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Kratz CP, Lupo PJ, Zelley K, Schienda J, Nichols KE, Stewart DR, Malkin D, Brodeur GM, Maxwell K, Plon SE, Walsh MF. Adult-Onset Cancer Predisposition Syndromes in Children and Adolescents-To Test or not to Test? Clin Cancer Res 2024; 30:1733-1738. [PMID: 38411636 DOI: 10.1158/1078-0432.ccr-23-3683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/17/2024] [Accepted: 02/20/2024] [Indexed: 02/28/2024]
Abstract
With the increasing use of comprehensive germline genetic testing of children and adolescents with cancer, it has become evident that pathogenic variants (PV) in adult-onset cancer predisposition genes (aoCPG) underlying adult-onset cancer predisposition syndromes, such as Lynch syndrome or hereditary breast and ovarian cancer, are enriched and reported in 1% to 2% of children and adolescents with cancer. However, the causal relationship between PVs in aoCPGs and childhood cancer is still under investigation. The best-studied examples include heterozygous PVs in mismatch repair genes associated with Lynch syndrome in children with mismatch repair deficient high-grade glioma, heterozygous PVs in BARD1 in childhood neuroblastoma, and heterozygous PVs in BRCA2 in children with rhabdomyosarcoma. The low penetrance for pediatric cancers is considered to result from a combination of the low baseline risk of cancer in childhood and the report of only a modest relative risk of disease in childhood. Therefore, we do not advise that healthy children empirically be tested for PVs in an aoCPG before adulthood outside a research study. However, germline panel testing is increasingly being performed in children and adolescents with cancer, and exome and genome sequencing may be offered more commonly in this population in the future. The precise pediatric cancer risks and spectra associated with PVs in aoCPGs, underlying cellular mechanisms and somatic mutational signatures, as well as treatment response, second neoplasm risks, and psycho-oncological aspects require further research.
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Affiliation(s)
- Christian P Kratz
- Department of Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Philip J Lupo
- Department of Pediatrics, Division of Hematology/Oncology, Texas Children's Cancer Center, Texas Children's Hospital, Baylor College of Medicine, Houston, Texas
| | - Kristin Zelley
- Division of Oncology at the Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Jaclyn Schienda
- Department of Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, Massachusetts
| | - Kim E Nichols
- Department of Oncology, St Jude Children's Research Hospital, Memphis, Tennessee
| | - Douglas R Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, NCI, NIH, Rockville, Maryland
| | - David Malkin
- Division of Hematology/Oncology, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Garrett M Brodeur
- Division of Oncology, Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kara Maxwell
- Department of Medicine, Hematology-Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Sharon E Plon
- Department of Pediatrics, Division of Hematology/Oncology, Texas Children's Cancer Center, Texas Children's Hospital, Baylor College of Medicine, Houston, Texas
| | - Michael F Walsh
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
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Stoltze UK, Foss-Skiftesvik J, Hansen TVO, Rasmussen S, Karczewski KJ, Wadt KAW, Schmiegelow K. The evolutionary impact of childhood cancer on the human gene pool. Nat Commun 2024; 15:1881. [PMID: 38424437 PMCID: PMC10904397 DOI: 10.1038/s41467-024-45975-9] [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: 03/16/2023] [Accepted: 02/08/2024] [Indexed: 03/02/2024] Open
Abstract
Germline pathogenic variants associated with increased childhood mortality must be subject to natural selection. Here, we analyze publicly available germline genetic metadata from 4,574 children with cancer [11 studies; 1,083 whole exome sequences (WES), 1,950 whole genome sequences (WGS), and 1,541 gene panel] and 141,456 adults [125,748 WES and 15,708 WGS]. We find that pediatric cancer predisposition syndrome (pCPS) genes [n = 85] are highly constrained, harboring only a quarter of the loss-of-function variants that would be expected. This strong indication of selective pressure on pCPS genes is found across multiple lines of germline genomics data from both pediatric and adult cohorts. For six genes [ELP1, GPR161, VHL and SDHA/B/C], a clear lack of mutational constraint calls the pediatric penetrance and/or severity of associated cancers into question. Conversely, out of 23 known pCPS genes associated with biallelic risk, two [9%, DIS3L2 and MSH2] show significant constraint, indicating that they may monoallelically increase childhood cancer risk. In summary, we show that population genetic data provide empirical evidence that heritable childhood cancer leads to natural selection powerful enough to have significantly impacted the present-day gene pool.
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Affiliation(s)
- Ulrik Kristoffer Stoltze
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet, Blegdamsvej 9, Copenhagen, The Capital Region, Denmark.
- Department of Clinical Genetics, Rigshospitalet, Blegdamsvej 9, Copenhagen, The Capital Region, Denmark.
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Merkin Building, 415 Main St, Cambridge, MA, 02142, USA.
| | - Jon Foss-Skiftesvik
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet, Blegdamsvej 9, Copenhagen, The Capital Region, Denmark
- Department of Neurosurgery, Rigshospitalet, Blegdamsvej 9, Copenhagen, The Capital Region, Denmark
| | - Thomas van Overeem Hansen
- Department of Clinical Genetics, Rigshospitalet, Blegdamsvej 9, Copenhagen, The Capital Region, Denmark
- Department of Clinical Medicine, University of Copenhagen, Blegdamsvej 3B, Copenhagen, Denmark
| | - Simon Rasmussen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3B, Copenhagen, Denmark
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Konrad J Karczewski
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Merkin Building, 415 Main St, Cambridge, MA, 02142, USA
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Center for Genomic Medicine, Massachusetts General Hospital, 55 Fruit St, Boston, MA, 02114, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, 55 Fruit St, Boston, MA, 02114, USA
| | - Karin A W Wadt
- Department of Clinical Genetics, Rigshospitalet, Blegdamsvej 9, Copenhagen, The Capital Region, Denmark
- Department of Clinical Medicine, University of Copenhagen, Blegdamsvej 3B, Copenhagen, Denmark
| | - Kjeld Schmiegelow
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet, Blegdamsvej 9, Copenhagen, The Capital Region, Denmark.
- Department of Clinical Medicine, University of Copenhagen, Blegdamsvej 3B, Copenhagen, Denmark.
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Haas-Kogan DA, Aboian MS, Minturn JE, Leary SE, Abdelbaki MS, Goldman S, Elster JD, Kraya A, Lueder MR, Ramakrishnan D, von Reppert M, Liu KX, Rokita JL, Resnick AC, Solomon DA, Phillips JJ, Prados M, Molinaro AM, Waszak SM, Mueller S. Everolimus for Children With Recurrent or Progressive Low-Grade Glioma: Results From the Phase II PNOC001 Trial. J Clin Oncol 2024; 42:441-451. [PMID: 37978951 PMCID: PMC10824388 DOI: 10.1200/jco.23.01838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 10/09/2023] [Accepted: 10/17/2023] [Indexed: 11/19/2023] Open
Abstract
PURPOSE The PNOC001 phase II single-arm trial sought to estimate progression-free survival (PFS) associated with everolimus therapy for progressive/recurrent pediatric low-grade glioma (pLGG) on the basis of phosphatidylinositol 3-kinase (PI3K)/AKT/mammalian target of rapamycin (mTOR) pathway activation as measured by phosphorylated-ribosomal protein S6 and to identify prognostic and predictive biomarkers. PATIENTS AND METHODS Patients, age 3-21 years, with progressive/recurrent pLGG received everolimus orally, 5 mg/m2 once daily. Frequency of driver gene alterations was compared among independent pLGG cohorts of newly diagnosed and progressive/recurrent patients. PFS at 6 months (primary end point) and median PFS (secondary end point) were estimated for association with everolimus therapy. RESULTS Between 2012 and 2019, 65 subjects with progressive/recurrent pLGG (median age, 9.6 years; range, 3.0-19.9; 46% female) were enrolled, with a median follow-up of 57.5 months. The 6-month PFS was 67.4% (95% CI, 60.0 to 80.0) and median PFS was 11.1 months (95% CI, 7.6 to 19.8). Hypertriglyceridemia was the most common grade ≥3 adverse event. PI3K/AKT/mTOR pathway activation did not correlate with clinical outcomes (6-month PFS, active 68.4% v nonactive 63.3%; median PFS, active 11.2 months v nonactive 11.1 months; P = .80). Rare/novel KIAA1549::BRAF fusion breakpoints were most frequent in supratentorial midline pilocytic astrocytomas, in patients with progressive/recurrent disease, and correlated with poor clinical outcomes (median PFS, rare/novel KIAA1549::BRAF fusion breakpoints 6.1 months v common KIAA1549::BRAF fusion breakpoints 16.7 months; P < .05). Multivariate analysis confirmed their independent risk factor status for disease progression in PNOC001 and other, independent cohorts. Additionally, rare pathogenic germline variants in homologous recombination genes were identified in 6.8% of PNOC001 patients. CONCLUSION Everolimus is a well-tolerated therapy for progressive/recurrent pLGGs. Rare/novel KIAA1549::BRAF fusion breakpoints may define biomarkers for progressive disease and should be assessed in future clinical trials.
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Affiliation(s)
- Daphne A. Haas-Kogan
- Department of Radiation Oncology, Brigham and Women's Hospital, Dana-Farber Cancer Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Mariam S. Aboian
- Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT
| | - Jane E. Minturn
- Division of Oncology, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA
- Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Sarah E.S. Leary
- Cancer and Blood Disorders Center, Seattle Children's Hospital, Seattle, WA
- Department of Pediatrics, University of Washington, Seattle, WA
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, WA
| | - Mohamed S. Abdelbaki
- Department of Pediatrics, Washington University School of Medicine, St Louis, MO
| | - Stewart Goldman
- Phoenix Children's Hospital, Phoenix, AZ
- University of Arizona College of Medicine, Phoenix, AZ
| | - Jennifer D. Elster
- Division of Hematology Oncology, Department of Pediatrics, Rady Children's Hospital, University of California, San Diego, San Diego, CA
| | - Adam Kraya
- Division of Neurosurgery, Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Matthew R. Lueder
- Division of Neurosurgery, Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Divya Ramakrishnan
- Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT
| | - Marc von Reppert
- Department of Radiology and Biomedical Imaging, Yale School of Medicine, New Haven, CT
- University of Leipzig, Leipzig, Germany
| | - Kevin X. Liu
- Department of Radiation Oncology, Brigham and Women's Hospital, Dana-Farber Cancer Institute, Boston Children's Hospital, Harvard Medical School, Boston, MA
| | - Jo Lynne Rokita
- Division of Neurosurgery, Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Adam C. Resnick
- Division of Neurosurgery, Center for Data-Driven Discovery in Biomedicine, Children's Hospital of Philadelphia, Philadelphia, PA
| | - David A. Solomon
- Department of Pathology, University of California, San Francisco, San Francisco, CA
| | - Joanna J. Phillips
- Department of Pathology, University of California, San Francisco, San Francisco, CA
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA
| | - Michael Prados
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA
| | - Annette M. Molinaro
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA
| | - Sebastian M. Waszak
- Laboratory of Computational Neuro-Oncology, Swiss Institute for Experimental Cancer Research, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
- Department of Neurology, University of California, San Francisco, San Francisco, CA
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Sabine Mueller
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA
- Department of Neurology, University of California, San Francisco, San Francisco, CA
- Department of Pediatrics, University of Zurich, Zurich, Switzerland
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4
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Freycon C, Lupo PJ, Witkowski L, Budd C, Foulkes WD, Goudie C. A systematic review of the prevalence of pathogenic or likely pathogenic germline variants in individuals with FOXO1 fusion-positive rhabdomyosarcoma. Pediatr Blood Cancer 2023; 70:e30651. [PMID: 37638828 DOI: 10.1002/pbc.30651] [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: 07/05/2023] [Revised: 08/15/2023] [Accepted: 08/20/2023] [Indexed: 08/29/2023]
Abstract
Several cancer predisposition syndromes (CPS) are reported to predispose to rhabdomyosarcoma, most frequently in children with embryonal rhabdomyosarcoma. There are lingering questions over the role of CPS in individuals with alveolar rhabdomyosarcoma (ARMS), which are frequently driven by FOXO1 fusion oncoproteins. We conducted a systematic review to identify patients with FOXO1 fusion-positive ARMS (FP-ARMS) who underwent germline DNA sequencing. We estimated the prevalence of pathogenic/likely pathogenic (P/LP) variants in cancer predisposing genes (CPGs) and of CPSs. We included 19 publications reporting on 191 patients with FP-ARMS. P/LP variants in CPGs were identified in 26/191 (13.6%) patients, nine (4.9%) of which were associated with a CPS diagnosis. Evidence for causal associations between CPSs and FP-ARMS could not be assessed with available data from this review. Only one patient was affected with a CPS known to predispose to rhabdomyosarcoma, Li-Fraumeni syndrome. Typical CPS associations with rhabdomyosarcoma are rare, but not nonexistent, in patients with FP-ARMS. FOXO1 fusion status, alone, is insufficient for clinicians to rely on to distinguish between patients with/without CPS.
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Affiliation(s)
- Claire Freycon
- Department of Pediatrics, Division of Hematology-Oncology, Montreal Children's Hospital, McGill University Health Centre, Montreal, Quebec, Canada
- Department of Child Health and Human Development, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Philip J Lupo
- Section of Hematology-Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
| | - Leora Witkowski
- Department of Child Health and Human Development, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University Health Centre, Montreal, Quebec, Canada
| | - Crystal Budd
- Department of Child Health and Human Development, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | | | - Catherine Goudie
- Department of Pediatrics, Division of Hematology-Oncology, Montreal Children's Hospital, McGill University Health Centre, Montreal, Quebec, Canada
- Department of Child Health and Human Development, Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
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5
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Hanson H, Astiazaran-Symonds E, Amendola LM, Balmaña J, Foulkes WD, James P, Klugman S, Ngeow J, Schmutzler R, Voian N, Wick MJ, Pal T, Tischkowitz M, Stewart DR. Management of individuals with germline pathogenic/likely pathogenic variants in CHEK2: A clinical practice resource of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2023; 25:100870. [PMID: 37490054 PMCID: PMC10623578 DOI: 10.1016/j.gim.2023.100870] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/21/2023] [Accepted: 04/24/2023] [Indexed: 07/26/2023] Open
Abstract
PURPOSE Although the role of CHEK2 germline pathogenic variants in cancer predisposition is well known, resources for managing CHEK2 heterozygotes in clinical practice are limited. METHODS An international workgroup developed guidance on clinical management of CHEK2 heterozygotes informed by peer-reviewed publications from PubMed. RESULTS Although CHEK2 is considered a moderate penetrance gene, cancer risks may be considered as a continuous variable, which are influenced by family history and other modifiers. Consequently, early cancer detection and prevention for CHEK2 heterozygotes should be guided by personalized risk estimates. Such estimates may result in both downgrading lifetime breast cancer risks to those similar to the general population or upgrading lifetime risk to a level at which CHEK2 heterozygotes are offered high-risk breast surveillance according to country-specific guidelines. Risk-reducing mastectomy should be guided by personalized risk estimates and shared decision making. Colorectal and prostate cancer surveillance should be considered based on assessment of family history. For CHEK2 heterozygotes who develop cancer, no specific targeted medical treatment is recommended at this time. CONCLUSION Systematic prospective data collection is needed to establish the spectrum of CHEK2-associated cancer risks and to determine yet-unanswered questions, such as the outcomes of surveillance, response to cancer treatment, and survival after cancer diagnosis.
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Affiliation(s)
- Helen Hanson
- Southwest Thames Regional Genetics Service, St George's University Hospitals NHS Foundation Trust, London, United Kingdom
| | - Esteban Astiazaran-Symonds
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD; Department of Medicine, College of Medicine-Tucson, University of Arizona, Tucson, AZ
| | | | - Judith Balmaña
- Hereditary Cancer Genetics Group, Vall d'Hebron Institute of Oncology (VHIO), Barcelona, Spain; Medical Oncology Department, Hospital Universitari Vall d'Hebron, Vall d'Hebron Hospital Campus, Barcelona, Spain
| | - William D Foulkes
- Departments of Human Genetics, Oncology and Medicine, McGill University, Montréal, QC, Canada
| | - Paul James
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia; Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Susan Klugman
- Division of Reproductive & Medical Genetics, Department of Obstetrics & Gynecology and Women's Health, Montefiore Medical Center/Albert Einstein College of Medicine, Bronx, NY
| | - Joanne Ngeow
- Genomic Medicine, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore; Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Rita Schmutzler
- Center of Integrated Oncology (CIO), University of Cologne, Cologne, Germany; Center for Hereditary Breast and Ovarian Cancer, University Hospital of Cologne, Cologne, Germany
| | - Nicoleta Voian
- Providence Genetic Risk Clinic, Providence Cancer Institute, Portland, OR
| | - Myra J Wick
- Departments of Obstetrics and Gynecology and Clinical Genomics, Mayo Clinic, Rochester, MN
| | - Tuya Pal
- Department of Medicine, Vanderbilt University Medical Center/Vanderbilt-Ingram Cancer Center, Nashville, TN
| | - Marc Tischkowitz
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, United Kingdom
| | - Douglas R Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD
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6
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Seligson ND, Kolesar JM, Alam B, Baker L, Lamba JK, Fridley BL, Salahudeen AA, Hertz DL, Hicks JK. Integrating pharmacogenomic testing into paired germline and somatic genomic testing in patients with cancer. Pharmacogenomics 2023; 24:731-738. [PMID: 37702060 DOI: 10.2217/pgs-2023-0125] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023] Open
Abstract
Precision medicine has revolutionized clinical care for patients with cancer through the development of targeted therapy, identification of inherited cancer predisposition syndromes and the use of pharmacogenetics to optimize pharmacotherapy for anticancer drugs and supportive care medications. While germline (patient) and somatic (tumor) genomic testing have evolved separately, recent interest in paired germline/somatic testing has led to an increase in integrated genomic testing workflows. However, paired germline/somatic testing has generally lacked the incorporation of germline pharmacogenomics. Integrating pharmacogenomics into paired germline/somatic genomic testing would be an efficient method for increasing access to pharmacogenomic testing. In this perspective, the authors argue for the benefits of implementing a comprehensive approach integrating somatic and germline testing that is inclusive of pharmacogenomics in clinical practice.
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Affiliation(s)
- Nathan D Seligson
- Department of Pharmacotherapy & Translational Research, The University of Florida, Jacksonville, FL 32209, USA
- Center for Pharmacogenomics & Translational Research, Nemours Children's Health, Jacksonville, FL 32207, USA
| | - Jill M Kolesar
- Markey Cancer Center, University of Kentucky, Lexington, KY 40536, USA
- Department of Pharmacy Practice & Science, University of Kentucky, Lexington, KY 40536, USA
| | - Benish Alam
- Department of Clinical Pharmacy, University of Michigan College of Pharmacy, Ann Arbor, MI 48109, USA
| | - Laura Baker
- Nemours Center for Cancer & Blood Disorders, Nemours Children's Health, Wilmington, DE 19803, USA
| | - Jatinder K Lamba
- Department of Pharmacotherapy & Translational Research, The University of Florida, Gainesville, FL 32611, USA
| | - Brooke L Fridley
- Department of Biostatistics & Bioinformatics, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Ameen A Salahudeen
- Department of Medicine, University of Illinois at Chicago, Chicago, IL 60612, USA
- Tempus Labs Inc., Chicago, IL 60654, USA
| | - Daniel L Hertz
- Department of Clinical Pharmacy, University of Michigan College of Pharmacy, Ann Arbor, MI 48109, USA
| | - J Kevin Hicks
- Department of Individualized Cancer Management, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
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7
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Wadensten E, Wessman S, Abel F, Diaz De Ståhl T, Tesi B, Orsmark Pietras C, Arvidsson L, Taylan F, Fransson S, Vogt H, Poluha A, Pradhananga S, Hellberg M, Lagerstedt-Robinson K, Raj Somarajan P, Samuelsson S, Orrsjö S, Maqbool K, Henning K, Strid T, Ek T, Fagman H, Olsson Bontell T, Martinsson T, Puls F, Kogner P, Wirta V, Pronk CJ, Wille J, Rosenquist R, Nistér M, Mertens F, Sabel M, Norén-Nyström U, Grillner P, Nordgren A, Ljungman G, Sandgren J, Gisselsson D. Diagnostic Yield From a Nationwide Implementation of Precision Medicine for all Children With Cancer. JCO Precis Oncol 2023; 7:e2300039. [PMID: 37384868 PMCID: PMC10581599 DOI: 10.1200/po.23.00039] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 04/20/2023] [Accepted: 05/24/2023] [Indexed: 07/01/2023] Open
Abstract
PURPOSE Several studies have indicated that broad genomic characterization of childhood cancer provides diagnostically and/or therapeutically relevant information in selected high-risk cases. However, the extent to which such characterization offers clinically actionable data in a prospective broadly inclusive setting remains largely unexplored. METHODS We implemented prospective whole-genome sequencing (WGS) of tumor and germline, complemented by whole-transcriptome sequencing (RNA-Seq) for all children diagnosed with a primary or relapsed solid malignancy in Sweden. Multidisciplinary molecular tumor boards were set up to integrate genomic data in the clinical decision process along with a medicolegal framework enabling secondary use of sequencing data for research purposes. RESULTS During the study's first 14 months, 118 solid tumors from 117 patients were subjected to WGS, with complementary RNA-Seq for fusion gene detection in 52 tumors. There was no significant geographic bias in patient enrollment, and the included tumor types reflected the annual national incidence of pediatric solid tumor types. Of the 112 tumors with somatic mutations, 106 (95%) exhibited alterations with a clear clinical correlation. In 46 of 118 tumors (39%), sequencing only corroborated histopathological diagnoses, while in 59 cases (50%), it contributed to additional subclassification or detection of prognostic markers. Potential treatment targets were found in 31 patients (26%), most commonly ALK mutations/fusions (n = 4), RAS/RAF/MEK/ERK pathway mutations (n = 14), FGFR1 mutations/fusions (n = 5), IDH1 mutations (n = 2), and NTRK2 gene fusions (n = 2). In one patient, the tumor diagnosis was revised based on sequencing. Clinically relevant germline variants were detected in 8 of 94 patients (8.5%). CONCLUSION Up-front, large-scale genomic characterization of pediatric solid malignancies provides diagnostically valuable data in the majority of patients also in a largely unselected cohort.
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Affiliation(s)
- Elisabeth Wadensten
- Section of Clinical Genetics, Pathology and Molecular Diagnostics, Medical Services, Region Skåne, University Hospital, SE-22185, Lund, Sweden
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, BMC C13, SE-221 84, Lund, Sweden
| | - Sandra Wessman
- Clinical Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Frida Abel
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | | | - Bianca Tesi
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics, Karolinska University Hospital, Solna, Sweden
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Christina Orsmark Pietras
- Section of Clinical Genetics, Pathology and Molecular Diagnostics, Medical Services, Region Skåne, University Hospital, SE-22185, Lund, Sweden
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, BMC C13, SE-221 84, Lund, Sweden
| | - Linda Arvidsson
- Section of Clinical Genetics, Pathology and Molecular Diagnostics, Medical Services, Region Skåne, University Hospital, SE-22185, Lund, Sweden
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, BMC C13, SE-221 84, Lund, Sweden
| | - Fulya Taylan
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics, Karolinska University Hospital, Solna, Sweden
| | - Susanne Fransson
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Hartmut Vogt
- Crown Princess Victoria's Child and Youth Hospital in Linköping, and Division of Children's and Women's Health, Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Anna Poluha
- Clinical Genetics, Uppsala University Hospital, Uppsala, Sweden
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Sailendra Pradhananga
- Section of Clinical Genetics, Pathology and Molecular Diagnostics, Medical Services, Region Skåne, University Hospital, SE-22185, Lund, Sweden
| | - Maria Hellberg
- Section of Clinical Genetics, Pathology and Molecular Diagnostics, Medical Services, Region Skåne, University Hospital, SE-22185, Lund, Sweden
| | - Kristina Lagerstedt-Robinson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics, Karolinska University Hospital, Solna, Sweden
| | | | - Sofie Samuelsson
- Section of Clinical Genetics, Pathology and Molecular Diagnostics, Medical Services, Region Skåne, University Hospital, SE-22185, Lund, Sweden
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, BMC C13, SE-221 84, Lund, Sweden
| | - Sara Orrsjö
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Khurram Maqbool
- Department of Microbiology, Tumor and Cell Biology, Clinical Genomics Stockholm, Science Life Laboratory, Karolinska Institutet, Solna, Sweden
| | - Karin Henning
- Section for Pediatric Hematology and Oncology, Karolinska University Hospital, Stockholm, Sweden
- Childhood Cancer Research Unit, Department for Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Tobias Strid
- Department of Clinical Pathology and Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Torben Ek
- Department of Pediatrics, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg
- Queen Silvia Children's Hospital, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Henrik Fagman
- Department of Clinical Pathology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Thomas Olsson Bontell
- Department of Clinical Pathology, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Physiology, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Tommy Martinsson
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Florian Puls
- Department of Clinical Pathology, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Per Kogner
- Section for Pediatric Hematology and Oncology, Karolinska University Hospital, Stockholm, Sweden
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institute, Stockholm, Sweden
| | - Valtteri Wirta
- Department of Microbiology, Tumor and Cell Biology, Clinical Genomics Stockholm, Science Life Laboratory, Karolinska Institutet, Solna, Sweden
- Genomic Medicine Center Karolinska, Karolinska University Hospital, Stockholm, Sweden
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Clinical Genomics Stockholm, Science Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | | | - Joakim Wille
- Childhood Cancer Centre, Skåne University Hospital, Lund, Sweden
| | - Richard Rosenquist
- Clinical Genetics, Karolinska University Hospital, Solna, Sweden
- Genomic Medicine Center Karolinska, Karolinska University Hospital, Stockholm, Sweden
| | - Monica Nistér
- Clinical Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Fredrik Mertens
- Section of Clinical Genetics, Pathology and Molecular Diagnostics, Medical Services, Region Skåne, University Hospital, SE-22185, Lund, Sweden
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, BMC C13, SE-221 84, Lund, Sweden
| | - Magnus Sabel
- Department of Pediatrics, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg
- Queen Silvia Children's Hospital, Sahlgrenska University Hospital, Gothenburg, Sweden
| | | | - Pernilla Grillner
- Section for Pediatric Hematology and Oncology, Karolinska University Hospital, Stockholm, Sweden
| | - Ann Nordgren
- Department of Clinical Genetics and Genomics, Sahlgrenska University Hospital, Gothenburg, Sweden
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics, Karolinska University Hospital, Solna, Sweden
| | - Gustaf Ljungman
- Department of Women's and Children's Health, Uppsala University, Sweden
- Department of Pediatric Oncology, Uppsala University Children's Hospital, 751 35 Uppsala, Sweden
| | - Johanna Sandgren
- Clinical Pathology and Cancer Diagnostics, Karolinska University Hospital, Stockholm, Sweden
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - David Gisselsson
- Section of Clinical Genetics, Pathology and Molecular Diagnostics, Medical Services, Region Skåne, University Hospital, SE-22185, Lund, Sweden
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, BMC C13, SE-221 84, Lund, Sweden
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8
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Stoltze UK, Foss-Skiftesvik J, van Overeem Hansen T, Byrjalsen A, Sehested A, Scheie D, Stamm Mikkelsen T, Rasmussen S, Bak M, Okkels H, Thude Callesen M, Skjøth-Rasmussen J, Gerdes AM, Schmiegelow K, Mathiasen R, Wadt K. Genetic predisposition and evolutionary traces of pediatric cancer risk: a prospective 5-year population-based genome sequencing study of children with CNS tumors. Neuro Oncol 2023; 25:761-773. [PMID: 35902210 PMCID: PMC10076945 DOI: 10.1093/neuonc/noac187] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND The etiology of central nervous system (CNS) tumors in children is largely unknown and population-based studies of genetic predisposition are lacking. METHODS In this prospective, population-based study, we performed germline whole-genome sequencing in 128 children with CNS tumors, supplemented by a systematic pedigree analysis covering 3543 close relatives. RESULTS Thirteen children (10%) harbored pathogenic variants in known cancer genes. These children were more likely to have medulloblastoma (OR 5.9, CI 1.6-21.2) and develop metasynchronous CNS tumors (P = 0.01). Similar carrier frequencies were seen among children with low-grade glioma (12.8%) and high-grade tumors (12.2%). Next, considering the high mortality of childhood CNS tumors throughout most of human evolution, we explored known pediatric-onset cancer genes, showing that they are more evolutionarily constrained than genes associated with risk of adult-onset malignancies (P = 5e-4) and all other genes (P = 5e-17). Based on this observation, we expanded our analysis to 2986 genes exhibiting high evolutionary constraint in 141,456 humans. This analysis identified eight directly causative loss-of-functions variants, and showed a dose-response association between degree of constraint and likelihood of pathogenicity-raising the question of the role of other highly constrained gene alterations detected. CONCLUSIONS Approximately 10% of pediatric CNS tumors can be attributed to rare variants in known cancer genes. Genes associated with high risk of childhood cancer show evolutionary evidence of constraint.
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Affiliation(s)
- Ulrik Kristoffer Stoltze
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet - Copenhagen University Hospital, Copenhagen, Denmark
- Department of Clinical Genetics, Rigshospitalet - Copenhagen University Hospital, Copenhagen, Denmark
| | - Jon Foss-Skiftesvik
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet - Copenhagen University Hospital, Copenhagen, Denmark
- Department of Neurosurgery, Rigshospitalet - Copenhagen University Hospital, Copenhagen, Denmark
| | - Thomas van Overeem Hansen
- Department of Clinical Genetics, Rigshospitalet - Copenhagen University Hospital, Copenhagen, Denmark
| | - Anna Byrjalsen
- Department of Clinical Genetics, Rigshospitalet - Copenhagen University Hospital, Copenhagen, Denmark
| | - Astrid Sehested
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet - Copenhagen University Hospital, Copenhagen, Denmark
| | - David Scheie
- Department of Pathology, Rigshospitalet - Copenhagen University Hospital, Copenhagen, Denmark
| | - Torben Stamm Mikkelsen
- Department of Pediatrics and Adolescent Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Simon Rasmussen
- Novo Nordisk Foundation Center for Protein Research, Copenhagen University, Copenhagen, Denmark
| | - Mads Bak
- Department of Clinical Genetics, Rigshospitalet - Copenhagen University Hospital, Copenhagen, Denmark
| | - Henrik Okkels
- Department of Molecular Diagnostics, Aalborg University Hospital, Aalborg, Denmark
| | - Michael Thude Callesen
- Department of Pediatrics and Adolescent Medicine, Odense University Hospital, Odense, Denmark
| | - Jane Skjøth-Rasmussen
- Department of Neurosurgery, Rigshospitalet - Copenhagen University Hospital, Copenhagen, Denmark
| | - Anne-Marie Gerdes
- Department of Clinical Genetics, Rigshospitalet - Copenhagen University Hospital, Copenhagen, Denmark
| | - Kjeld Schmiegelow
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet - Copenhagen University Hospital, Copenhagen, Denmark
| | - René Mathiasen
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet - Copenhagen University Hospital, Copenhagen, Denmark
| | - Karin Wadt
- Department of Clinical Genetics, Rigshospitalet - Copenhagen University Hospital, Copenhagen, Denmark
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9
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Keller KM, Koetsier J, Schild L, Amo-Addae V, Eising S, van den Handel K, Ober K, Koopmans B, Essing A, van den Boogaard ML, Langenberg KPS, Jäger N, Kool M, Pfister S, Dolman MEM, Molenaar JJ, van Hooff SR. The potential of PARP as a therapeutic target across pediatric solid malignancies. BMC Cancer 2023; 23:310. [PMID: 37020198 PMCID: PMC10077757 DOI: 10.1186/s12885-022-10319-7] [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: 09/27/2022] [Accepted: 11/15/2022] [Indexed: 04/07/2023] Open
Abstract
BACKGROUND Pediatric cancer is the leading cause of disease-related death in children and the need for better therapeutic options remains urgent. Due to the limited number of patients, target and drug development for pediatrics is often supplemented by data from studies focused on adult cancers. Recent evidence shows that pediatric cancers possess different vulnerabilities that should be explored independently from adult cancers. METHODS Using the publicly available Genomics of Drug Sensitivity in Cancer database, we explore therapeutic targets and biomarkers specific to the pediatric solid malignancies Ewing sarcoma, medulloblastoma, neuroblastoma, osteosarcoma, and rhabdomyosarcoma. Results are validated using cell viability assays and high-throughput drug screens are used to identify synergistic combinations. RESULTS Using published drug screening data, PARP is identified as a drug target of interest across multiple different pediatric malignancies. We validate these findings, and we show that efficacy can be improved when combined with conventional chemotherapeutics, namely topoisomerase inhibitors. Additionally, using gene set enrichment analysis, we identify ribosome biogenesis as a potential biomarker for PARP inhibition in pediatric cancer cell lines. CONCLUSION Collectively, our results provide evidence to support the further development of PARP inhibition and the combination with TOP1 inhibition as a therapeutic approach in solid pediatric malignancies. Additionally, we propose ribosome biogenesis as a component to PARP inhibitor sensitivity that should be further investigated to help maximize the potential utility of PARP inhibition and combinations across pediatric solid malignancies.
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Affiliation(s)
- Kaylee M Keller
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Joost Koetsier
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Linda Schild
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Vicky Amo-Addae
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Selma Eising
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | | | - Kimberley Ober
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Bianca Koopmans
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Anke Essing
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | | | | | - Natalie Jäger
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Paediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Marcel Kool
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Paediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Stefan Pfister
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany
- Division of Paediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), Heidelberg, Germany
| | - M Emmy M Dolman
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
- School of Women's and Children's Health, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Jan J Molenaar
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.
- Department of Pharmaceutical Sciences, University Utrecht, Utrecht, the Netherlands.
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10
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McGee RB, Oak N, Harrison L, Xu K, Nuccio R, Blake AK, Mostafavi R, Lewis S, Taylor LM, Kubal M, Ouma A, Hines-Dowell SJ, Cheng C, Furtado LV, Nichols KE. Pathogenic Variants in Adult-Onset Cancer Predisposition Genes in Pediatric Cancer: Prevalence and Impact on Tumor Molecular Features and Clinical Management. Clin Cancer Res 2023; 29:1243-1251. [PMID: 36693186 PMCID: PMC10642481 DOI: 10.1158/1078-0432.ccr-22-2482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 12/09/2022] [Accepted: 01/23/2023] [Indexed: 01/25/2023]
Abstract
PURPOSE Clinical genomic sequencing of pediatric tumors is increasingly uncovering pathogenic variants in adult-onset cancer predisposition genes (aoCPG). Nevertheless, it remains poorly understood how often aoCPG variants are of germline origin and whether they influence tumor molecular profiles and/or clinical care. In this study, we examined the prevalence, spectrum, and impacts of aoCPG variants on tumor genomic features and patient management at our institution. EXPERIMENTAL DESIGN This is a retrospective study of 1,018 children with cancer who underwent clinical genomic sequencing of their tumors. Tumor genomic data were queried for pathogenic variants affecting 24 preselected aoCPGs. Available tumor whole-genome sequencing (WGS) data were evaluated for second hit mutations, loss of heterozygosity (LOH), DNA mutational signatures, and homologous recombination deficiency (HRD). Patients whose tumors harbored one or more pathogenic aoCPG variants underwent subsequent germline testing based on hereditary cancer evaluation and family or provider preference. RESULTS Thirty-three patients (3%) had tumors harboring pathogenic variants affecting one or more aoCPGs. Among 21 tumors with sufficient WGS sequencing data, six (29%) harbored a second hit or LOH affecting the remaining aoCPG allele with four of these six tumors (67%) also exhibiting a DNA mutational signature consistent with the altered aoCPG. Two additional tumors demonstrated HRD, of uncertain relation to the identified aoCPG variant. Twenty-one of 26 patients (81%) completing germline testing were positive for the aoCPG variant in the germline. All germline-positive patients were counseled regarding future cancer risks, surveillance, and risk-reducing measures. No patients had immediate cancer therapy changed due to aoCPG data. CONCLUSIONS AoCPG variants are rare in pediatric tumors; however, many originate in the germline. Almost one third of tumor aoCPG variants examined exhibited a second hit and/or conferred an abnormal DNA mutational profile suggesting a role in tumor formation. aoCPG information aids in cancer risk prediction but is not commonly used to alter the treatment of pediatric cancers.
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Affiliation(s)
- Rose B. McGee
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, Tennessee
| | - Ninad Oak
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, Tennessee
| | - Lynn Harrison
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, Tennessee
| | - Ke Xu
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, Tennessee
| | - Regina Nuccio
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, Tennessee
| | - Alise K. Blake
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, Tennessee
| | - Roya Mostafavi
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, Tennessee
| | - Sara Lewis
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, Tennessee
| | - Leslie M. Taylor
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, Tennessee
| | - Manish Kubal
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, Tennessee
| | - Annastasia Ouma
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, Tennessee
| | | | - Cheng Cheng
- Department of Biostatistics, St. Jude Children’s Research Hospital, Memphis, Tennessee
| | - Larissa V. Furtado
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, Tennessee
| | - Kim E. Nichols
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, Tennessee
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11
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Kratz CP, Smirnov D, Autry R, Jäger N, Waszak SM, Großhennig A, Berutti R, Wendorff M, Hainaut P, Pfister SM, Prokisch H, Ripperger T, Malkin D. Heterozygous BRCA1 and BRCA2 and Mismatch Repair Gene Pathogenic Variants in Children and Adolescents With Cancer. J Natl Cancer Inst 2022; 114:1523-1532. [PMID: 35980168 DOI: 10.1093/jnci/djac151] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 03/21/2022] [Accepted: 07/20/2022] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Genetic predisposition is has been identified as a cause of cancer, yet little is known about the role of adult cancer predisposition syndromes in childhood cancer. We examined the extent to which heterozygous pathogenic germline variants in BRCA1, BRCA2, PALB2, ATM, CHEK2, MSH2, MSH6, MLH1, and PMS2 contribute to cancer risk in children and adolescents. METHODS We conducted a meta-analysis of 11 studies that incorporated comprehensive germline testing for children and adolescents with cancer. ClinVar pathogenic or likely pathogenic variants (PVs) in genes of interest were compared with 2 control groups. Results were validated in a cohort of mainly European patients and controls. We employed the Proxy External Controls Association Test to account for different pipelines. RESULTS Among 3975 children and adolescents with cancer, statistically significant associations with cancer risk were observed for PVs in BRCA1 and 2 (26 PVs vs 63 PVs among 27 501 controls, odds ratio = 2.78, 95% confidence interval = 1.69 to 4.45; P < .001) and mismatch repair genes (19 PVs vs 14 PVs among 27 501 controls, odds ratio = 7.33, 95% confidence interval = 3.64 to 14.82; P <.001). Associations were seen in brain and other solid tumors but not in hematologic neoplasms. We confirmed similar findings in 1664 pediatric cancer patients primarily of European descent. CONCLUSION These data suggest that heterozygous PVs in BRCA1 and 2 and mismatch repair genes contribute with reduced penetrance to cancer risk in children and adolescents. No changes to predictive genetic testing and surveillance recommendations are required.
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Affiliation(s)
- Christian P Kratz
- Department of Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Dmitrii Smirnov
- Institute of Human Genetics, School of Medicine, Technische Universität München, München, Germany.,Institute of Neurogenomics, Computational Health Center, Helmholtz Zentrum München, Neuherberg, Germany
| | - Robert Autry
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Division of Paediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Natalie Jäger
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Division of Paediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Sebastian M Waszak
- Centre for Molecular Medicine Norway (NCMM), Nordic European Molecular Biology Laboratory (EMBL) Partnership, University of Oslo and Oslo University Hospital, Oslo, Norway.,Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Anika Großhennig
- Institute of Biostatistics, Hannover Medical School, Hannover, Germany
| | - Riccardo Berutti
- Institute of Human Genetics, School of Medicine, Technische Universität München, München, Germany.,Institute of Neurogenomics, Computational Health Center, Helmholtz Zentrum München, Neuherberg, Germany
| | - Mareike Wendorff
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - Pierre Hainaut
- Univ. Grenoble Alpes, Inserm 1209, CNRS 5309, Institute for Advanced Biosciences, F38000, Grenoble, France
| | - Stefan M Pfister
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Division of Paediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany.,German Cancer Consortium (DKTK), Heidelberg, Germany.,Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Holger Prokisch
- Institute of Human Genetics, School of Medicine, Technische Universität München, München, Germany.,Institute of Neurogenomics, Computational Health Center, Helmholtz Zentrum München, Neuherberg, Germany
| | - Tim Ripperger
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - David Malkin
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada.,Division of Hematology/Oncology, The Hospital for Sick Children, Toronto, ON, Canada.,Department of Paediatrics, University of Toronto, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
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12
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Genetic predisposition to central nervous system tumors in children - what the neurosurgeon should know. Acta Neurochir (Wien) 2022; 164:3025-3034. [PMID: 35660974 DOI: 10.1007/s00701-022-05258-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 05/17/2022] [Indexed: 02/01/2023]
Abstract
BACKGROUND Historically, few pediatric central nervous system (CNS) tumors were thought to result from genetic predisposition. However, within the last decade, new DNA sequencing methods have led to an increased recognition of high-risk cancer predisposition syndromes in children with CNS tumors. Thus, genetic predisposition is increasingly impacting clinical pediatric neuro-oncology. METHODS In this narrative review, we discuss the current understanding of genetic predisposition to childhood CNS tumors and provide a general overview of involved research methodologies and terminology. Moreover, we consider how germline genetics may influence neurosurgical practice. RESULTS Introduction of next-generation DNA sequencing has greatly increased our understanding of genetic predisposition to pediatric CNS tumors by enabling whole-exome/-genome sequencing of large cohorts. To date, the scientific literature has reported germline sequencing findings for more than 2000 children with CNS tumors. Although varying between tumor types, at least 10% of childhood CNS tumors can currently be explained by rare pathogenic germline variants in known cancer-related genes. Novel methodologies continue to uncover new mechanisms, suggesting that a much higher proportion of children with CNS tumors have underlying genetic causes. Understanding how genetic predisposition influences tumor biology and the clinical course in a given patient may mandate adjustments to neurosurgical treatment. CONCLUSION Germline genetics is becoming increasingly important to clinicians, including neurosurgeons. This review provides an updated overview of genetic predisposition to childhood CNS tumors with focus on aspects relevant to pediatric neurosurgeons.
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13
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Foss-Skiftesvik J, Stoltze UK, van Overeem Hansen T, Ahlborn LB, Sørensen E, Ostrowski SR, Kullegaard SMA, Laspiur AO, Melchior LC, Scheie D, Kristensen BW, Skjøth-Rasmussen J, Schmiegelow K, Wadt K, Mathiasen R. Redefining germline predisposition in children with molecularly characterized ependymoma: a population-based 20-year cohort. Acta Neuropathol Commun 2022; 10:123. [PMID: 36008825 PMCID: PMC9404601 DOI: 10.1186/s40478-022-01429-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 08/11/2022] [Indexed: 11/10/2022] Open
Abstract
Ependymoma is the second most common malignant brain tumor in children. The etiology is largely unknown and germline DNA sequencing studies focusing on childhood ependymoma are limited. We therefore performed germline whole-genome sequencing on a population-based cohort of children diagnosed with ependymoma in Denmark over the past 20 years (n = 43). Single nucleotide and structural germline variants in 457 cancer related genes and 2986 highly evolutionarily constrained genes were assessed in 37 children with normal tissue available for sequencing. Molecular ependymoma classification was performed using DNA methylation profiling for 39 children with available tumor tissue. Pathogenic germline variants in known cancer predisposition genes were detected in 11% (4/37; NF2, LZTR1, NF1 & TP53). However, DNA methylation profiling resulted in revision of the histopathological ependymoma diagnosis to non-ependymoma tumor types in 8% (3/39). This included the two children with pathogenic germline variants in TP53 and NF1 whose tumors were reclassified to a diffuse midline glioma and a rosette-forming glioneuronal tumor, respectively. Consequently, 50% (2/4) of children with pathogenic germline variants in fact had other tumor types. A meta-analysis combining our findings with pediatric pan-cancer germline sequencing studies showed an overall frequency of pathogenic germline variants of 3.4% (7/207) in children with ependymoma. In summary, less than 4% of childhood ependymoma is explained by genetic predisposition, virtually restricted to pathogenic variants in NF2 and NF1. For children with other cancer predisposition syndromes, diagnostic reconsideration is recommended for ependymomas without molecular classification. Additionally, LZTR1 is suggested as a novel putative ependymoma predisposition gene.
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Affiliation(s)
- Jon Foss-Skiftesvik
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet University Hospital, Copenhagen, Denmark. .,Department of Neurosurgery, Rigshospitalet University Hospital, Copenhagen, Denmark. .,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. .,Department of Neurosurgery, Section 6031, Rigshospitalet University Hospital, Inge Lehmanns Vej 6, 2100, Copenhagen, Denmark. .,The Pediatric Oncology Research Laboratory, Section 5704, Department of Pediatrics and Adolescent Medicine, Rigshospitalet University Hospital, Henrik Harpestrengs Vej 6A, 2100, Copenhagen, Denmark.
| | - Ulrik Kristoffer Stoltze
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet University Hospital, Copenhagen, Denmark.,Department of Clinical Genetics, University of Copenhagen, Copenhagen, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Thomas van Overeem Hansen
- Department of Clinical Genetics, University of Copenhagen, Copenhagen, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lise Barlebo Ahlborn
- Department of Genomic Medicine, Rigshospitalet University Hospital, Copenhagen, Denmark
| | - Erik Sørensen
- Department of Clinical Immunology, Rigshospitalet University Hospital, Copenhagen, Denmark
| | - Sisse Rye Ostrowski
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Clinical Immunology, Rigshospitalet University Hospital, Copenhagen, Denmark
| | | | - Adrian Otamendi Laspiur
- Department of Health Technology, Cancer Systems Biology and Bioinformatics, Technical University of Denmark, Lyngby, Denmark
| | | | - David Scheie
- Department of Pathology, Rigshospitalet University Hospital, Copenhagen, Denmark
| | - Bjarne Winther Kristensen
- Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Pathology, Rigshospitalet University Hospital, Copenhagen, Denmark.,Biotech Research and Innovation Center, University of Copenhagen, Copenhagen, Denmark
| | - Jane Skjøth-Rasmussen
- Department of Neurosurgery, Rigshospitalet University Hospital, Copenhagen, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kjeld Schmiegelow
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet University Hospital, Copenhagen, Denmark.,Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Karin Wadt
- Department of Clinical Genetics, University of Copenhagen, Copenhagen, Denmark
| | - René Mathiasen
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet University Hospital, Copenhagen, Denmark
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14
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Gargallo P, Oltra S, Yáñez Y, Juan-Ribelles A, Calabria I, Segura V, Lázaro M, Balaguer J, Tormo T, Dolz S, Fernández JM, Fuentes C, Torres B, Andrés M, Tasso M, Castel V, Font de Mora J, Cañete A. Germline Predisposition to Pediatric Cancer, from Next Generation Sequencing to Medical Care. Cancers (Basel) 2021; 13:5339. [PMID: 34771502 PMCID: PMC8582391 DOI: 10.3390/cancers13215339] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/18/2021] [Accepted: 10/21/2021] [Indexed: 11/16/2022] Open
Abstract
Knowledge about genetic predisposition to pediatric cancer is constantly expanding. The categorization and clinical management of the best-known syndromes has been refined over the years. Meanwhile, new genes for pediatric cancer susceptibility are discovered every year. Our current work shares the results of genetically studying the germline of 170 pediatric patients diagnosed with cancer. Patients were prospectively recruited and studied using a custom panel, OncoNano V2. The well-categorized predisposing syndromes incidence was 9.4%. Likely pathogenic variants for predisposition to the patient's tumor were identified in an additional 5.9% of cases. Additionally, a high number of pathogenic variants associated with recessive diseases was detected, which required family genetic counseling as well. The clinical utility of the Jongmans MC tool was evaluated, showing a high sensitivity for detecting the best-known predisposing syndromes. Our study confirms that the Jongmans MC tool is appropriate for a rapid assessment of patients; however, the updated version of Ripperger T criteria would be more accurate. Meaningfully, based on our findings, up to 9.4% of patients would present genetic alterations predisposing to cancer. Notably, up to 20% of all patients carry germline pathogenic or likely pathogenic variants in genes related to cancer and, thereby, they also require expert genetic counseling. The most important consideration is that the detection rate of genetic causality outside Jongmans MC et al. criteria was very low.
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Affiliation(s)
- Pablo Gargallo
- Pediatric Oncology Department, Hospital Universitario y Politécnico La Fe de Valencia, 46026 Valencia, Spain; (Y.Y.); (A.J.-R.); (V.S.); (J.B.); (T.T.); (J.M.F.); (C.F.); (B.T.); (M.A.); (V.C.); (A.C.)
- Imegen–Health in Code Group, Department of Oncology, Paterna, 46980 Valencia, Spain; (I.C.); (M.L.)
| | - Silvestre Oltra
- Genetics Unit, Hospital Universitario y Politécnico La Fe de Valencia, 46026 Valencia, Spain;
- Genetics Department, Universidad de Valencia, 46010 Valencia, Spain
| | - Yania Yáñez
- Pediatric Oncology Department, Hospital Universitario y Politécnico La Fe de Valencia, 46026 Valencia, Spain; (Y.Y.); (A.J.-R.); (V.S.); (J.B.); (T.T.); (J.M.F.); (C.F.); (B.T.); (M.A.); (V.C.); (A.C.)
| | - Antonio Juan-Ribelles
- Pediatric Oncology Department, Hospital Universitario y Politécnico La Fe de Valencia, 46026 Valencia, Spain; (Y.Y.); (A.J.-R.); (V.S.); (J.B.); (T.T.); (J.M.F.); (C.F.); (B.T.); (M.A.); (V.C.); (A.C.)
| | - Inés Calabria
- Imegen–Health in Code Group, Department of Oncology, Paterna, 46980 Valencia, Spain; (I.C.); (M.L.)
| | - Vanessa Segura
- Pediatric Oncology Department, Hospital Universitario y Politécnico La Fe de Valencia, 46026 Valencia, Spain; (Y.Y.); (A.J.-R.); (V.S.); (J.B.); (T.T.); (J.M.F.); (C.F.); (B.T.); (M.A.); (V.C.); (A.C.)
| | - Marián Lázaro
- Imegen–Health in Code Group, Department of Oncology, Paterna, 46980 Valencia, Spain; (I.C.); (M.L.)
| | - Julia Balaguer
- Pediatric Oncology Department, Hospital Universitario y Politécnico La Fe de Valencia, 46026 Valencia, Spain; (Y.Y.); (A.J.-R.); (V.S.); (J.B.); (T.T.); (J.M.F.); (C.F.); (B.T.); (M.A.); (V.C.); (A.C.)
| | - Teresa Tormo
- Pediatric Oncology Department, Hospital Universitario y Politécnico La Fe de Valencia, 46026 Valencia, Spain; (Y.Y.); (A.J.-R.); (V.S.); (J.B.); (T.T.); (J.M.F.); (C.F.); (B.T.); (M.A.); (V.C.); (A.C.)
| | - Sandra Dolz
- Laboratory of Cellular and Molecular Biology, Clinical and Translational Research in Cancer, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (S.D.); (J.F.d.M.)
| | - José María Fernández
- Pediatric Oncology Department, Hospital Universitario y Politécnico La Fe de Valencia, 46026 Valencia, Spain; (Y.Y.); (A.J.-R.); (V.S.); (J.B.); (T.T.); (J.M.F.); (C.F.); (B.T.); (M.A.); (V.C.); (A.C.)
| | - Carolina Fuentes
- Pediatric Oncology Department, Hospital Universitario y Politécnico La Fe de Valencia, 46026 Valencia, Spain; (Y.Y.); (A.J.-R.); (V.S.); (J.B.); (T.T.); (J.M.F.); (C.F.); (B.T.); (M.A.); (V.C.); (A.C.)
| | - Bárbara Torres
- Pediatric Oncology Department, Hospital Universitario y Politécnico La Fe de Valencia, 46026 Valencia, Spain; (Y.Y.); (A.J.-R.); (V.S.); (J.B.); (T.T.); (J.M.F.); (C.F.); (B.T.); (M.A.); (V.C.); (A.C.)
| | - Mara Andrés
- Pediatric Oncology Department, Hospital Universitario y Politécnico La Fe de Valencia, 46026 Valencia, Spain; (Y.Y.); (A.J.-R.); (V.S.); (J.B.); (T.T.); (J.M.F.); (C.F.); (B.T.); (M.A.); (V.C.); (A.C.)
| | - María Tasso
- Pediatric Oncology Department, Hospital General de Alicante, 03010 Alicante, Spain;
| | - Victoria Castel
- Pediatric Oncology Department, Hospital Universitario y Politécnico La Fe de Valencia, 46026 Valencia, Spain; (Y.Y.); (A.J.-R.); (V.S.); (J.B.); (T.T.); (J.M.F.); (C.F.); (B.T.); (M.A.); (V.C.); (A.C.)
| | - Jaime Font de Mora
- Laboratory of Cellular and Molecular Biology, Clinical and Translational Research in Cancer, Instituto de Investigación Sanitaria La Fe, 46026 Valencia, Spain; (S.D.); (J.F.d.M.)
| | - Adela Cañete
- Pediatric Oncology Department, Hospital Universitario y Politécnico La Fe de Valencia, 46026 Valencia, Spain; (Y.Y.); (A.J.-R.); (V.S.); (J.B.); (T.T.); (J.M.F.); (C.F.); (B.T.); (M.A.); (V.C.); (A.C.)
- Department of Pediatrics, Obstetrics and Gynecology, University of Valencia, 46010 Valencia, Spain
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