GeneticsUT MD Anderson Cancer CenterHoustonTexasUSA
| | | | - Susan K. Peterson
- Department of Behavioral ScienceUT MD Anderson Cancer CenterHoustonTexasUSA
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McDonald JT, Ricks-Santi LJ. Hereditary variants of unknown significance in African American women with breast cancer. PLoS One 2022; 17:e0273835. [PMID: 36315513 PMCID: PMC9621418 DOI: 10.1371/journal.pone.0273835] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 08/17/2022] [Indexed: 11/06/2022] Open
Abstract
Expanded implementation of genetic sequencing has precipitously increased the discovery of germline and somatic variants. The direct benefit of identifying variants in actionable genes may lead to risk reduction strategies such as increased surveillance, prophylactic surgery, as well as lifestyle modifications to reduce morbidity and mortality. However, patients with African ancestry are more likely to receive inconclusive genetic testing results due to an increased number of variants of unknown significance decreasing the utility and impact on disease management and prevention. This study examines whole exome sequencing results from germline DNA samples in African American women with a family history of cancer including 37 cases that were diagnosed with breast cancer and 51 family members. Self-identified ancestry was validated and compared to the 1000 genomes population. The analysis of sequencing results was limited to 85 genes from three clinically available common genetic screening platforms. This target region had a total of 993 variants of which 6 (<1%) were pathogenic or likely pathogenic, 736 (74.1%) were benign, and 170 (17.1%) were classified as a variant of unknown significance. There was an average of 3.4±1.8 variants with an unknown significance per individual and 85 of 88 individuals (96.6%) harbored at least one of these in the targeted genes. Pathogenic or likely pathogenic variants were only found in 6 individuals for the BRCA1 (p.R1726fs, rs80357867), BRCA2 (p.K589fs, rs397507606 & p.L2805fs, rs397507402), RAD50 (p.E995fs, rs587780154), ATM (p.V2424G, rs28904921), or MUTYH (p.G396D, rs36053993) genes. Strategies to functionally validate the remaining variants of unknown significance, especially in understudied and hereditary cancer populations, are greatly needed to increase the clinical utility and utilization of clinical genetic screening platforms to reduce cancer incidence and mortality.
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Affiliation(s)
- J. Tyson McDonald
- Department of Radiation Medicine, Georgetown University School of Medicine, Washington, DC, United States of America
| | - Luisel J. Ricks-Santi
- Cancer Research Center, Hampton University, Hampton, VA, United States of America
- Department of Pharmacotherapy and Translational Research, College of Medicine, University of Florida, Gainesville, FL, United States of America
- * E-mail:
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Cocorpus J, Hager MM, Benchimol C, Bijol V, Salem F, Punj S, Castellanos L, Singer P, Sethna CB, Basalely A. COL4A4 variant recently identified: lessons learned in variant interpretation-a case report. BMC Nephrol 2022; 23:253. [PMID: 35842573 PMCID: PMC9287857 DOI: 10.1186/s12882-022-02866-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 06/28/2022] [Indexed: 11/10/2022] Open
Abstract
Background Alport syndrome is a hereditary kidney disease characterized by hematuria and proteinuria. Although there have been reports of autosomal dominant COL4A4 variants, this is likely an underdiagnosed condition. Improved access to affordable genetic testing has increased the diagnosis of Alport syndrome. As genetic testing becomes ubiquitous, it is imperative that clinical nephrologists understand the benefits and challenges associated with clinical genetic testing. Case Presentation We present a family of Mexican descent with a heterozygous COL4A4 variant (c.5007delC, ClinVar accession numbers: SCV001580980.2, SCV001993731.1) not previously discussed in detail in the literature. The proband received a biopsy diagnosis suggestive of Fabry disease 18 years after she first developed hematuria and progressed to chronic kidney disease stage III. One year later, the proband was provisionally diagnosed with Alport syndrome after a variant of uncertain significance in the COL4A4 gene was identified following targeted family variant testing of her daughter. Upon review of the medical histories of the proband’s children and niece, all but one had the same variant. Of the four with the variant, three display clinical symptoms of hematuria, and/or proteinuria. The youngest of the four, only months old, has yet to exhibit clinical symptoms. Despite these findings there was a considerable delay in synthesizing this data, as patients were tested in different commercial genetic testing laboratories. Subsequently, understanding this family’s inheritance pattern, family history, and clinical symptoms, as well as the location of the COL4A4 variant resulted in the upgrade of the variant’s classification. Although the classification of this variant varied among different clinical genetic testing laboratories, the consensus was that this variant is likely pathogenic. Conclusions This COL4A4 variant (c.5007delC) not yet discussed in detail in the literature is associated with Alport syndrome. The inheritance pattern is suggestive of autosomal dominant inheritance. This report highlights the intricacies of variant interpretation and classification, the siloed nature of commercial genetic testing laboratories, and the importance of a thorough family history for proper variant interpretation. Additionally, the cases demonstrate the varied clinical presentations of Alport syndrome and suggest the utility of early screening, diagnosis, monitoring, and treatment.
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Affiliation(s)
- Jenelle Cocorpus
- Pediatric Nephrology, Cohen Children's Medical Center of New York, 269-01 76th Avenue, New Hyde Park, NY, 11040, USA
| | | | | | - Vanesa Bijol
- Renal Pathology, Northwell Health, Lake Success, NY, USA
| | - Fadi Salem
- Pathology, Molecular and Cell Based Medicine, Mount Sinai, New York, NY, USA
| | | | - Laura Castellanos
- Pediatric Nephrology, Cohen Children's Medical Center of New York, 269-01 76th Avenue, New Hyde Park, NY, 11040, USA
| | - Pamela Singer
- Pediatric Nephrology, Cohen Children's Medical Center of New York, 269-01 76th Avenue, New Hyde Park, NY, 11040, USA
| | - Christine B Sethna
- Pediatric Nephrology, Cohen Children's Medical Center of New York, 269-01 76th Avenue, New Hyde Park, NY, 11040, USA
| | - Abby Basalely
- Pediatric Nephrology, Cohen Children's Medical Center of New York, 269-01 76th Avenue, New Hyde Park, NY, 11040, USA.
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Health Disparities in Germline Genetic Testing for Cancer Susceptibility. CURRENT BREAST CANCER REPORTS 2020. [DOI: 10.1007/s12609-020-00354-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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A pediatric perspective on genomics and prevention in the twenty-first century. Pediatr Res 2020; 87:338-344. [PMID: 31578042 DOI: 10.1038/s41390-019-0597-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 09/18/2019] [Indexed: 12/19/2022]
Abstract
We present evidence from diverse disciplines and populations to identify the current and emerging role of genomics in prevention from both medical and public health perspectives as well as key challenges and potential untoward consequences of increasing the role of genomics in these endeavors. We begin by comparing screening in healthy populations (newborn screening), with testing in symptomatic populations, which may incidentally identify secondary findings and at-risk relatives. Emerging evidence suggests that variants in genes subject to the reporting of secondary findings are more common than expected in patients who otherwise would not meet the criteria for testing and population testing for variants in these genes may more precisely identify discrete populations to target for various prevention strategies starting in childhood. Conversely, despite its theoretical promise, recent studies attempting to demonstrate benefits of next-generation sequencing for newborn screening have instead demonstrated numerous barriers and pitfalls to this approach. We also examine the special cases of pharmacogenomics and polygenic risk scores as examples of ways genomics can contribute to prevention amongst a broader population than that affected by rare Mendelian disease. We conclude with unresolved questions which will benefit from future investigations of the role of genomics in disease prevention.
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