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Kannan P, A HB, N MP, D TK, Ramanathan G, Eswaramoorthy R, Ramasamy M. Unravelling the Relacatib activity against the CTSK proteins causing pycnodysostosis: a molecular docking and dynamics approach. J Biomol Struct Dyn 2024; 42:4121-4132. [PMID: 37255004 DOI: 10.1080/07391102.2023.2218927] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 05/22/2023] [Indexed: 06/01/2023]
Abstract
Pycnodysostosis is an atypical autosomal recessive condition of Lysosomal storage disorder that originated due to the deficit of the enzyme Cathepsin K which is vital for normal osteoclast action in bone resorption. Abnormal degradation of type 1 collagen and accumulation of toxic undigested collagen fibers in lysosomes of the osteoclast cells resulting in high bone density, brittle bones, and a short stature is caused in CTSK protein-carrying individuals. The broad aim of this study is to identify the most significant variant through various computational pipelines. This study was initiated by retrieving a total number of thirty-six variants from NCBI, HGMD, and UniProt databases, and the Y283C variant was found to be more significant by various standard computational tools. A structural investigation was performed to understand and gain a better knowledge about the interaction profile for the native (1BY8) and variant (Y283C) with Relacatib (a small-molecule drug that blocks the function of Cathepsin K, an enzyme that has been linked to osteoporosis, osteoarthritis, and other bone-degrading diseases). The interaction profile was analyzed using molecular docking. Relacatib (ligand) had an average binding affinity for both native (-7.16 kcal/mol) and Y283C (-6.76 kcal/mol). Finally, Molecular dynamics simulations were done in duplicates to recognize the variant (Y283C) activity of the protein structure against Relacatib for 100 ns. This study assists in comprehending the most pathogenic amino-acid variant, the ligand interaction with the protein structure, and paves the way for understanding the steadiness of the ligand with the native and selected significant amino-acid variant.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Priyanka Kannan
- Department of Biotechnology, Sri Ramachandra Institute of Higher Education and Research (DU), Chennai, India
| | - Hadeefa Begum A
- Department of Biotechnology, Sri Ramachandra Institute of Higher Education and Research (DU), Chennai, India
| | - Madhana Priya N
- Department of Biotechnology, Sri Ramachandra Institute of Higher Education and Research (DU), Chennai, India
| | - Thirumal Kumar D
- Faculty of Allied Health Science, Meenakshi Academy of Higher Education and Research, Chennai, India
| | - Gnansambandan Ramanathan
- Department of Biomedical Science, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Rajalakshmanan Eswaramoorthy
- Department of Prosthodontics, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Chennai, India
| | - Magesh Ramasamy
- Department of Biotechnology, Sri Ramachandra Institute of Higher Education and Research (DU), Chennai, India
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2
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K P, Madhana PN, Eswaramoorthy R, Ramasamy M. A computational approach to analyzing the functional and structural impacts of Tripeptidyl-Peptidase 1 missense mutations in neuronal ceroid lipofuscinosis. Metab Brain Dis 2024; 39:545-558. [PMID: 38185715 DOI: 10.1007/s11011-024-01341-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 12/18/2023] [Indexed: 01/09/2024]
Abstract
Neuronal ceroid-lipofuscinosis (NCLs) are a group of severe neurodegenerative conditions, most likely present in infantile, late infantile, juvenile, and adult-onset forms. Their phenotypic characteristics comprise eyesight damage, reduced motor activity and cognitive function, and sometimes tend to die in the initial stage. In recent studies, NCLs have been categorized into at least 14 genetic collections (CLN1-14). CLN2 gene encodes Tripeptidyl peptidase 1 (TPP1), which affects late infantile-onset form. In this study, we retrieved a mutational dataset screening for TPP1 protein from various databases (ClinVar, UniProt, HGMD). Fifty-six missense mutants were enumerated with computational methods to perceive the significant mutants (G475R and G501C) and correlated with clinical and literature data. A structure-based screening method was initiated to understand protein-ligand interaction and dynamic simulation. The docking procedure was performed for the native (3EDY) and mutant (G473R and G501C) structures with Gemfibrozil (gem), which lowers the lipid level, decreases the triglycerides amount in the blood circulation, and controls hyperlipidemia. The Native had an interaction score of -5.57 kcal/mol, and the mutants had respective average binding scores of -6.24 (G473R) and - 5.17 (G501C) kcal/mol. Finally, molecular dynamics simulation showed that G473R and G501C mutants had better flexible and stable orientation in all trajectory analyses. Therefore, this work gives an extended understanding of both functional and structural levels of influence for the mutant form that leads to NCL disorder.
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Affiliation(s)
- Priyanka K
- Department of Biotechnology, Sri Ramachandra Institute of Higher Education and Research (DU), Porur, Chennai, TamilNadu, 600116, India
| | - Priya N Madhana
- Department of Biotechnology, Sri Ramachandra Institute of Higher Education and Research (DU), Porur, Chennai, TamilNadu, 600116, India
| | - Rajalakshmanan Eswaramoorthy
- Department of Prosthodontics, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences (SIMATS), Chennai, TamilNadu, India
| | - Magesh Ramasamy
- Department of Biotechnology, Sri Ramachandra Institute of Higher Education and Research (DU), Porur, Chennai, TamilNadu, 600116, India.
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3
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Aguirre J, Padilla N, Özkan S, Riera C, Feliubadaló L, de la Cruz X. Choosing Variant Interpretation Tools for Clinical Applications: Context Matters. Int J Mol Sci 2023; 24:11872. [PMID: 37511631 PMCID: PMC10380979 DOI: 10.3390/ijms241411872] [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: 06/09/2023] [Revised: 07/10/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
Pathogenicity predictors are computational tools that classify genetic variants as benign or pathogenic; this is currently a major challenge in genomic medicine. With more than fifty such predictors available, selecting the most suitable tool for clinical applications like genetic screening, molecular diagnostics, and companion diagnostics has become increasingly challenging. To address this issue, we have developed a cost-based framework that naturally considers the various components of the problem. This framework encodes clinical scenarios using a minimal set of parameters and treats pathogenicity predictors as rejection classifiers, a common practice in clinical applications where low-confidence predictions are routinely rejected. We illustrate our approach in four examples where we compare different numbers of pathogenicity predictors for missense variants. Our results show that no single predictor is optimal for all clinical scenarios and that considering rejection yields a different perspective on classifiers.
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Affiliation(s)
- Josu Aguirre
- Research Unit in Clinical and Translational Bioinformatics, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, P/Vall d'Hebron, 119-129, 08035 Barcelona, Spain
| | - Natàlia Padilla
- Research Unit in Clinical and Translational Bioinformatics, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, P/Vall d'Hebron, 119-129, 08035 Barcelona, Spain
| | - Selen Özkan
- Research Unit in Clinical and Translational Bioinformatics, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, P/Vall d'Hebron, 119-129, 08035 Barcelona, Spain
| | - Casandra Riera
- Research Unit in Clinical and Translational Bioinformatics, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, P/Vall d'Hebron, 119-129, 08035 Barcelona, Spain
| | - Lídia Feliubadaló
- Hereditary Cancer Program, Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Catalan Institute of Oncology, 08908 L'Hospitalet de Llobregat, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), 28929 Madrid, Spain
| | - Xavier de la Cruz
- Research Unit in Clinical and Translational Bioinformatics, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, P/Vall d'Hebron, 119-129, 08035 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
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Liu Y, Yeung WSB, Chiu PCN, Cao D. Computational approaches for predicting variant impact: An overview from resources, principles to applications. Front Genet 2022; 13:981005. [PMID: 36246661 PMCID: PMC9559863 DOI: 10.3389/fgene.2022.981005] [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: 06/29/2022] [Accepted: 08/08/2022] [Indexed: 11/13/2022] Open
Abstract
One objective of human genetics is to unveil the variants that contribute to human diseases. With the rapid development and wide use of next-generation sequencing (NGS), massive genomic sequence data have been created, making personal genetic information available. Conventional experimental evidence is critical in establishing the relationship between sequence variants and phenotype but with low efficiency. Due to the lack of comprehensive databases and resources which present clinical and experimental evidence on genotype-phenotype relationship, as well as accumulating variants found from NGS, different computational tools that can predict the impact of the variants on phenotype have been greatly developed to bridge the gap. In this review, we present a brief introduction and discussion about the computational approaches for variant impact prediction. Following an innovative manner, we mainly focus on approaches for non-synonymous variants (nsSNVs) impact prediction and categorize them into six classes. Their underlying rationale and constraints, together with the concerns and remedies raised from comparative studies are discussed. We also present how the predictive approaches employed in different research. Although diverse constraints exist, the computational predictive approaches are indispensable in exploring genotype-phenotype relationship.
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Affiliation(s)
- Ye Liu
- Shenzhen Key Laboratory of Fertility Regulation, Reproductive Medicine Center, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - William S. B. Yeung
- Shenzhen Key Laboratory of Fertility Regulation, Reproductive Medicine Center, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
- Department of Obstetrics and Gynaecology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Philip C. N. Chiu
- Shenzhen Key Laboratory of Fertility Regulation, Reproductive Medicine Center, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
- Department of Obstetrics and Gynaecology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- *Correspondence: Philip C. N. Chiu, ; Dandan Cao,
| | - Dandan Cao
- Shenzhen Key Laboratory of Fertility Regulation, Reproductive Medicine Center, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
- *Correspondence: Philip C. N. Chiu, ; Dandan Cao,
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5
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Clark KA, Paquette A, Tao K, Bell R, Boyle JL, Rosenthal J, Snow AK, Stark AW, Thompson BA, Unger J, Gertz J, Varley KE, Boucher KM, Goldgar DE, Foulkes WD, Thomas A, Tavtigian SV. Comprehensive evaluation and efficient classification of BRCA1 RING domain missense substitutions. Am J Hum Genet 2022; 109:1153-1174. [PMID: 35659930 PMCID: PMC9247830 DOI: 10.1016/j.ajhg.2022.05.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 05/09/2022] [Indexed: 11/21/2022] Open
Abstract
BRCA1 is a high-risk susceptibility gene for breast and ovarian cancer. Pathogenic protein-truncating variants are scattered across the open reading frame, but all known missense substitutions that are pathogenic because of missense dysfunction are located in either the amino-terminal RING domain or the carboxy-terminal BRCT domain. Heterodimerization of the BRCA1 and BARD1 RING domains is a molecularly defined obligate activity. Hence, we tested every BRCA1 RING domain missense substitution that can be created by a single nucleotide change for heterodimerization with BARD1 in a mammalian two-hybrid assay. Downstream of the laboratory assay, we addressed three additional challenges: assay calibration, validation thereof, and integration of the calibrated results with other available data, such as computational evidence and patient/population observational data to achieve clinically applicable classification. Overall, we found that 15%-20% of BRCA1 RING domain missense substitutions are pathogenic. Using a Bayesian point system for data integration and variant classification, we achieved clinical classification of 89% of observed missense substitutions. Moreover, among missense substitutions not present in the human observational data used here, we find an additional 45 with concordant computational and functional assay evidence in favor of pathogenicity plus 223 with concordant evidence in favor of benignity; these are particularly likely to be classified as likely pathogenic and likely benign, respectively, once human observational data become available.
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Affiliation(s)
- Kathleen A Clark
- Huntsman Cancer Institute at the University of Utah, Salt Lake City, UT 84112, USA
| | - Andrew Paquette
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Kayoko Tao
- Huntsman Cancer Institute at the University of Utah, Salt Lake City, UT 84112, USA
| | - Russell Bell
- Huntsman Cancer Institute at the University of Utah, Salt Lake City, UT 84112, USA
| | - Julie L Boyle
- Huntsman Cancer Institute at the University of Utah, Salt Lake City, UT 84112, USA
| | - Judith Rosenthal
- Huntsman Cancer Institute at the University of Utah, Salt Lake City, UT 84112, USA
| | - Angela K Snow
- Huntsman Cancer Institute at the University of Utah, Salt Lake City, UT 84112, USA
| | - Alex W Stark
- Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Bryony A Thompson
- Huntsman Cancer Institute at the University of Utah, Salt Lake City, UT 84112, USA
| | - Joshua Unger
- Huntsman Cancer Institute at the University of Utah, Salt Lake City, UT 84112, USA
| | - Jason Gertz
- Huntsman Cancer Institute at the University of Utah, Salt Lake City, UT 84112, USA; Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Katherine E Varley
- Huntsman Cancer Institute at the University of Utah, Salt Lake City, UT 84112, USA; Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Kenneth M Boucher
- Huntsman Cancer Institute at the University of Utah, Salt Lake City, UT 84112, USA; Division of Epidemiology, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT 84108, USA
| | - David E Goldgar
- Huntsman Cancer Institute at the University of Utah, Salt Lake City, UT 84112, USA; Department of Dermatology, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - William D Foulkes
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC H3T 1E2, Canada; Research Institute McGill University Health Center, Montreal, QC H3T 1E2, Canada; Departments of Medicine, Human Genetics, and Oncology, McGill University, Montreal, QC H3T 1E2, Canada
| | - Alun Thomas
- Division of Epidemiology, Department of Internal Medicine, University of Utah School of Medicine, Salt Lake City, UT 84108, USA
| | - Sean V Tavtigian
- Huntsman Cancer Institute at the University of Utah, Salt Lake City, UT 84112, USA; Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
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6
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Ben-Cohen G, Doffe F, Devir M, Leroy B, Soussi T, Rosenberg S. TP53_PROF: a machine learning model to predict impact of missense mutations in TP53. Brief Bioinform 2022; 23:6510957. [PMID: 35043155 PMCID: PMC8921628 DOI: 10.1093/bib/bbab524] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 11/04/2021] [Accepted: 11/15/2021] [Indexed: 11/27/2022] Open
Abstract
Correctly identifying the true driver mutations in a patient’s tumor is a major challenge in precision oncology. Most efforts address frequent mutations, leaving medium- and low-frequency variants mostly unaddressed. For TP53, this identification is crucial for both somatic and germline mutations, with the latter associated with the Li-Fraumeni syndrome (LFS), a multiorgan cancer predisposition. We present TP53_PROF (prediction of functionality), a gene specific machine learning model to predict the functional consequences of every possible missense mutation in TP53, integrating human cell- and yeast-based functional assays scores along with computational scores. Variants were labeled for the training set using well-defined criteria of prevalence in four cancer genomics databases. The model’s predictions provided accuracy of 96.5%. They were validated experimentally, and were compared to population data, LFS datasets, ClinVar annotations and to TCGA survival data. Very high accuracy was shown through all methods of validation. TP53_PROF allows accurate classification of TP53 missense mutations applicable for clinical practice. Our gene specific approach integrated machine learning, highly reliable features and biological knowledge, to create an unprecedented, thoroughly validated and clinically oriented classification model. This approach currently addresses TP53 mutations and will be applied in the future to other important cancer genes.
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Affiliation(s)
- Gil Ben-Cohen
- Corresponding authors: Gil Ben Cohen, Gaffin Center for Neuro-Oncology, Sharett Institute for Oncology, The Wohl Institute for Translational Medicine. Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Israel. Tel.: +972549410946. E-mail: ; Shai Rosenberg, Gaffin Center for Neuro-Oncology, Sharett Institute for Oncology, The Wohl Institute for Translational Medicine. Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Israel. Tel.: 972-2-6776289. E-mail:
| | - Flora Doffe
- INSERM UMR 1186, Integrative Tumor Immunology and Immunotherapy, Gustave Roussy, Faculté de Médecine, Université Paris-Sud, Université Paris-Saclay, 94805 Villejuif, France
| | - Michal Devir
- Gaffin Center for Neuro-Oncology, Sharett Institute for Oncology, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Israel
- The Wohl Institute for Translational Medicine, Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Israel
| | - Bernard Leroy
- Sorbonne Université, UPMC Univ Paris 06, F- 75005 Paris, France
| | | | - Shai Rosenberg
- Corresponding authors: Gil Ben Cohen, Gaffin Center for Neuro-Oncology, Sharett Institute for Oncology, The Wohl Institute for Translational Medicine. Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Israel. Tel.: +972549410946. E-mail: ; Shai Rosenberg, Gaffin Center for Neuro-Oncology, Sharett Institute for Oncology, The Wohl Institute for Translational Medicine. Hadassah Medical Center and Faculty of Medicine, Hebrew University of Jerusalem, Israel. Tel.: 972-2-6776289. E-mail:
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7
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Tamana S, Xenophontos M, Minaidou A, Stephanou C, Harteveld CL, Bento C, Traeger-Synodinos J, Fylaktou I, Yasin NM, Abdul Hamid FS, Esa E, Halim-Fikri H, Zilfalil BA, Kakouri AC, Kleanthous M, Kountouris P. Evaluation of in silico predictors on short nucleotide variants in HBA1, HBA2, and HBB associated with haemoglobinopathies. eLife 2022; 11:79713. [PMID: 36453528 PMCID: PMC9731569 DOI: 10.7554/elife.79713] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 10/31/2022] [Indexed: 12/03/2022] Open
Abstract
Haemoglobinopathies are the commonest monogenic diseases worldwide and are caused by variants in the globin gene clusters. With over 2400 variants detected to date, their interpretation using the American College of Medical Genetics and Genomics (ACMG)/Association for Molecular Pathology (AMP) guidelines is challenging and computational evidence can provide valuable input about their functional annotation. While many in silico predictors have already been developed, their performance varies for different genes and diseases. In this study, we evaluate 31 in silico predictors using a dataset of 1627 variants in HBA1, HBA2, and HBB. By varying the decision threshold for each tool, we analyse their performance (a) as binary classifiers of pathogenicity and (b) by using different non-overlapping pathogenic and benign thresholds for their optimal use in the ACMG/AMP framework. Our results show that CADD, Eigen-PC, and REVEL are the overall top performers, with the former reaching moderate strength level for pathogenic prediction. Eigen-PC and REVEL achieve the highest accuracies for missense variants, while CADD is also a reliable predictor of non-missense variants. Moreover, SpliceAI is the top performing splicing predictor, reaching strong level of evidence, while GERP++ and phyloP are the most accurate conservation tools. This study provides evidence about the optimal use of computational tools in globin gene clusters under the ACMG/AMP framework.
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Affiliation(s)
- Stella Tamana
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and GeneticsNicosiaCyprus
| | - Maria Xenophontos
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and GeneticsNicosiaCyprus
| | - Anna Minaidou
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and GeneticsNicosiaCyprus
| | - Coralea Stephanou
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and GeneticsNicosiaCyprus
| | - Cornelis L Harteveld
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and GeneticsNicosiaCyprus,Leiden University Medical CenterLeidenNetherlands
| | - Celeste Bento
- Centro Hospitalar e Universitário de CoimbraCoimbraPortugal
| | | | - Irene Fylaktou
- Division of Endocrinology, Metabolism and Diabetes, First Department of Pediatrics, National and Kapodistrian University of AthensAthensGreece
| | - Norafiza Mohd Yasin
- Haematology Unit, Cancer Research Centre, Institute for Medical Research, National Health of Institutes (NIH), Ministry of Health MalaysiaSelangorMalaysia
| | - Faidatul Syazlin Abdul Hamid
- Haematology Unit, Cancer Research Centre, Institute for Medical Research, National Health of Institutes (NIH), Ministry of Health MalaysiaSelangorMalaysia
| | - Ezalia Esa
- Haematology Unit, Cancer Research Centre, Institute for Medical Research, National Health of Institutes (NIH), Ministry of Health MalaysiaSelangorMalaysia
| | - Hashim Halim-Fikri
- Malaysian Node of the Human Variome Project, School of Medical Sciences, Health Campus, Universiti Sains MalaysiaKelantanMalaysia
| | - Bin Alwi Zilfalil
- Human Genome Centre, School of Medical Sciences, Health Campus, Universiti Sains MalaysiaKelantanMalaysia
| | - Andrea C Kakouri
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and GeneticsNicosiaCyprus
| | | | - Marina Kleanthous
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and GeneticsNicosiaCyprus
| | - Petros Kountouris
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and GeneticsNicosiaCyprus
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8
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Siraj AK, Masoodi T, Bu R, Parvathareddy SK, Iqbal K, Azam S, Al-Rasheed M, Ajarim D, Tulbah A, Al-Dayel F, Al-Kuraya KS. Prevalence of germline TP53 mutation among early onset middle eastern breast cancer patients. Hered Cancer Clin Pract 2021; 19:49. [PMID: 34906214 PMCID: PMC8670057 DOI: 10.1186/s13053-021-00206-w] [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: 08/16/2021] [Accepted: 11/29/2021] [Indexed: 11/22/2022] Open
Abstract
Background The data on prevalence and clinical relevance of TP53 germline mutations in early onset Middle-Eastern breast cancer (BC) is limited. Methods We determined TP53 germline mutations in a cohort of 464 early onset BC patients from Saudi Arabia using capture sequencing based next generation sequencing. Results Germline TP53 pathogenic mutations were found in 1.5% (7/464) of early onset Saudi BC patients. A total of six pathogenic missense mutations, one stop gain mutation and two variants of uncertain significance (VUS) were detected in our cohort. No TP53 pathogenic mutations were detected among 463 healthy controls. TP53 mutations carriers were significantly more likely to have bilateral breast cancer (p = 0.0008). At median follow-up of 41 months, TP53 mutations were an unfavorable factor for overall survival in univariate analysis. All the patients carrying TP53 mutations were negative for BRCA1 and BRCA2 mutations. Majority of patients (85.7%; 6/7) carrying TP53 mutation had no family history suggestive of Li-Fraumeni Syndrome (LFS) or personal history of multiple LFS related tumors. Only one patient had a positive family history suggestive of LFS. Conclusions TP53 germline mutation screening detects a clinically meaningful risk of early onset BC from this ethnicity and should be considered in all early onset BC regardless of the family history of cancer, especially in young patients that are negative for BRCA mutations. Supplementary Information The online version contains supplementary material available at 10.1186/s13053-021-00206-w.
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Affiliation(s)
- Abdul Khalid Siraj
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Center, P.O. Box 3354, 11211, Riyadh, Saudi Arabia
| | - Tariq Masoodi
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Center, P.O. Box 3354, 11211, Riyadh, Saudi Arabia
| | - Rong Bu
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Center, P.O. Box 3354, 11211, Riyadh, Saudi Arabia
| | - Sandeep Kumar Parvathareddy
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Center, P.O. Box 3354, 11211, Riyadh, Saudi Arabia
| | - Kaleem Iqbal
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Center, P.O. Box 3354, 11211, Riyadh, Saudi Arabia
| | - Saud Azam
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Center, P.O. Box 3354, 11211, Riyadh, Saudi Arabia
| | - Maha Al-Rasheed
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Center, P.O. Box 3354, 11211, Riyadh, Saudi Arabia
| | - Dahish Ajarim
- Department of Oncology, King Faisal Specialist Hospital and Research Centre, P.O. Box 3354, 11211, Riyadh, Saudi Arabia
| | - Asma Tulbah
- Department of Pathology, King Faisal Specialist Hospital and Research Centre, P.O. Box 3354, 11211, Riyadh, Saudi Arabia
| | - Fouad Al-Dayel
- Department of Pathology, King Faisal Specialist Hospital and Research Centre, P.O. Box 3354, 11211, Riyadh, Saudi Arabia
| | - Khawla Sami Al-Kuraya
- Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Center, P.O. Box 3354, 11211, Riyadh, Saudi Arabia. .,Research Center, Human Cancer Genomic Research, King Faisal Specialist Hospital and Research Center, MBC#98-16, P.O. Box 3354, 11211, Riyadh, Saudi Arabia.
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9
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Douglass DP, Stine KC, Farrar JE. A Novel Germline TP53 Mutation in a Patient With Li-Fraumeni Syndrome: Resolving a Variant of Uncertain Significance. J Pediatr Hematol Oncol 2021; 43:e1220-e1222. [PMID: 33633026 DOI: 10.1097/mph.0000000000002115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 01/15/2021] [Indexed: 11/25/2022]
Abstract
Increasing availability of genomic testing poses new challenges to clinicians, particularly where variant interpretation from commercial sources may be equivocal. The authors report a patient with recurrent rhabdomyosarcoma and subsequent bilateral breast cancer who was found to harbor a previously undescribed germline TP53 sequence alteration annotated by the commercial laboratory as a variant of uncertain significance. By investigating publicly available databases of aggregated normal germline and malignant somatic genomic sequences, the authors conclude that this missense variant, c.476C>T (p.A159V), is a novel, pathogenic Li-Fraumeni syndrome mutation and demonstrate the utility of these resources in clinical pediatric hematology and oncology practice.
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Affiliation(s)
- David P Douglass
- Department of Pediatrics, Arkansas Children's Research Institute, University of Arkansas for Medical Sciences, Little Rock, AR
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10
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Pinto EM, Maxwell KN, Halalsheh H, Phillips A, Powers J, MacFarland S, Walsh MF, Breen K, Formiga MN, Kriwacki R, Nichols KE, Mostafavi R, Wang J, Clay MR, Rodriguez-Galindo C, Ribeiro RC, Zambetti GP. Clinical and Functional Significance of TP53 Exon 4-Intron 4 Splice Junction Variants. Mol Cancer Res 2021; 20:207-216. [PMID: 34675114 DOI: 10.1158/1541-7786.mcr-21-0583] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 09/15/2021] [Accepted: 10/19/2021] [Indexed: 11/16/2022]
Abstract
Germline TP53 splicing variants are uncommon, and their clinical relevance is unknown. However, splice-altering variants at exon 4-intron 4 junctions are relatively enriched in pediatric adrenocortical tumors (ACT). Nevertheless, family histories of cancer compatible with classic Li-Fraumeni syndrome are rarely seen in these patients. We used conventional and in silico assays to determine protein stability, splicing, and transcriptional activity of 10 TP53 variants at exon 4-intron 4 junctions and analyzed their clinical correlates. We reviewed public databases that report the impact of TP53 variants in human cancer and examined individual reports, focusing on family history of cancer. TP53 exon 4-intron 4 junction germline variants were identified in 9 of 75 pediatric ACTs enrolled in the International Pediatric Adrenocortical Tumor Registry and Children's Oncology Group ARAR0332 study. An additional eight independent TP53 variants involving exon 4 splicing were identified in the Pediatric Cancer Genome Project (n = 5,213). These variants resulted in improper expression due to ineffective splicing, protein instability, altered subcellular localization, and loss of function. Clinical case review of carriers of TP53 exon 4-intron 4 junction variants revealed a high incidence of pediatric ACTs and atypical tumor types not consistent with classic Li-Fraumeni syndrome. Germline variants involving TP53 exon 4-intron 4 junctions are frequent in ACT and rare in other pediatric tumors. The collective impact of these germline TP53 variants on the fidelity of splicing, protein structure, and function must be considered in evaluating cancer susceptibility. IMPLICATIONS: Taken together, the data indicate that splice variants at TP53 codon 125 and surrounding bases differentially impacted p53 gene expression and function.
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Affiliation(s)
- Emilia M Pinto
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee.
| | - Kara N Maxwell
- Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | | | - Aaron Phillips
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jacquelyn Powers
- Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Suzanne MacFarland
- Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania
| | - Michael F Walsh
- Department of Pediatrics and Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kelsey Breen
- Department of Pediatrics and Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Maria N Formiga
- Department of Oncogenetics, A.C. Camargo Center, Sao Paulo, Brazil
| | - Richard Kriwacki
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Kim E Nichols
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Roya Mostafavi
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jinling Wang
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Michael R Clay
- Department of Pathology, University of Colorado, Boulder, Colorado
| | - Carlos Rodriguez-Galindo
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee
- Global Pediatric Medicine at St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Raul C Ribeiro
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee.
| | - Gerard P Zambetti
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee.
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11
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Fortuno C, Pesaran T, Dolinsky J, Yussuf A, McGoldrick K, Tavtigian SV, Goldgar D, Spurdle AB, James PA. An updated quantitative model to classify missense variants in the TP53 gene: A novel multifactorial strategy. Hum Mutat 2021; 42:1351-1361. [PMID: 34273903 DOI: 10.1002/humu.24264] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 06/25/2021] [Accepted: 07/15/2021] [Indexed: 11/07/2022]
Abstract
Multigene panel testing has led to an increase in the number of variants of uncertain significance identified in the TP53 gene, associated with Li-Fraumeni syndrome. We previously developed a quantitative model for predicting the pathogenicity of P53 missense variants based on the combination of calibrated bioinformatic information and somatic to germline ratio. Here, we extended this quantitative model for the classification of P53 predicted missense variants by adding new pieces of evidence (personal and family history parameters, loss-of-function results, population allele frequency, healthy individual status by age 60, and breast tumor pathology). We also annotated which missense variants might have an effect on splicing based on bioinformatic predictions. This updated model plus annotation led to the classification of 805 variants into a clinically relevant class, which correlated well with existing ClinVar classifications, and resolved a large number of conflicting and uncertain classifications. We propose this model as a reliable approach to TP53 germline variant classification and emphasize its use in contributing to optimize TP53-specific ACMG/AMP guidelines.
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Affiliation(s)
- Cristina Fortuno
- Genetics and Computational Division, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | | | | | - Amal Yussuf
- Ambry Genetics, Aliso Viejo, California, USA
| | | | - Sean V Tavtigian
- Huntsman Cancer Institute and Department of Dermatology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - David Goldgar
- Huntsman Cancer Institute and Department of Dermatology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Amanda B Spurdle
- Genetics and Computational Division, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Paul A James
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Melbourne, Australia
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12
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Targeted Sequencing of Sorted Esophageal Adenocarcinoma Cells Unveils Known and Novel Mutations in the Separated Subpopulations. Clin Transl Gastroenterol 2021; 11:e00202. [PMID: 33094962 PMCID: PMC7508445 DOI: 10.14309/ctg.0000000000000202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
INTRODUCTION Our study aimed at investigating tumor heterogeneity in esophageal adenocarcinoma (EAC) cells regarding clinical outcomes. METHODS Thirty-eight surgical EAC cases who underwent gastroesophageal resection with lymph node dissection in 3 university centers were included. Archival material was analyzed via high-throughput cell sorting technology and targeted sequencing of 63 cancer-related genes. Low-pass sequencing and immunohistochemistry (IHC) were used to validate the results. RESULTS Thirty-five of 38 EACs carried at least one somatic mutation that was absent in the stromal cells; 73.7%, 10.5%, and 10.5% carried mutations in tumor protein 53, cyclin dependent kinase inhibitor 2A, and SMAD family member 4, respectively. In addition, 2 novel mutations were found for hepatocyte nuclear factor-1 alpha in 2 of 38 cases. Tumor protein 53 gene abnormalities were more informative than p53 IHC. Conversely, loss of SMAD4 was more frequently noted with IHC (53%) and was associated with a higher recurrence rate (P = 0.015). Only through cell sorting we were able to detect the presence of hyperdiploid and pseudodiploid subclones in 7 EACs that exhibited different mutational loads and/or additional copy number amplifications, indicating the high genetic heterogeneity of these cancers. DISCUSSION Selective cell sorting allowed the characterization of multiple molecular defects in EAC subclones that were missed in a significant number of cases when whole-tumor samples were analyzed. Therefore, this approach can reveal subtle differences in cancer cell subpopulations. Future studies are required to investigate whether these subclones are responsible for treatment response and disease recurrence.
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13
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Doffe F, Carbonnier V, Tissier M, Leroy B, Martins I, Mattsson JSM, Micke P, Pavlova S, Pospisilova S, Smardova J, Joerger AC, Wiman KG, Kroemer G, Soussi T. Identification and functional characterization of new missense SNPs in the coding region of the TP53 gene. Cell Death Differ 2021; 28:1477-1492. [PMID: 33257846 PMCID: PMC8166836 DOI: 10.1038/s41418-020-00672-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 11/03/2020] [Accepted: 11/04/2020] [Indexed: 02/06/2023] Open
Abstract
Infrequent and rare genetic variants in the human population vastly outnumber common ones. Although they may contribute significantly to the genetic basis of a disease, these seldom-encountered variants may also be miss-identified as pathogenic if no correct references are available. Somatic and germline TP53 variants are associated with multiple neoplastic diseases, and thus have come to serve as a paradigm for genetic analyses in this setting. We searched 14 independent, globally distributed datasets and recovered TP53 SNPs from 202,767 cancer-free individuals. In our analyses, 19 new missense TP53 SNPs, including five novel variants specific to the Asian population, were recurrently identified in multiple datasets. Using a combination of in silico, functional, structural, and genetic approaches, we showed that none of these variants displayed loss of function compared to the normal TP53 gene. In addition, classification using ACMG criteria suggested that they are all benign. Considered together, our data reveal that the TP53 coding region shows far more polymorphism than previously thought and present high ethnic diversity. They furthermore underline the importance of correctly assessing novel variants in all variant-calling pipelines associated with genetic diagnoses for cancer.
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Affiliation(s)
- Flora Doffe
- Equipe Labellisée par la Ligue Contre le Cancer, Université Paris Descartes, Université Sorbonne Paris Cité, Université Paris Diderot, Sorbonne Université, INSERM U1138, Centre de Recherche des Cordeliers, Paris, France
- Department of Oncology-Pathology, Bioclinicum, Karolinska Institutet, Stockholm, Sweden
| | - Vincent Carbonnier
- Equipe Labellisée par la Ligue Contre le Cancer, Université Paris Descartes, Université Sorbonne Paris Cité, Université Paris Diderot, Sorbonne Université, INSERM U1138, Centre de Recherche des Cordeliers, Paris, France
| | - Manon Tissier
- Equipe Labellisée par la Ligue Contre le Cancer, Université Paris Descartes, Université Sorbonne Paris Cité, Université Paris Diderot, Sorbonne Université, INSERM U1138, Centre de Recherche des Cordeliers, Paris, France
| | - Bernard Leroy
- Department of Life Science, Sorbonne Université, Paris, France
| | - Isabelle Martins
- Equipe Labellisée par la Ligue Contre le Cancer, Université Paris Descartes, Université Sorbonne Paris Cité, Université Paris Diderot, Sorbonne Université, INSERM U1138, Centre de Recherche des Cordeliers, Paris, France
- Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France
| | - Johanna S M Mattsson
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Patrick Micke
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Sarka Pavlova
- Department of Internal Medicine-Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Sarka Pospisilova
- Department of Internal Medicine-Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Jana Smardova
- Faculty of Science, Department of Experimental Biology, Masaryk University, Brno, Czech Republic
| | - Andreas C Joerger
- Institute of Pharmaceutical Chemistry, Johann Wolfgang Goethe University, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences and Structural Genomics Consortium (SGC), Max-von-Laue-Str. 15, 60438, Frankfurt am Main, Germany
| | - Klas G Wiman
- Department of Oncology-Pathology, Bioclinicum, Karolinska Institutet, Stockholm, Sweden
| | - Guido Kroemer
- Equipe Labellisée par la Ligue Contre le Cancer, Université Paris Descartes, Université Sorbonne Paris Cité, Université Paris Diderot, Sorbonne Université, INSERM U1138, Centre de Recherche des Cordeliers, Paris, France
- Metabolomics and Cell Biology Platforms, Institut Gustave Roussy, Villejuif, France
- Pôle de Biologie, Hôpital Européen Georges Pompidou, AP-HP, Paris, France
- Department of Women's and Children's Health, Karolinska University Hospital, Stockholm, Sweden
| | - Thierry Soussi
- Equipe Labellisée par la Ligue Contre le Cancer, Université Paris Descartes, Université Sorbonne Paris Cité, Université Paris Diderot, Sorbonne Université, INSERM U1138, Centre de Recherche des Cordeliers, Paris, France.
- Department of Oncology-Pathology, Bioclinicum, Karolinska Institutet, Stockholm, Sweden.
- Department of Life Science, Sorbonne Université, Paris, France.
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
- Cell Death and Drug Resistance in Lymphoproliferative Disorders Team, INSERM U1138, Centre de Recherche des Cordeliers, Paris, France.
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14
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Fortuno C, Lee K, Olivier M, Pesaran T, Mai PL, de Andrade KC, Attardi LD, Crowley S, Evans DG, Feng BJ, Major Foreman AK, Frone MN, Huether R, James PA, McGoldrick K, Mester J, Seifert BA, Slavin TP, Witkowski L, Zhang L, Plon SE, Spurdle AB, Savage SA. Specifications of the ACMG/AMP variant interpretation guidelines for germline TP53 variants. Hum Mutat 2021; 42:223-236. [PMID: 33300245 PMCID: PMC8374922 DOI: 10.1002/humu.24152] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 11/05/2020] [Accepted: 12/07/2020] [Indexed: 12/28/2022]
Abstract
Germline pathogenic variants in TP53 are associated with Li-Fraumeni syndrome, a cancer predisposition disorder inherited in an autosomal dominant pattern associated with a high risk of malignancy, including early-onset breast cancers, sarcomas, adrenocortical carcinomas, and brain tumors. Intense cancer surveillance for individuals with TP53 germline pathogenic variants is associated with reduced cancer-related mortality. Accurate and consistent classification of germline variants across clinical and research laboratories is important to ensure appropriate cancer surveillance recommendations. Here, we describe the work performed by the Clinical Genome Resource TP53 Variant Curation Expert Panel (ClinGen TP53 VCEP) focused on specifying the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP) guidelines for germline variant classification to the TP53 gene. Specifications were developed for 20 ACMG/AMP criteria, while nine were deemed not applicable. The original strength level for the 10 criteria was also adjusted due to current evidence. Use of TP53-specific guidelines and sharing of clinical data among experts and clinical laboratories led to a decrease in variants of uncertain significance from 28% to 12% compared with the original guidelines. The ClinGen TP53 VCEP recommends the use of these TP53-specific ACMG/AMP guidelines as the standard strategy for TP53 germline variant classification.
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Affiliation(s)
- Cristina Fortuno
- QIMR Berghofer Medical Research Institute, Brisbane City, Australia, AUS
| | - Kristy Lee
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | | | - Phuong L. Mai
- Magee-Womens Hospital, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
| | - Kelvin C. de Andrade
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Laura D. Attardi
- Departments of Radiation-Oncology and Genetics, Stanford University, Stanford, CA, USA
| | - Stephanie Crowley
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | | | | | - Megan N. Frone
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | | | - Paul A. James
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Australia
| | | | | | - Bryce A. Seifert
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Leora Witkowski
- Laboratory for Molecular Medicine, Partners Healthcare Personalized Medicine, Cambridge, MA, USA
| | - Liying Zhang
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sharon E. Plon
- Department of Pediatrics/Hematology-Oncology, Baylor College of Medicine, Houston, TX, USA
| | - Amanda B. Spurdle
- QIMR Berghofer Medical Research Institute, Brisbane City, Australia, AUS
| | - Sharon A. Savage
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
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15
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Raad S, Rolain M, Coutant S, Derambure C, Lanos R, Charbonnier F, Bou J, Bouvignies E, Lienard G, Vasseur S, Farrell M, Ingster O, Baert Desurmont S, Kasper E, Bougeard G, Frébourg T, Tournier I. Blood functional assay for rapid clinical interpretation of germline TP53 variants. J Med Genet 2020; 58:796-805. [PMID: 33051313 PMCID: PMC8639931 DOI: 10.1136/jmedgenet-2020-107059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 08/05/2020] [Accepted: 09/01/2020] [Indexed: 12/11/2022]
Abstract
BACKGROUND The interpretation of germline TP53 variants is critical to ensure appropriate medical management of patients with cancer and follow-up of variant carriers. This interpretation remains complex and is becoming a growing challenge considering the exponential increase in TP53 tests. We developed a functional assay directly performed on patients' blood. METHODS Peripheral blood mononuclear cells were cultured, activated, exposed to doxorubicin and the p53-mediated transcriptional response was quantified using reverse transcription-multiplex ligation probe amplification and RT-QMPSF assays, including 10 p53 targets selected from transcriptome analysis, and two amplicons to measure p53 mRNA levels. We applied this blood functional assay to 77 patients addressed for TP53 analysis. RESULTS In 51 wild-type TP53 individuals, the mean p53 functionality score was 12.7 (range 7.5-22.8). Among eight individuals harbouring likely pathogenic or pathogenic variants, the scores were reduced (mean 4.8, range 3.1-7.1), and p53 mRNA levels were reduced in patients harbouring truncating variants. We tested 14 rare unclassified variants (p.(Pro72His), p.(Gly105Asp), p.(Arg110His), p.(Phe134Leu), p.(Arg158Cys), p.(Pro191Arg), p.(Pro278Arg), p.(Arg283Cys), p.(Leu348Ser), p.(Asp352Tyr), p.(Gly108_Phe109delinsVal), p.(Asn131del), p.(Leu265del), c.-117G>T) and 12 yielded functionally abnormal scores. Remarkably, the assay revealed that the c.*1175A>C polymorphic variant within TP53 poly-adenylation site can impact p53 function with the same magnitude as a null variant, when present on both alleles, and may act as a modifying factor in pathogenic variant carriers. CONCLUSION This blood p53 assay should therefore be a useful tool for the rapid clinical classification of germline TP53 variants and detection of non-coding functional variants.
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Affiliation(s)
- Sabine Raad
- Normandie University, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics, F76000, Normandy Centre for Genomic and Personalized Medicine, University of Rouen Faculty of Medicine and Pharmacy, Rouen, France
| | - Marion Rolain
- Normandie University, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics, F76000, Normandy Centre for Genomic and Personalized Medicine, University of Rouen Faculty of Medicine and Pharmacy, Rouen, France
| | - Sophie Coutant
- Normandie University, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics, F76000, Normandy Centre for Genomic and Personalized Medicine, University of Rouen Faculty of Medicine and Pharmacy, Rouen, France
| | - Céline Derambure
- Normandie University, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics, F76000, Normandy Centre for Genomic and Personalized Medicine, University of Rouen Faculty of Medicine and Pharmacy, Rouen, France
| | - Raphael Lanos
- Normandie University, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics, F76000, Normandy Centre for Genomic and Personalized Medicine, University of Rouen Faculty of Medicine and Pharmacy, Rouen, France
| | - Françoise Charbonnier
- Normandie University, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics, F76000, Normandy Centre for Genomic and Personalized Medicine, University of Rouen Faculty of Medicine and Pharmacy, Rouen, France
| | - Jacqueline Bou
- Normandie University, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics, F76000, Normandy Centre for Genomic and Personalized Medicine, University of Rouen Faculty of Medicine and Pharmacy, Rouen, France
| | - Emilie Bouvignies
- Normandie University, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics, F76000, Normandy Centre for Genomic and Personalized Medicine, University of Rouen Faculty of Medicine and Pharmacy, Rouen, France
| | - Gwendoline Lienard
- Normandie University, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics, F76000, Normandy Centre for Genomic and Personalized Medicine, University of Rouen Faculty of Medicine and Pharmacy, Rouen, France
| | - Stéphanie Vasseur
- Normandie University, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics, F76000, Normandy Centre for Genomic and Personalized Medicine, University of Rouen Faculty of Medicine and Pharmacy, Rouen, France
| | - Michael Farrell
- Cancer Genetics Service, Mater Private Hospital, Dublin, Leinster, Ireland
| | - Olivier Ingster
- Department of Genetics, University Hospital Centre Angers, Angers, Pays de la Loire, France
| | - Stéphanie Baert Desurmont
- Normandie University, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics, F76000, Normandy Centre for Genomic and Personalized Medicine, University of Rouen Faculty of Medicine and Pharmacy, Rouen, France
| | - Edwige Kasper
- Normandie University, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics, F76000, Normandy Centre for Genomic and Personalized Medicine, University of Rouen Faculty of Medicine and Pharmacy, Rouen, France
| | - Gaëlle Bougeard
- Normandie University, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics, F76000, Normandy Centre for Genomic and Personalized Medicine, University of Rouen Faculty of Medicine and Pharmacy, Rouen, France
| | - Thierry Frébourg
- Normandie University, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics, F76000, Normandy Centre for Genomic and Personalized Medicine, University of Rouen Faculty of Medicine and Pharmacy, Rouen, France
| | - Isabelle Tournier
- Normandie University, UNIROUEN, Inserm U1245 and Rouen University Hospital, Department of Genetics, F76000, Normandy Centre for Genomic and Personalized Medicine, University of Rouen Faculty of Medicine and Pharmacy, Rouen, France
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16
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Bittar CM, Vieira IA, Sabato CS, Andreis TF, Alemar B, Artigalás O, Galvão HDCR, Macedo GS, Palmero EI, Ashton-Prolla P. TP53 variants of uncertain significance: increasing challenges in variant interpretation and genetic counseling. Fam Cancer 2020; 18:451-456. [PMID: 31321604 DOI: 10.1007/s10689-019-00140-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Li-Fraumeni syndrome (LFS) and Li-Fraumeni Like (LFL) are autosomal dominant cancer predisposition syndromes caused by pathogenic germline variants in the TP53 gene. Recent studies have shown that the incorporation of next-generation sequencing by using multigene panels in clinical practice has resulted in the frequent identification of variants of uncertain significance (VUS). Given that there is no established medical management for VUS carriers, the identification of these variants may cause confusion and anxiety for both patients and practitioners. Herein, we aimed to verify VUS frequency and review VUS classification and interpretation in 1844 patients submitted for comprehensive germline TP53 testing independent of clinical criteria. Variant characterization was done assessing clinical information whenever available, variant frequency in population databases, pathogenicity predictions using in silico tools and previous functional studies. All variants were classified based on the guidelines proposed by the American College of Medical Genetics and Genomics (2015) and by the Sherloc framework (2017). Of the twelve VUS (0.65%) identified in TP53, two were classified as likely pathogenic and two were classified as likely benign after re-evaluation, potentially resulting in significant management modification for the proband and relatives. This report cases highlights the challenges and impact of TP53 variant interpretation especially when there is no clear LFS/LFL phenotype.
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Affiliation(s)
- Camila Matzenbacher Bittar
- Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 9500 - Prédio 43323 M, Porto Alegre, RS, 91501-970, Brazil.,Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Rua Ramiro Barcelos, 2350, Porto Alegre, RS, 90035-903, Brazil
| | - Igor Araujo Vieira
- Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 9500 - Prédio 43323 M, Porto Alegre, RS, 91501-970, Brazil.,Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Rua Ramiro Barcelos, 2350, Porto Alegre, RS, 90035-903, Brazil
| | - Cristina Silva Sabato
- Molecular Oncology Research Center, Barretos Cancer Hospital, Rua Antenor Duarte Viléla, 1331 - Dr. Paulo Prata, Barretos, SP, 14784-400, Brazil
| | - Tiago Finger Andreis
- Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 9500 - Prédio 43323 M, Porto Alegre, RS, 91501-970, Brazil.,Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Rua Ramiro Barcelos, 2350, Porto Alegre, RS, 90035-903, Brazil
| | - Bárbara Alemar
- Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 9500 - Prédio 43323 M, Porto Alegre, RS, 91501-970, Brazil.,Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Rua Ramiro Barcelos, 2350, Porto Alegre, RS, 90035-903, Brazil
| | - Osvaldo Artigalás
- Hospital Moinhos de Vento (HMV), Rua Ramiro Barcelos, 910, Porto Alegre, RS, 91790-560, Brazil
| | - Henrique de Campos Reis Galvão
- Molecular Oncology Research Center, Barretos Cancer Hospital, Rua Antenor Duarte Viléla, 1331 - Dr. Paulo Prata, Barretos, SP, 14784-400, Brazil
| | - Gabriel S Macedo
- Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 9500 - Prédio 43323 M, Porto Alegre, RS, 91501-970, Brazil.,Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Rua Ramiro Barcelos, 2350, Porto Alegre, RS, 90035-903, Brazil
| | - Edenir Inez Palmero
- Molecular Oncology Research Center, Barretos Cancer Hospital, Rua Antenor Duarte Viléla, 1331 - Dr. Paulo Prata, Barretos, SP, 14784-400, Brazil.,Barretos School of Health Sciences, Dr. Paulo Prata - FACISB, Barretos, SP, 14784-400, Brazil
| | - Patricia Ashton-Prolla
- Programa de Pós-Graduação em Genética e Biologia Molecular (PPGBM), Universidade Federal do Rio Grande do Sul (UFRGS), Av. Bento Gonçalves, 9500 - Prédio 43323 M, Porto Alegre, RS, 91501-970, Brazil. .,Laboratório de Medicina Genômica, Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Rua Ramiro Barcelos, 2350, Porto Alegre, RS, 90035-903, Brazil. .,Serviço de Genética Médica, Hospital de Clínicas de Porto Alegre (HCPA), Rua Ramiro Barcelos, 2350, Porto Alegre, RS, 90035-903, Brazil.
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17
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Li H, LaDuca H, Pesaran T, Chao EC, Dolinsky JS, Parsons M, Spurdle AB, Polley EC, Shimelis H, Hart SN, Hu C, Couch FJ, Goldgar DE. Classification of variants of uncertain significance in BRCA1 and BRCA2 using personal and family history of cancer from individuals in a large hereditary cancer multigene panel testing cohort. Genet Med 2019; 22:701-708. [PMID: 31853058 PMCID: PMC7118020 DOI: 10.1038/s41436-019-0729-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 12/02/2019] [Indexed: 02/07/2023] Open
Abstract
Purpose Genetic testing of individuals often results in identification of genomic variants of unknown significance (VUS). Multiple lines of evidence are used to help determine the clinical significance of these variants. Methods We analyzed ~138,000 individuals tested by multigene panel testing (MGPT). We used logistic regression to predict carrier status based on personal and family history of cancer. This was applied to 4644 tested individuals carrying 2383 BRCA1/2 variants to calculate likelihood ratios informing pathogenicity for each. Heterogeneity tests were performed for specific classes of variants defined by in silico predictions. Results Twenty-two variants labeled as VUS had odds of >10:1 in favor of pathogenicity. The heterogeneity analysis found that among variants in functional domains that were predicted to be benign by in silico tools, a significantly higher proportion of variants were estimated to be pathogenic than previously indicated; that missense variants outside of functional domains should be considered benign; and that variants predicted to create de novo donor sites were also largely benign. Conclusion The evidence presented here supports the use of personal and family history from MGPT in the classification of VUS and will be integrated into ongoing efforts to provide large-scale multifactorial classification.
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Affiliation(s)
- Hongyan Li
- Huntsman Cancer Institute, Salt Lake City, UT, USA
| | - Holly LaDuca
- Ambry Genetics Laboratories, Aliso Viejo, CA, USA
| | - Tina Pesaran
- Ambry Genetics Laboratories, Aliso Viejo, CA, USA
| | - Elizabeth C Chao
- Ambry Genetics Laboratories, Aliso Viejo, CA, USA.,Department of Pediatrics, University of California Irvine, Irvine, CA, USA
| | | | - Michael Parsons
- Molecular Cancer Epidemiology Lab, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Amanda B Spurdle
- Molecular Cancer Epidemiology Lab, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Eric C Polley
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Hermela Shimelis
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Steven N Hart
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Chunling Hu
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Fergus J Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - David E Goldgar
- Huntsman Cancer Institute, Salt Lake City, UT, USA. .,Department of Dermatology, University of Utah School of Medicine, Salt Lake City, UT, USA.
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18
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Fortuno C, Pesaran T, Dolinsky J, Yussuf A, McGoldrick K, Kho PF, James PA, Spurdle AB. p53 major hotspot variants are associated with poorer prognostic features in hereditary cancer patients. Cancer Genet 2019; 235-236:21-27. [PMID: 31296311 DOI: 10.1016/j.cancergen.2019.05.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 05/08/2019] [Accepted: 05/29/2019] [Indexed: 12/16/2022]
Abstract
TP53 pathogenic germline variation is associated with the multi-cancer predisposition Li-Fraumeni syndrome (LFS). Next-generation sequencing and multigene panel testing are highlighting variability in the clinical presentation of patients with TP53 positive results. We aimed to investigate if the p53 variants considered as major hotspots at both germline and somatic levels (p.Arg175His, p.Gly245Asp, p.Gly245Ser, p.Arg248Gln, p.Arg248Trp, p.Arg273Cys, p.Arg273His, and p.Arg282Trp) were associated with poorer prognostic features compared to other pathogenic missense variants in the DNA-binding domain. To do so, we assessed clinical features from 1025 carriers of germline TP53 pathogenic variants (749 probands and 276 relatives) from three independent datasets (IARC TP53 Database, Ambry Single Gene Testing, and Ambry Multigene Panel Testing). We observed that, compared to carriers of non-hotspot germline variants, individuals that carried a hotspot germline variant were more likely to present with a Classic LFS phenotype, earlier age of first breast cancer onset, and shorter time to diagnosis to any cancer. Further studies with larger datasets addressing differences in cancer phenotypes by genotype are thus needed to replicate our findings and consider variant effect and position, towards future personalized clinical management of pathogenic variant carriers.
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Affiliation(s)
- Cristina Fortuno
- Genetics and Computational Biology Division, QIMR Berghofer Medical Research Institute, 300 Herston Rd, Herston QLD 4006, Australia
| | | | | | | | | | - Pik Fang Kho
- Genetics and Computational Biology Division, QIMR Berghofer Medical Research Institute, 300 Herston Rd, Herston QLD 4006, Australia
| | - Paul A James
- Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and Royal Melbourne Hospital, Australia
| | - Amanda B Spurdle
- Genetics and Computational Biology Division, QIMR Berghofer Medical Research Institute, 300 Herston Rd, Herston QLD 4006, Australia.
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19
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Spurdle AB, Greville-Heygate S, Antoniou AC, Brown M, Burke L, de la Hoya M, Domchek S, Dörk T, Firth HV, Monteiro AN, Mensenkamp A, Parsons MT, Radice P, Robson M, Tischkowitz M, Tudini E, Turnbull C, Vreeswijk MP, Walker LC, Tavtigian S, Eccles DM. Towards controlled terminology for reporting germline cancer susceptibility variants: an ENIGMA report. J Med Genet 2019; 56:347-357. [PMID: 30962250 DOI: 10.1136/jmedgenet-2018-105872] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 02/09/2019] [Accepted: 02/11/2019] [Indexed: 12/18/2022]
Abstract
The vocabulary currently used to describe genetic variants and their consequences reflects many years of studying and discovering monogenic disease with high penetrance. With the recent rapid expansion of genetic testing brought about by wide availability of high-throughput massively parallel sequencing platforms, accurate variant interpretation has become a major issue. The vocabulary used to describe single genetic variants in silico, in vitro, in vivo and as a contributor to human disease uses terms in common, but the meaning is not necessarily shared across all these contexts. In the setting of cancer genetic tests, the added dimension of using data from genetic sequencing of tumour DNA to direct treatment is an additional source of confusion to those who are not experienced in cancer genetics. The language used to describe variants identified in cancer susceptibility genetic testing typically still reflects an outdated paradigm of Mendelian inheritance with dichotomous outcomes. Cancer is a common disease with complex genetic architecture; an improved lexicon is required to better communicate among scientists, clinicians and patients, the risks and implications of genetic variants detected. This review arises from a recognition of, and discussion about, inconsistencies in vocabulary usage by members of the ENIGMA international multidisciplinary consortium focused on variant classification in breast-ovarian cancer susceptibility genes. It sets out the vocabulary commonly used in genetic variant interpretation and reporting, and suggests a framework for a common vocabulary that may facilitate understanding and clarity in clinical reporting of germline genetic tests for cancer susceptibility.
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Affiliation(s)
- Amanda B Spurdle
- Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | | | - Antonis C Antoniou
- Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge, UK
| | - Melissa Brown
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Leslie Burke
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, Queensland, Australia
| | - Miguel de la Hoya
- Medical Oncology Department, Hospital Clínico San Carlos, Madrid, Spain
| | - Susan Domchek
- Basser Center for BRCA, Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Thilo Dörk
- Gynaecology Research Unit, Hannover Medical School, Hannover, Germany
| | - Helen V Firth
- Cambridge University Hospitals National Health Service Foundation Trust, Cambridge, UK
| | - Alvaro N Monteiro
- Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - Arjen Mensenkamp
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Michael T Parsons
- Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Paolo Radice
- Department of Research, Fondazione IRCCS Istituto Nazionale dei Tumori, Milano, Italy
| | - Mark Robson
- Clinical Genetics Service, Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | - Marc Tischkowitz
- Department of Medical Genetics, Cambridge University, Cambridge, UK
| | - Emma Tudini
- Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Clare Turnbull
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
- William Harvey Research Institute, Queen Mary Hospital, London, UK
| | | | - Logan C Walker
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Sean Tavtigian
- Oncological Sciences, University of Utah School of Medicine, Salt Lake City, Utah, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah, USA
| | - Diana M Eccles
- Faculty of Medicine, University of Southampton, Southampton, UK
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20
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Fortuno C, Cipponi A, Ballinger ML, Tavtigian SV, Olivier M, Ruparel V, Haupt Y, Haupt S, Study ISK, Tucker K, Spurdle AB, Thomas DM, James PA. A quantitative model to predict pathogenicity of missense variants in the TP53 gene. Hum Mutat 2019; 40:788-800. [PMID: 30840781 DOI: 10.1002/humu.23739] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 02/27/2019] [Accepted: 03/04/2019] [Indexed: 12/20/2022]
Abstract
Germline pathogenic variants in the TP53 gene cause Li-Fraumeni syndrome, a condition that predisposes individuals to a wide range of cancer types. Identification of individuals carrying a TP53 pathogenic variant is linked to clinical management decisions, such as the avoidance of radiotherapy and use of high-intensity screening programs. The aim of this study was to develop an evidence-based quantitative model that integrates independent in silico data (Align-GVGD and BayesDel) and somatic to germline ratio (SGR), to assign pathogenicity to every possible missense variant in the TP53 gene. To do this, a likelihood ratio for pathogenicity (LR) was derived from each component calibrated using reference sets of assumed pathogenic and benign missense variants. A posterior probability of pathogenicity was generated by combining LRs, and algorithm outputs were validated using different approaches. A total of 730 TP53 missense variants could be assigned to a clinically interpretable class. The outputs of the model correlated well with existing clinical information, functional data, and ClinVar classifications. In conclusion, these quantitative outputs provide the basis for individualized assessment of cancer risk useful for clinical interpretation. In addition, we propose the value of the novel SGR approach for use within the ACMG/AMP guidelines for variant classification.
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Affiliation(s)
- Cristina Fortuno
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - Arcadi Cipponi
- Cancer Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Mandy L Ballinger
- Cancer Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Sean V Tavtigian
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah
| | - Magali Olivier
- Molecular Mechanisms and Biomarkers Group, International Agency for Research on Cancer, Lyon, France
| | - Vatsal Ruparel
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Ygal Haupt
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Sue Haupt
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - International Sarcoma Kindred Study
- Research Division, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Kathy Tucker
- Hereditary Cancer Clinic, Prince of Wales Hospital, Randwick, New South Wales, Australia
- Prince of Wales Medical School, University of New South Wales, Randwick, New South Wales, Australia
| | - Amanda B Spurdle
- Genetics and Computational Biology Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | - David M Thomas
- Cancer Division, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Paul A James
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
- Familial Cancer Centre, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
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21
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Leung GMK, Zhang C, Ng NKL, Yang N, Lam SSY, Au CH, Chan TL, Ma ESK, Tsui SP, Ip HW, So JCC, Ng MHL, Cheng KCK, Wong KF, Siu LLP, Yip SF, Lin SY, Lau JSM, Luk TH, Lee HKK, Lau CK, Kho B, Kwong YL, Leung AYH. Distinct mutation spectrum, clinical outcome and therapeutic responses of typical complex/monosomy karyotype acute myeloid leukemia carrying TP53 mutations. Am J Hematol 2019; 94:650-657. [PMID: 30900772 DOI: 10.1002/ajh.25469] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/18/2019] [Accepted: 03/20/2019] [Indexed: 12/29/2022]
Abstract
The present study aimed to define a subtype of complex/monosomal karyotype (CK/MK) acute myeloid leukemia (AML) by its distinct clinical features, p53 signaling and responses to p53 targeting agents. Ninety-eight young adults (range: 21-60 years; median: 49 years) with CK/MK AML were studied. They received standard induction, consolidation and allogeneic hematopoietic stem cell transplantation from siblings or matched unrelated donors if available. Chromosomal abnormalities most commonly affected chromosome 5 (30%), 7 (22%) and 17 (21%). Next generation sequencing of a 54-myeloid gene panel were available in 76 patients. Tumor protein 53 (TP53) mutations were most common (49%) and associated with the presence of -5/5q- (P < .001) and -17/17p- (P < .001), but not -7/7q- (P = .370). This "typical" CK/MK AML subtype was associated with significantly lower presenting white cell counts, higher number of karyotypic abnormalities, and inferior leukemia-free and overall survivals, compared with CK/MK AML without the typical features. Blood or bone marrow samples from typical CK/MK AML patients showed defective p53 signaling upon induction by etoposide. In vitro drug sensitivity analysis showed that they were sensitive to APR-246 that targeted mutant p53, but resistant to MDM2 antagonist MI-77301. Novel therapeutic strategies targeting TP53 mutations in CK/MK AML should be developed and tested in clinical trials.
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Affiliation(s)
- Garret M. K. Leung
- Division of Haematology, Department of Medicine, LKS Faculty of MedicineUniversity of Hong Kong Hong Kong China
| | - Chunxiao Zhang
- Division of Haematology, Department of Medicine, LKS Faculty of MedicineUniversity of Hong Kong Hong Kong China
| | - Nelson K. L. Ng
- Division of Haematology, Department of Medicine, LKS Faculty of MedicineUniversity of Hong Kong Hong Kong China
| | - Ning Yang
- Division of Haematology, Department of Medicine, LKS Faculty of MedicineUniversity of Hong Kong Hong Kong China
| | - Stephen S. Y. Lam
- Division of Haematology, Department of Medicine, LKS Faculty of MedicineUniversity of Hong Kong Hong Kong China
| | - Chun H. Au
- Department of PathologyHong Kong Sanatorium and Hospital Hong Kong China
| | - Tsun L. Chan
- Department of PathologyHong Kong Sanatorium and Hospital Hong Kong China
| | - Edmond S. K. Ma
- Department of PathologyHong Kong Sanatorium and Hospital Hong Kong China
| | - Sze P. Tsui
- Division of Haematology, Department of PathologyQueen Mary Hospital Hong Kong China
| | - Ho W. Ip
- Division of Haematology, Department of PathologyQueen Mary Hospital Hong Kong China
| | - Jason C. C. So
- Division of Haematology, Department of PathologyQueen Mary Hospital Hong Kong China
| | - Margaret H. L. Ng
- Department of Anatomical and Cellular PathologyThe Chinese University of Hong Kong Hong Kong China
| | - Kelvin C. K. Cheng
- Department of Anatomical and Cellular PathologyThe Chinese University of Hong Kong Hong Kong China
| | - Kit F. Wong
- Department of PathologyQueen Elizabeth Hospital Hong Kong China
| | - Lisa L. P. Siu
- Department of PathologyQueen Elizabeth Hospital Hong Kong China
| | - Sze F. Yip
- Department of MedicineTuen Mun Hospital Hong Kong China
| | - Shek Y. Lin
- Department of Medicine and GeriatricsUnited Christian Hospital Hong Kong China
| | - June S. M. Lau
- Department of MedicineQueen Elizabeth Hospital Hong Kong China
| | - Tsan H. Luk
- Department of MedicineQueen Elizabeth Hospital Hong Kong China
| | - Harold K. K. Lee
- Department of MedicinePrincess Margaret Hospital Hong Kong China
| | - Chi K. Lau
- Department of MedicineTseung Kwan O Hospital Hong Kong China
| | - Bonnie Kho
- Department of MedicinePamela Youde Nethersole Eastern Hospital Hong Kong China
| | - Yok L. Kwong
- Division of Haematology, Department of Medicine, LKS Faculty of MedicineUniversity of Hong Kong Hong Kong China
| | - Anskar Y. H. Leung
- Division of Haematology, Department of Medicine, LKS Faculty of MedicineUniversity of Hong Kong Hong Kong China
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22
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Rana HQ, Clifford J, Hoang L, LaDuca H, Black MH, Li S, McGoldrick K, Speare V, Dolinsky JS, Gau CL, Garber JE. Genotype–phenotype associations among panel-based TP53+ subjects. Genet Med 2019; 21:2478-2484. [DOI: 10.1038/s41436-019-0541-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 04/30/2019] [Indexed: 11/09/2022] Open
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23
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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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