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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Nelson AT, Harris AK, Watson D, Kamihara J, Chen KS, Stall JN, Devins KM, Young RH, Olson DR, Mallinger PHR, Mitchell SG, Hoffman LM, Halliday G, Suleymanova AM, Glade Bender JL, Messinger YH, Herzog CE, Field AL, Frazier AL, Stewart DR, Dehner LP, Hill DA, Billmire DF, Schneider DT, Schultz KAP. Outcomes in ovarian Sertoli-Leydig cell tumor: A report from the International Pleuropulmonary Blastoma/DICER1 and Ovarian and Testicular Stromal Tumor Registries. Gynecol Oncol 2024; 186:117-125. [PMID: 38657450 DOI: 10.1016/j.ygyno.2024.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/02/2024] [Accepted: 04/06/2024] [Indexed: 04/26/2024]
Abstract
OBJECTIVE Sertoli-Leydig cell tumors (SLCTs) are rare sex cord-stromal tumors, representing <0.5% of all ovarian tumors. We sought to describe prognostic factors, treatment and outcomes for individuals with ovarian SLCT. METHODS Individuals with SLCT were enrolled in the International Pleuropulmonary Blastoma/DICER1 Registry and/or the International Ovarian and Testicular Stromal Tumor Registry. Medical records were systematically abstracted, and pathology was centrally reviewed when available. RESULTS In total, 191 participants with ovarian SLCT enrolled, with most (92%, 175/191) presenting with FIGO stage I disease. Germline DICER1 results were available for 156 patients; of these 58% had a pathogenic or likely pathogenic germline variant. Somatic (tumor) DICER1 testing showed RNase IIIb hotspot variants in 97% (88/91) of intermediately and poorly differentiated tumors. Adjuvant chemotherapy was administered in 40% (77/191) of cases, and among these, nearly all patients received platinum-based regimens (95%, 73/77), and 30% (23/77) received regimens that included an alkylating agent. Three-year recurrence-free survival for patients with stage IA tumors was 93.6% (95% CI: 88.2-99.3%) compared to 67.1% (95% CI: 55.2-81.6%) for all stage IC and 60.6% (95% CI: 40.3-91.0%) for stage II-IV (p < .001) tumors. Among patients with FIGO stage I tumors, those with mesenchymal heterologous elements treated with surgery alone were at higher risk for recurrence (HR: 74.18, 95% CI: 17.99-305.85). CONCLUSION Most individuals with SLCT fare well, though specific risk factors such as mesenchymal heterologous elements are associated with poor prognosis. We also highlight the role of DICER1 surveillance in early detection of SLCT, facilitating stage IA resection.
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Affiliation(s)
- Alexander T Nelson
- International Pleuropulmonary Blastoma/DICER1 Registry, Children's Minnesota, Minneapolis, MN, USA; International Ovarian and Testicular Stromal Tumor Registry, Children's Minnesota, Minneapolis, MN, USA; Cancer and Blood Disorders, Children's Minnesota, Minneapolis, MN, USA; University of Minnesota Medical School, Minneapolis, MN, USA
| | - Anne K Harris
- International Pleuropulmonary Blastoma/DICER1 Registry, Children's Minnesota, Minneapolis, MN, USA; International Ovarian and Testicular Stromal Tumor Registry, Children's Minnesota, Minneapolis, MN, USA; Cancer and Blood Disorders, Children's Minnesota, Minneapolis, MN, USA
| | - Dave Watson
- Research Institute, Children's Minnesota, Minneapolis, MN, USA
| | - Junne Kamihara
- Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA, USA
| | - Kenneth S Chen
- Department of Pediatrics, UT Southwestern Medical Center, Dallas, TX, USA; Children's Medical Center Research Institute, UT Southwestern Medical Center, Dallas, TX, USA
| | | | - Kyle M Devins
- James Homer Wright Pathology Laboratories, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Robert H Young
- James Homer Wright Pathology Laboratories, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Damon R Olson
- Department of Pathology and Laboratory Medicine, Children's Minnesota, Minneapolis, MN, USA
| | - Paige H R Mallinger
- International Pleuropulmonary Blastoma/DICER1 Registry, Children's Minnesota, Minneapolis, MN, USA; International Ovarian and Testicular Stromal Tumor Registry, Children's Minnesota, Minneapolis, MN, USA; Cancer and Blood Disorders, Children's Minnesota, Minneapolis, MN, USA
| | - Sarah G Mitchell
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA, USA
| | - Lindsey M Hoffman
- Center for Cancer and Blood Disorders, Phoenix Children's Hospital, Phoenix, AZ, USA
| | - Gail Halliday
- Department of Paediatric Oncology, Great North Children's Hospital, Newcastle-upon-Tyne, UK
| | - Amina M Suleymanova
- Institute of Pediatric Oncology, Federal State Budgetary Institution N.N. Blokhin National Medical Research Center of Oncology of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Julia L Glade Bender
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Yoav H Messinger
- International Pleuropulmonary Blastoma/DICER1 Registry, Children's Minnesota, Minneapolis, MN, USA; International Ovarian and Testicular Stromal Tumor Registry, Children's Minnesota, Minneapolis, MN, USA; Cancer and Blood Disorders, Children's Minnesota, Minneapolis, MN, USA
| | - Cynthia E Herzog
- Division of Pediatrics, Department of Pediatric Patient Care, The University of Texas MD Anderson Cancer Care Center, Houston, TX, USA
| | | | - A Lindsay Frazier
- Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA, USA
| | - Douglas R Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Louis P Dehner
- Lauren V. Ackerman Laboratory of Surgical Pathology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - D Ashley Hill
- ResourcePath LLC, Sterling, VA, USA; Lauren V. Ackerman Laboratory of Surgical Pathology, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Deborah F Billmire
- Division of Pediatric Surgery, Department of Surgery, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Dominik T Schneider
- Clinic of Pediatrics, Municipal Hospital Dortmund, University Witten/Herdecke, Germany
| | - Kris Ann P Schultz
- International Pleuropulmonary Blastoma/DICER1 Registry, Children's Minnesota, Minneapolis, MN, USA; International Ovarian and Testicular Stromal Tumor Registry, Children's Minnesota, Minneapolis, MN, USA; Cancer and Blood Disorders, Children's Minnesota, Minneapolis, MN, USA.
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3
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Hansford JR, Das A, McGee RB, Nakano Y, Brzezinski J, Scollon SR, Rednam SP, Schienda J, Michaeli O, Kim SY, Greer MLC, Weksberg R, Stewart DR, Foulkes WD, Tabori U, Pajtler KW, Pfister SM, Brodeur GM, Kamihara J. Update on cancer predisposition syndromes and surveillance guidelines for childhood brain tumors. Clin Cancer Res 2024:742912. [PMID: 38573059 DOI: 10.1158/1078-0432.ccr-23-4033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/27/2024] [Accepted: 04/04/2024] [Indexed: 04/05/2024]
Abstract
Tumors of the central nervous system (CNS) comprise the second most common group of neoplasms in childhood. The incidence of germline predisposition among children with brain tumors continues to grow as our knowledge on disease aetiology increases. Some children with brain tumors may present with non-malignant phenotypic features of specific syndromes (e.g. nevoid basal cell carcinoma syndrome, neurofibromatosis type 1 and type 2, DICER1 syndrome, and constitutional mismatch repair deficiency), while others may present with a strong family history of cancer (e.g. Li-Fraumeni syndrome), or with a rare tumor commonly found in the context of germline predisposition (e.g. rhabdoid tumor predisposition syndrome). Approximately 50% of patients with a brain tumor may be the first in a family identified to have a predisposition. The past decade has witnessed a rapid expansion in our molecular understanding of CNS tumors. A significant proportion of CNS tumors are now well characterized and known to harbor specific genetic changes that can be found in the germline. Additional novel predisposition syndromes are also being described. Identification of these germline syndromes in individual patients has not only enabled cascade testing of family members and early tumor surveillance but increasingly has also impacted cancer management in those patients. Therefore, the AACR Cancer Predisposition Working Group chose to highlight these advances in CNS tumor predisposition and summarize and/or generate surveillance recommendations for established and more recently emerging pediatric brain tumor predisposition syndromes.
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Affiliation(s)
| | | | - Rose B McGee
- St. Jude Children's Research Hospital, Memphis, TN, United States
| | | | | | | | | | | | - Orli Michaeli
- Schneider Children's Medical Center of Israel, Patach Tikva, Israel
| | - Sun Young Kim
- Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States
| | | | | | | | | | - Uri Tabori
- Hospital for Sick Children, Toronto, Ontario, Canada
| | | | - Stefan M Pfister
- Hopp Children's Cancer Center at the NCT Heidelberg (KiTZ), Heidelberg, Germany
| | - Garrett M Brodeur
- Children's Hospital of Philadelphia, Philadelphia, PA, United States
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4
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Pyle LC, Kim J, Bradfield J, Damrauer SM, D'Andrea K, Einhorn LH, Godse R, Hakonarson H, Kanetsky PA, Kember RL, Jacobs LA, Maxwell KN, Rader DJ, Vaughn DJ, Weathers B, Wubbenhorst B, Regeneron Genetics Center Research Team, Cancer Genomics Research Laboratory, Greene MH, Nathanson KL, Stewart DR. Germline Exome Sequencing for Men with Testicular Germ Cell Tumor Reveals Coding Defects in Chromosomal Segregation and Protein-targeting Genes. Eur Urol 2024; 85:337-345. [PMID: 37246069 PMCID: PMC10676450 DOI: 10.1016/j.eururo.2023.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 04/21/2023] [Accepted: 05/09/2023] [Indexed: 05/30/2023]
Abstract
BACKGROUND Testicular germ cell tumor (TGCT) is the most common cancer among young White men. TGCT is highly heritable, although there are no known high-penetrance predisposition genes. CHEK2 is associated with moderate TGCT risk. OBJECTIVE To identify coding genomic variants associated with predisposition to TGCT. DESIGN, SETTING, AND PARTICIPANTS The study involved 293 men with familial or bilateral (high risk; HR)-TGCT representing 228 unique families and 3157 cancer-free controls. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS We carried out exome sequencing and gene burden analysis to identify associations with TGCT risk. RESULTS AND LIMITATIONS Gene burden association identified several genes, including loss-of-function variants of NIN and QRSL1. We identified no statistically significant association with the sex- and germ-cell development pathways (hypergeometric overlap test: p = 0.65 for truncating variants, p = 0.47 for all variants) or evidence of associations with the regions previously identified via genome-wide association studies (GWAS). When considering all significant coding variants together with genes associated with TGCT on GWAS, there were associations with three major pathways: mitosis/cell cycle (Gene Ontology identity GO:1903047: observed/expected variant ratio [O/E] 6.17, false discovery rate [FDR] 1.53 × 10-11), co-translational protein targeting (GO:0006613: O/E 18.62, FDR 1.35 × 10-10), and sex differentiation (GO:0007548: O/E 5.25, FDR 1.90 × 10-4). CONCLUSIONS To the best of our knowledge, this study is the largest to date on men with HR-TGCT. As in previous studies, we identified associations with variants for several genes, suggesting multigenic heritability. We identified associations with co-translational protein targeting, and chromosomal segregation and sex determination, identified via GWAS. Our results suggest potentially druggable targets for TGCT prevention or treatment. PATIENT SUMMARY We searched for gene variations that increase the risk of testicular cancer and found numerous new specific variants that contribute to this risk. Our results support the idea that many gene variants inherited together contribute to the risk of testicular cancer.
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Affiliation(s)
- Louise C Pyle
- Rare Disease Institute, Center for Genetic Medicine, Children's National Hospital, Washington, DC, USA; Department of Precision Medicine, George Washington University, Washington, DC, USA; Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Jung Kim
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | | | - Scott M Damrauer
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kurt D'Andrea
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | - Rama Godse
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Hakon Hakonarson
- Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Peter A Kanetsky
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Rachel L Kember
- Department of Psychiatry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Linda A Jacobs
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kara N Maxwell
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Daniel J Rader
- Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - David J Vaughn
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Benita Weathers
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Bradley Wubbenhorst
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | - Mark H Greene
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Katherine L Nathanson
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA; Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Douglas R Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA.
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5
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Nelson AT, Vasta LM, Watson D, Kim J, Harris AK, Best AF, Harney LA, Carr AG, Frederickson N, Dehner LP, Kratz CP, Hagedorn KN, Mize WA, Ling A, Messinger YH, Hill DA, Schultz KAP, Stewart DR. Prevalence of lung cysts in adolescents and adults with a germline DICER1 pathogenic/likely pathogenic variant: a report from the National Institutes of Health and International Pleuropulmonary Blastoma/ DICER1 Registry. Thorax 2024:thorax-2023-221024. [PMID: 38508719 DOI: 10.1136/thorax-2023-221024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 01/17/2024] [Indexed: 03/22/2024]
Abstract
BACKGROUND Pleuropulmonary blastoma (PPB), the hallmark tumour associated with DICER1-related tumour predisposition, is characterised by an age-related progression from a cystic lesion (type I) to a high-grade sarcoma with mixed cystic and solid features (type II) or purely solid lesion (type III). Not all cystic PPBs progress; type Ir (regressed), hypothesised to represent regressed or non-progressed type I PPB, is an air-filled, cystic lesion lacking a primitive sarcomatous component. This study aims to evaluate the prevalence of non-progressed lung cysts detected by CT scan in adolescents and adults with germline DICER1 pathogenic/likely pathogenic (P/LP) variants. METHODS Individuals were enrolled in the National Cancer Institute Natural History of DICER1 Syndrome study, the International PPB/DICER1 Registry and/or the International Ovarian and Testicular Stromal Tumor Registry. Individuals with a germline DICER1 P/LP variant with first chest CT at 12 years of age or older were selected for this analysis. RESULTS In the combined databases, 110 individuals with a germline DICER1 P/LP variant who underwent first chest CT at or after the age of 12 were identified. Cystic lung lesions were identified in 38% (42/110) with a total of 72 cystic lesions detected. No demographic differences were noted between those with lung cysts and those without lung cysts. Five cysts were resected with four centrally reviewed as type Ir PPB. CONCLUSION Lung cysts are common in adolescents and adults with germline DICER1 variation. Further study is needed to understand the mechanism of non-progression or regression of lung cysts in childhood to guide judicious intervention.
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Affiliation(s)
- Alexander T Nelson
- University of Minnesota Medical School, Minneapolis, Minnesota, USA
- International Pleuropulomary Blastoma/DICER1 Registry, Children's Minnesota, Minneapolis, Minnesota, USA
- International Ovarian and Testicular Stromal Tumor Registry, Children's Minnesota, Minneapolis, Minnesota, USA
- Cancer and Blood Disorders, Children's Minnesota, Minneapolis, Minnesota, USA
| | - Lauren M Vasta
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | - Dave Watson
- Research Institute, Children's Minnesota, Minneapolis, Minnesota, USA
| | - Jung Kim
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | - Anne K Harris
- International Pleuropulomary Blastoma/DICER1 Registry, Children's Minnesota, Minneapolis, Minnesota, USA
- International Ovarian and Testicular Stromal Tumor Registry, Children's Minnesota, Minneapolis, Minnesota, USA
- Cancer and Blood Disorders, Children's Minnesota, Minneapolis, Minnesota, USA
| | - Ana F Best
- Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | | | | | - Nicole Frederickson
- International Pleuropulomary Blastoma/DICER1 Registry, Children's Minnesota, Minneapolis, Minnesota, USA
- International Ovarian and Testicular Stromal Tumor Registry, Children's Minnesota, Minneapolis, Minnesota, USA
- Cancer and Blood Disorders, Children's Minnesota, Minneapolis, Minnesota, USA
| | - Louis P Dehner
- Lauren V. Ackerman Laboratory of Surgical Pathology, Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri, USA
| | - Christian P Kratz
- Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Niedersachsen, Germany
| | - Kelly N Hagedorn
- Department of Radiology, Children's Minnesota, Minneapolis, Minnesota, USA
| | - William A Mize
- Department of Radiology, Children's Minnesota, Minneapolis, Minnesota, USA
| | - Alexander Ling
- Department of Radiology, NIH Clinical Center, Bethesda, Maryland, USA
| | - Yoav H Messinger
- International Pleuropulomary Blastoma/DICER1 Registry, Children's Minnesota, Minneapolis, Minnesota, USA
- International Ovarian and Testicular Stromal Tumor Registry, Children's Minnesota, Minneapolis, Minnesota, USA
- Cancer and Blood Disorders, Children's Minnesota, Minneapolis, Minnesota, USA
| | - D Ashley Hill
- Lauren V. Ackerman Laboratory of Surgical Pathology, Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri, USA
- ResourcePath LLC, Sterling, Virginia, USA
| | - Kris Ann P Schultz
- International Pleuropulomary Blastoma/DICER1 Registry, Children's Minnesota, Minneapolis, Minnesota, USA
- International Ovarian and Testicular Stromal Tumor Registry, Children's Minnesota, Minneapolis, Minnesota, USA
- Cancer and Blood Disorders, Children's Minnesota, Minneapolis, Minnesota, USA
| | - Douglas R Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
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6
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Martin-Giacalone BA, Li H, Scheurer ME, Casey DL, Dugan-Perez S, Marquez-Do DA, Muzny D, Gibbs RA, Barkauskas DA, Hall D, Stewart DR, Schiffman JD, McEvoy MT, Khan J, Malkin D, Linardic CM, Crompton BD, Shern JF, Skapek SX, Venkatramani R, Hawkins DS, Sabo A, Plon SE, Lupo PJ. Germline Genetic Testing and Survival Outcomes Among Children With Rhabdomyosarcoma: A Report From the Children's Oncology Group. JAMA Netw Open 2024; 7:e244170. [PMID: 38546643 PMCID: PMC10979319 DOI: 10.1001/jamanetworkopen.2024.4170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 02/01/2024] [Indexed: 04/01/2024] Open
Abstract
Importance Determining the impact of germline cancer-predisposition variants (CPVs) on outcomes could inform novel approaches to testing and treating children with rhabdomyosarcoma. Objective To assess whether CPVs are associated with outcome among children with rhabdomyosarcoma. Design, Setting, and Participants In this cohort study, data were obtained for individuals, aged 0.01-23.23 years, newly diagnosed with rhabdomyosarcoma who were treated across 171 Children's Oncology Group sites from March 15, 1999, to December 8, 2017. Data analysis was performed from June 16, 2021, to May 15, 2023. Exposure The presence of a CPV in 24 rhabdomyosarcoma-associated cancer-predisposition genes (CPGs) or an expanded set of 63 autosomal-dominant CPGs. Main Outcomes and Measures Overall survival (OS) and event-free survival (EFS) were the main outcomes, using the Kaplan-Meier estimator to assess survival probabilities and the Cox proportional hazards regression model to adjust for clinical covariates. Analyses were stratified by tumor histology and the fusion status of PAX3 or PAX7 to the FOXO1 gene. Results In this study of 580 individuals with rhabdomyosarcoma, the median patient age was 5.9 years (range, 0.01-23.23 years), and the male-to-female ratio was 1.5 to 1 (351 [60.5%] male). For patients with CPVs in rhabdomyosarcoma-associated CPGs, EFS was 48.4% compared with 57.8% for patients without a CPV (P = .10), and OS was 53.7% compared with 65.3% for patients without a CPV (P = .06). After adjustment, patients with CPVs had significantly worse OS (adjusted hazard ratio [AHR], 2.49 [95% CI, 1.39-4.45]; P = .002), and the outcomes were not better among patients with embryonal histology (EFS: AHR, 2.25 [95% CI, 1.25-4.06]; P = .007]; OS: AHR, 2.83 [95% CI, 1.47-5.43]; P = .002]). These associations were not due to the development of a second malignant neoplasm, and importantly, patients with fusion-negative rhabdomyosarcoma who harbored a CPV had similarly inferior outcomes as patients with fusion-positive rhabdomyosarcoma without CPVs (EFS: AHR, 1.35 [95% CI, 0.71-2.59]; P = .37; OS: AHR, 1.71 [95% CI, 0.84-3.47]; P = .14). There were no significant differences in outcome by CPV status of the 63 CPG set. Conclusions and Relevance This cohort study identified a group of patients with embryonal rhabdomyosarcoma who had a particularly poor outcome. Other important clinical findings included that individuals with TP53 had poor outcomes independent of second malignant neoplasms and that patients with fusion-negative rhabdomyosarcoma who harbored a CPV had outcomes comparable to patients with fusion-positive rhabdomyosarcoma. These findings suggest that germline CPV testing may aid in clinical prognosis and should be considered in prospective risk-based clinical trials.
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Affiliation(s)
- Bailey A. Martin-Giacalone
- Division of Public Health Sciences, Department of Surgery, Washington University School of Medicine in St. Louis, St. Louis, Missouri
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, Texas
| | - He Li
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Michael E. Scheurer
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Dana L. Casey
- Department of Radiation Oncology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill
| | | | - Deborah A. Marquez-Do
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, Texas
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Donald A. Barkauskas
- Department of Population and Public Health Sciences, Keck School of Medicine of University of Southern California, Los Angeles
- QuadW Childhood Sarcoma Biostatistics and Annotation Office at the Children’s Oncology Group, Monrovia, California
| | - David Hall
- QuadW Childhood Sarcoma Biostatistics and Annotation Office at the Children’s Oncology Group, Monrovia, California
| | - Douglas R. Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland
| | - Joshua D. Schiffman
- Department of Pediatrics, Huntsman Cancer Institute, University of Utah, Salt Lake City
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City
| | - Matthew T. McEvoy
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, Texas
| | - Javed Khan
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - David Malkin
- Division of Haematology-Oncology, Department of Paediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Corinne M. Linardic
- Department of Pediatrics, Duke University School of Medicine, Durham, North Carolina
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, North Carolina
| | - Brian D. Crompton
- Department of Pediatric Oncology, Dana-Farber/Boston Children’s Cancer and Blood Disorders Center, Harvard Medical School, Boston, Massachusetts
| | - Jack F. Shern
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Stephen X. Skapek
- Department of Pediatrics, The University of Texas Southwestern Medical Center, Dallas
| | - Rajkumar Venkatramani
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, Texas
| | - Douglas S. Hawkins
- Division of Hematology-Oncology, Seattle Children’s Hospital, University of Washington School of Medicine, Seattle
| | - Aniko Sabo
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Sharon E. Plon
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, Texas
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Philip J. Lupo
- Department of Pediatrics, Section of Hematology-Oncology, Baylor College of Medicine, Houston, Texas
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
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7
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Kim J, Naqvi AS, Corbett RJ, Kaufman RS, Vaksman Z, Brown MA, Miller DP, Phul S, Geng Z, Storm PB, Resnick AC, Stewart DR, Rokita JL, Diskin SJ. AutoGVP: a dockerized workflow integrating ClinVar and InterVar germline sequence variant classification. Bioinformatics 2024; 40:btae114. [PMID: 38426335 PMCID: PMC10955249 DOI: 10.1093/bioinformatics/btae114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/09/2024] [Accepted: 02/27/2024] [Indexed: 03/02/2024] Open
Abstract
SUMMARY With the increasing rates of exome and whole genome sequencing, the ability to classify large sets of germline sequencing variants using up-to-date American College of Medical Genetics-Association for Molecular Pathology (ACMG-AMP) criteria is crucial. Here, we present Automated Germline Variant Pathogenicity (AutoGVP), a tool that integrates germline variant pathogenicity annotations from ClinVar and sequence variant classifications from a modified version of InterVar (PVS1 strength adjustments, removal of PP5/BP6). This tool facilitates large-scale, clinically focused classification of germline sequence variants in a research setting. AVAILABILITY AND IMPLEMENTATION AutoGVP is an open source dockerized workflow implemented in R and freely available on GitHub at https://github.com/diskin-lab-chop/AutoGVP.
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Affiliation(s)
- Jung Kim
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20850, United States
| | - Ammar S Naqvi
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, United States
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, United States
| | - Ryan J Corbett
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, United States
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, United States
| | - Rebecca S Kaufman
- Department of Bioinformatics and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, United States
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, United States
| | - Zalman Vaksman
- Department of Bioinformatics and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, United States
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, United States
| | - Miguel A Brown
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, United States
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, United States
| | - Daniel P Miller
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, United States
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, United States
| | - Saksham Phul
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, United States
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, United States
| | - Zhuangzhuang Geng
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, United States
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, United States
| | - Phillip B Storm
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, United States
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, United States
| | - Adam C Resnick
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, United States
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, United States
| | - Douglas R Stewart
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20850, United States
| | - Jo Lynne Rokita
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, United States
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, United States
| | - Sharon J Diskin
- Department of Bioinformatics and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, United States
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA 19104, United States
- Department of Pediatrics, University of Pennsylvania, Philadelphia, PA 19104, United States
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8
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Deng J, Altintas B, Haley JS, Kim J, Ramos M, Carey DJ, Stewart DR, McReynolds LJ. Most Fanconi anemia heterozygotes are not at increased cancer risk: A genome-first DiscovEHR cohort population study. Genet Med 2024; 26:101042. [PMID: 38063144 PMCID: PMC10939803 DOI: 10.1016/j.gim.2023.101042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 12/01/2023] [Accepted: 12/01/2023] [Indexed: 01/23/2024] Open
Abstract
PURPOSE Fanconi anemia (FA) is a bone marrow failure and cancer predisposition syndrome caused primarily by biallelic pathogenic variants in 1 of 22 genes involved in DNA interstrand cross-link repair. An enduring question concerns cancer risk of those with a single pathogenic FA gene variant. To investigate all FA genes, this study utilized the DiscovEHR cohort of 170,503 individuals with exome sequencing and electronic health data. METHODS 5822 subjects with a single pathogenic variant in an FA gene were identified. Two control groups were used in primary analysis deriving cancer risk signals. Secondary exploratory analysis was conducted using the UK Biobank and The Cancer Genome Atlas. RESULTS Signals for elevated cancer risk were found in all 5 known cancer predisposition genes. Among the remaining 15 genes associated with autosomal recessive inheritance cancer risk signals were found for 4 cancers across 3 genes in the primary cohort but were not validated in secondary cohorts. CONCLUSION To our knowledge, this is the first and largest FA heterozygote study to use genomic ascertainment and validates well-established cancer predispositions in 5 genes, whereas finding insufficient evidence of predisposition in 15 others. Our findings inform clinical surveillance given how common pathogenic FA variants are in the population.
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Affiliation(s)
- Joseph Deng
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD
| | - Burak Altintas
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD; Washington University, St. Louis Children's Hospital, St. Louis, MO
| | - Jeremy S Haley
- Department of Genomic Health, Weis Center for Research, Geisinger Medical Center, Danville, PA
| | - Jung Kim
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD
| | - Mark Ramos
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD
| | - David J Carey
- Department of Genomic Health, Weis Center for Research, Geisinger Medical Center, Danville, PA
| | - Douglas R Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD
| | - Lisa J McReynolds
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD.
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9
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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. Response to Stern. Genet Med 2024; 26:101030. [PMID: 38156990 DOI: 10.1016/j.gim.2023.101030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 11/14/2023] [Indexed: 01/03/2024] Open
Affiliation(s)
- Helen Hanson
- Peninsula Clinical Genetics Service, Royal Devon University Healthcare NHS Foundation Trust, Exeter, United Kingdom; Faculty of Health and Life Sciences, University of Exeter, Exeter, 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, Québec, Canada
| | - Paul James
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia; Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre, Melbourne, Victoria, 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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10
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de Andrade KC, Strande NT, Kim J, Haley JS, Hatton JN, Frone MN, Khincha PP, Thone GM, Mirshahi UL, Schneider C, Desai H, Dove JT, Smelser DT, Levine AJ, Maxwell KN, Stewart DR, Carey DJ, Savage SA. Genome-first approach of the prevalence and cancer phenotypes of pathogenic or likely pathogenic germline TP53 variants. HGG Adv 2024; 5:100242. [PMID: 37777824 PMCID: PMC10589747 DOI: 10.1016/j.xhgg.2023.100242] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/20/2023] [Accepted: 09/20/2023] [Indexed: 10/02/2023] Open
Abstract
Pathogenic or likely pathogenic (P/LP) germline TP53 variants are the primary cause of Li-Fraumeni syndrome (LFS), a hereditary cancer predisposition disorder characterized by early-onset cancers. The population prevalence of P/LP germline TP53 variants is estimated to be approximately one in every 3,500 to 20,000 individuals. However, these estimates are likely impacted by ascertainment biases and lack of clinical and genetic data to account for potential confounding factors, such as clonal hematopoiesis. Genome-first approaches of cohorts linked to phenotype data can further refine these estimates by identifying individuals with variants of interest and then assessing their phenotypes. This study evaluated P/LP germline (variant allele fraction ≥30%) TP53 variants in three cohorts: UK Biobank (UKB, n = 200,590), Geisinger (n = 170,503), and Penn Medicine Biobank (PMBB, n = 43,731). A total of 109 individuals were identified with P/LP germline TP53 variants across the three databases. The TP53 p.R181H variant was the most frequently identified (9 of 109 individuals, 8%). A total of 110 cancers, including 47 hematologic cancers (47 of 110, 43%), were reported in 71 individuals. The prevalence of P/LP germline TP53 variants was conservatively estimated as 1:10,439 in UKB, 1:3,790 in Geisinger, and 1:2,983 in PMBB. These estimates were calculated after excluding related individuals and accounting for the potential impact of clonal hematopoiesis by excluding heterozygotes who ever developed a hematologic cancer. These varying estimates likely reflect intrinsic selection biases of each database, such as healthcare or population-based contexts. Prospective studies of diverse, young cohorts are required to better understand the population prevalence of germline TP53 variants and their associated cancer penetrance.
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Affiliation(s)
- Kelvin C de Andrade
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Natasha T Strande
- Department of Genomic Health, Geisinger Clinic, Geisinger, Danville, PA, USA
| | - Jung Kim
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jeremy S Haley
- Department of Genomic Health, Geisinger Clinic, Geisinger, Danville, PA, USA
| | - Jessica N Hatton
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Megan N Frone
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Payal P Khincha
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Gretchen M Thone
- Department of Genomic Health, Geisinger Clinic, Geisinger, Danville, PA, USA
| | - Uyenlinh L Mirshahi
- Department of Genomic Health, Geisinger Clinic, Geisinger, Danville, PA, USA
| | - Cynthia Schneider
- Division of Hematology/Oncology, Department of Medicine and Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Heena Desai
- Division of Hematology/Oncology, Department of Medicine and Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - James T Dove
- Department of Genomic Health, Geisinger Clinic, Geisinger, Danville, PA, USA
| | - Diane T Smelser
- Department of Genomic Health, Geisinger Clinic, Geisinger, Danville, PA, USA
| | - Arnold J Levine
- Simons Center for Systems Biology, Institute for Advanced Study, Princeton, NJ, USA
| | - Kara N Maxwell
- Division of Hematology/Oncology, Department of Medicine and Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Douglas R Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - David J Carey
- Department of Genomic Health, Geisinger Clinic, Geisinger, Danville, PA, USA
| | - Sharon A Savage
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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11
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Kim J, Vaksman Z, Egolf LE, Kaufman R, Evans JP, Conkrite KL, Danesh A, Lopez G, Randall MP, Dent MH, Farra LM, Menghani NL, Dymek M, Desai H, Hausler R, Hicks B, Auvil JG, Gerhard DS, Hakonarson H, Maxwell KN, Cole KA, Pugh TJ, Bosse KR, Khan J, Wei JS, Maris JM, Stewart DR, Diskin SJ. Germline pathogenic variants in neuroblastoma patients are enriched in BARD1 and predict worse survival. J Natl Cancer Inst 2024; 116:149-159. [PMID: 37688579 PMCID: PMC10777667 DOI: 10.1093/jnci/djad183] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 08/02/2023] [Accepted: 08/25/2023] [Indexed: 09/11/2023] Open
Abstract
BACKGROUND Neuroblastoma is an embryonal cancer of the developing sympathetic nervous system. The genetic contribution of rare pathogenic or likely pathogenic germline variants in patients without a family history remains unclear. METHODS Germline DNA sequencing was performed on 786 neuroblastoma patients. The frequency of rare cancer predisposition gene pathogenic or likely pathogenic variants in patients was compared with 2 cancer-free control cohorts. Matched tumor DNA sequencing was evaluated for second hits, and germline DNA array data from 5585 neuroblastoma patients and 23 505 cancer-free control children were analyzed to identify rare germline copy number variants. Patients with germline pathogenic or likely pathogenic variants were compared with those without to test for association with clinical characteristics, tumor features, and survival. RESULTS We observed 116 pathogenic or likely pathogenic variants involving 13.9% (109 of 786) of neuroblastoma patients, representing a statistically significant excess burden compared with cancer-free participants (odds ratio [OR] = 1.60, 95% confidence interval [CI] = 1.27 to 2.00). BARD1 harbored the most statistically significant enrichment of pathogenic or likely pathogenic variants (OR = 32.30, 95% CI = 6.44 to 310.35). Rare germline copy number variants disrupting BARD1 were identified in patients but absent in cancer-free participants (OR = 29.47, 95% CI = 1.52 to 570.70). Patients harboring a germline pathogenic or likely pathogenic variant had a worse overall survival compared with those without (P = 8.6 x 10-3). CONCLUSIONS BARD1 is an important neuroblastoma predisposition gene harboring both common and rare germline pathogenic or likely pathogenic variations. The presence of any germline pathogenic or likely pathogenic variant in a cancer predisposition gene was independently predictive of worse overall survival. As centers move toward paired tumor-normal sequencing at diagnosis, efforts should be made to centralize data and provide an infrastructure to support cooperative longitudinal prospective studies of germline pathogenic variation.
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Affiliation(s)
- Jung Kim
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Zalman Vaksman
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Laura E Egolf
- Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Rebecca Kaufman
- Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - J Perry Evans
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Karina L Conkrite
- Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Arnavaz Danesh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, ON, Canada
| | - Gonzalo Lopez
- Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Michael P Randall
- Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Maiah H Dent
- Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Lance M Farra
- Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Neil L Menghani
- Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Malwina Dymek
- Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Heena Desai
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ryan Hausler
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Belynda Hicks
- Cancer Genome Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | | | - Daniela S Gerhard
- Office of Cancer Genomics, National Cancer Institute, Bethesda, MD, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kara N Maxwell
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kristina A Cole
- Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Trevor J Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Kristopher R Bosse
- Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Javed Khan
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jun S Wei
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - John M Maris
- Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Douglas R Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Sharon J Diskin
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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12
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Kim J, Naqvi AS, Corbett RJ, Kaufman RS, Vaksman Z, Brown MA, Miller DP, Phul S, Geng Z, Storm PB, Resnick AC, Stewart DR, Rokita JL, Diskin SJ. AutoGVP: a dockerized workflow integrating ClinVar and InterVar germline sequence variant classification. bioRxiv 2023:2023.11.29.569103. [PMID: 38076939 PMCID: PMC10705399 DOI: 10.1101/2023.11.29.569103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2023]
Abstract
With the increasing rates of exome and whole genome sequencing, the ability to classify large sets of germline sequencing variants using up-to-date American College of Medical Genetics - Association for Molecular Pathology (ACMG-AMP) criteria is crucial. Here, we present Automated Germline Variant Pathogenicity (AutoGVP), a tool that integrates germline variant pathogenicity annotations from ClinVar and sequence variant classifications from a modified version of InterVar (PVS1 strength adjustments, removal of PP5/BP6). This tool facilitates large-scale, clinically-focused classification of germline sequence variants in a research setting.
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Affiliation(s)
- Jung Kim
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD
| | - Ammar S. Naqvi
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Ryan J. Corbett
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Rebecca S. Kaufman
- Department of Bioinformatics and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Zalman Vaksman
- Department of Bioinformatics and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Miguel A. Brown
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Daniel P. Miller
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Saksham Phul
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Zhuangzhuang Geng
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Phillip B. Storm
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Adam C. Resnick
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Douglas R. Stewart
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD
| | - Jo Lynne Rokita
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA
| | - Sharon J. Diskin
- Department of Bioinformatics and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, PA
- Department of Pediatrics, University of Pennsylvania, Philadelphia, PA
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13
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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: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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14
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Venger K, Elbracht M, Carlens J, Deutz P, Zeppernick F, Lassay L, Kratz C, Zenker M, Kim J, Stewart DR, Wieland I, Schultz KAP, Schwerk N, Kurth I, Kontny U. Unusual phenotypes in patients with a pathogenic germline variant in DICER1. Fam Cancer 2023; 22:475-480. [PMID: 34331184 PMCID: PMC9743360 DOI: 10.1007/s10689-021-00271-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 07/20/2021] [Indexed: 02/02/2023]
Abstract
Pathogenic germline DICER1 variants are associated with pleuropulmonary blastoma, multinodular goiter, embryonal rhabdomyosarcoma and other tumour types, while mosaic missense DICER1 variants in the RNase IIIb domain are linked to cause GLOW (global developmental delay, lung cysts, overgrowth, and Wilms' tumor) syndrome. Here, we report four families with germline DICER1 pathogenic variants in which one member in each family had a more complex phenotype, including skeletal findings, facial dysmorphism and developmental abnormalities. The developmental features occur with a variable expressivity and incomplete penetrance as also described for the neoplastic and dysplastic lesions associated with DICER1 variants. Whole exome sequencing (WES) was performed on all four cases and revealed no further pathogenic or likely pathogenic dominant, homozygous or compound heterozygous variants in three of them. Notably, a frameshift variant in ARID1B was detected in one patient explaining part of her phenotype. This series of patients shows that pathogenic DICER1 variants may be associated with a broader phenotypic spectrum than initially assumed, including predisposition to different tumours, skeletal findings, dysmorphism and developmental abnormalities, but genetic work up in syndromic patients should be comprehensive in order not to miss additional underlying /modifying causes.
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Affiliation(s)
- Kateryna Venger
- Division of Pediatric Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Miriam Elbracht
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Julia Carlens
- Clinic for Pediatric Pulmonology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Peter Deutz
- Division of Pediatric Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Felix Zeppernick
- Department of Gynecology and Obstetrics, Medical Faculty, RWTH Aachen University, Aachen, Germany
- Department of Obstetrics and Gynecology, University Hospital Giessen, Giessen, Germany
| | - Lisa Lassay
- Division of Pediatric Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Christian Kratz
- Clinic for Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Martin Zenker
- Institute of Human Genetics, University Hospital Magdeburg, Magdeburg, Germany
| | - Jung Kim
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, USA
| | - Douglas R Stewart
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, USA
| | - Ilse Wieland
- Institute of Human Genetics, University Hospital Magdeburg, Magdeburg, Germany
| | - Kris Ann P Schultz
- International PPB/DICER1 Registry, Minneapolis, MN, USA
- Cancer and Blood Disorders, Children's Minnesota, Minneapolis, MN, USA
| | - Nicolaus Schwerk
- Clinic for Pediatric Pulmonology, Allergology and Neonatology, Hannover Medical School, Hannover, Germany
| | - Ingo Kurth
- Institute of Human Genetics, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | - Udo Kontny
- Division of Pediatric Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, Medical Faculty, RWTH Aachen University, Aachen, Germany.
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15
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Sargen MR, Kim J, Potjer TP, Velthuizen ME, Martir-Negron AE, Odia Y, Helgadottir H, Hatton JN, Haley JS, Thone G, Widemann BC, Gross AM, Yohe ME, Kaplan RN, Shern JF, Sundby RT, Astiazaran-Symonds E, Yang XR, Carey DJ, Tucker MA, Stewart DR, Goldstein AM. Estimated Prevalence, Tumor Spectrum, and Neurofibromatosis Type 1-Like Phenotype of CDKN2A-Related Melanoma-Astrocytoma Syndrome. JAMA Dermatol 2023; 159:1112-1118. [PMID: 37585199 PMCID: PMC10433137 DOI: 10.1001/jamadermatol.2023.2621] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 06/14/2023] [Indexed: 08/17/2023]
Abstract
Importance Knowledge about the prevalence and tumor types of CDKN2A-related melanoma-astrocytoma syndrome (MAS) is limited and could improve disease recognition. Objective To estimate the prevalence and describe the tumor types of MAS. Design, Setting, and Participants This retrospective cohort study analyzed all available MAS cases from medical centers in the US (2 sites) and Europe (2 sites) and from biomedical population genomic databases (UK Biobank [United Kingdom], Geisinger MyCode [US]) between January 1, 1976, and December 31, 2020. Patients with MAS with CDKN2A germline pathogenic variants and 1 or more neural tumors were included. Data were analyzed from June 1, 2022, to January 31, 2023. Main Outcomes and Measures Disease prevalence and tumor frequency. Results Prevalence of MAS ranged from 1 in 170 503 (n = 1 case; 95% CI, 1:30 098-1:965 887) in Geisinger MyCode (n = 170 503; mean [SD] age, 58.9 [19.1] years; 60.6% women; 96.2% White) to 1 in 39 149 (n = 12 cases; 95% CI, 1:22 396-1:68 434) in UK Biobank (n = 469 789; mean [SD] age, 70.0 [8.0] years; 54.2% women; 94.8% White). Among UK Biobank patients with MAS (n = 12) identified using an unbiased genomic ascertainment approach, brain neoplasms (4 of 12, 33%; 1 glioblastoma, 1 gliosarcoma, 1 astrocytoma, 1 unspecified type) and schwannomas (3 of 12, 25%) were the most common malignant and benign neural tumors, while cutaneous melanoma (2 of 12, 17%) and head and neck squamous cell carcinoma (2 of 12, 17%) were the most common nonneural malignant neoplasms. In a separate case series of 14 patients with MAS from the US and Europe, brain neoplasms (4 of 14, 29%; 2 glioblastomas, 2 unspecified type) and malignant peripheral nerve sheath tumor (2 of 14, 14%) were the most common neural cancers, while cutaneous melanoma (4 of 14, 29%) and sarcomas (2 of 14, 14%; 1 liposarcoma, 1 unspecified type) were the most common nonneural cancers. Cutaneous neurofibromas (7 of 14, 50%) and schwannomas (2 of 14, 14%) were also common. In 1 US family, a father and son with MAS had clinical diagnoses of neurofibromatosis type 1 (NF1). Genetic testing of the son detected a pathogenic CDKN2A splicing variant (c.151-1G>C) and was negative for NF1 genetic alterations. In UK Biobank, 2 in 150 (1.3%) individuals with clinical NF1 diagnoses had likely pathogenic variants in CDKN2A, including 1 individual with no detected variants in the NF1 gene. Conclusions and Relevance This cohort study estimates the prevalence and describes the tumors of MAS. Additional studies are needed in genetically diverse populations to further define population prevalence and disease phenotypes.
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Affiliation(s)
- Michael R. Sargen
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland
| | - Jung Kim
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland
| | - Thomas P. Potjer
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Mary E. Velthuizen
- Division Laboratories, Pharmacy and Biomedical Genetics, Department of Genetics, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Yazmin Odia
- Miami Cancer Institute, Baptist Health South Florida, Miami
| | - Hildur Helgadottir
- Department of Oncology and Pathology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Jessica N. Hatton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland
| | - Jeremy S. Haley
- Department of Genomic Health, Geisinger Clinic, Geisinger Health System, Danville, Pennsylvania
| | - Gretchen Thone
- Department of Genomic Health, Geisinger Clinic, Geisinger Health System, Danville, Pennsylvania
| | - Brigitte C. Widemann
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Andrea M. Gross
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Marielle E. Yohe
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
- Laboratory of Cell and Developmental Signaling, Center for Cancer Research, Frederick, Maryland
| | - Rosandra N. Kaplan
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Jack F. Shern
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - R. Taylor Sundby
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | | | - Xiaohong R. Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland
| | - David J. Carey
- Department of Genomic Health, Geisinger Clinic, Geisinger Health System, Danville, Pennsylvania
| | - Margaret A. Tucker
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland
| | - Douglas R. Stewart
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland
| | - Alisa M. Goldstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland
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16
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Fraire CR, Mallinger PR, Hatton JN, Kim J, Dickens DS, Argenta PA, Milanovich S, Hartshorne T, Carey DJ, Haley JS, Urban G, Lee J, Hill DA, Stewart DR, Schultz KAP, Chen KS. Intronic Germline DICER1 Variants in Patients With Sertoli-Leydig Cell Tumor. JCO Precis Oncol 2023; 7:e2300189. [PMID: 37883719 PMCID: PMC10860953 DOI: 10.1200/po.23.00189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 08/02/2023] [Accepted: 08/25/2023] [Indexed: 10/28/2023] Open
Abstract
Germline pathogenic loss-of-function (pLOF) variants in DICER1 are associated with a predisposition for a variety of solid neoplasms, including pleuropulmonary blastoma and Sertoli-Leydig cell tumor (SLCT). The most common DICER1 pLOF variants include small insertions or deletions leading to frameshifts, and base substitutions leading to nonsense codons or altered splice sites. Larger deletions and pathogenic missense variants occur less frequently. Identifying these variants can trigger surveillance algorithms with potential for early detection of DICER1-related cancers and cascade testing of family members. However, some patients with DICER1-associated tumors have no pLOF variants detected by germline or tumor testing. Here, we present two patients with SLCT whose tumor sequencing showed only a somatic missense DICER1 RNase IIIb variant. Conventional exon-directed germline sequencing revealed no pLOF variants. Using a custom capture panel, we discovered novel intronic variants, ENST00000343455.7: c.1752+213A>G and c.1509+16A>G, that appear to interfere with normal splicing. We suggest that when no DICER1 pLOF variants or large deletions are discovered in exonic regions despite strong clinical suspicion, intron sequencing and splicing analysis should be performed.
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Affiliation(s)
| | - Paige R. Mallinger
- International Pleuropulmonary Blastoma (PPB)/DICER1 Registry, Children's Minnesota, Minneapolis, MN
- International Ovarian and Testicular Stromal Tumor (OTST) Registry, Children's Minnesota, Minneapolis, MN
- Cancer and Blood Disorders, Children's Minnesota, Minneapolis, MN
| | - Jessica N. Hatton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD
| | - Jung Kim
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD
| | | | - Peter A. Argenta
- Department of Obstetrics, Gynecology and Women's Health, University of Minnesota, Minneapolis, MN
| | - Samuel Milanovich
- Pediatric Hematology and Oncology, Sanford Roger Maris Cancer Center, Fargo, ND
| | - Taylor Hartshorne
- Department of Pediatrics, UT Southwestern Medical Center, Dallas, TX
| | - David J. Carey
- Department of Genomic Health, Geisinger Clinic, Danville, PA
| | - Jeremy S. Haley
- Department of Genomic Health, Geisinger Clinic, Danville, PA
| | - Gretchen Urban
- Department of Genomic Health, Geisinger Clinic, Danville, PA
| | - Jeon Lee
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX
| | - D. Ashley Hill
- Department of Pathology and Immunology, Washington University, St Louis, MO
| | - Douglas R. Stewart
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD
| | - Kris Ann P. Schultz
- International Pleuropulmonary Blastoma (PPB)/DICER1 Registry, Children's Minnesota, Minneapolis, MN
- International Ovarian and Testicular Stromal Tumor (OTST) Registry, Children's Minnesota, Minneapolis, MN
- Cancer and Blood Disorders, Children's Minnesota, Minneapolis, MN
| | - Kenneth S. Chen
- Department of Pediatrics, UT Southwestern Medical Center, Dallas, TX
- Children's Medical Center Research Institute, UT Southwestern Medical Center, Dallas, TX
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17
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Miller DT, Lee K, Abul-Husn NS, Amendola LM, Brothers K, Chung WK, Gollob MH, Gordon AS, Harrison SM, Hershberger RE, Klein TE, Richards CS, Stewart DR, Martin CL. ACMG SF v3.2 list for reporting of secondary findings in clinical exome and genome sequencing: A policy statement of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2023; 25:100866. [PMID: 37347242 PMCID: PMC10524344 DOI: 10.1016/j.gim.2023.100866] [Citation(s) in RCA: 36] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 04/12/2023] [Indexed: 06/23/2023] Open
Abstract
Clinicians are encouraged to document the reasons for the use of a particular procedure or test, whether or not it is in conformance with this statement. Clinicians also are advised to take notice of the date this statement was adopted, and to consider other medical and scientific information that becomes available after that date. It also would be prudent to consider whether intellectual property interests may restrict the performance of certain tests and other procedures. Where individual authors are listed, the views expressed may not reflect those of authors’ employers or affiliated institutions.
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Affiliation(s)
- David T Miller
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA
| | - Kristy Lee
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Noura S Abul-Husn
- Department of Medicine, Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY; 23andMe, Inc., Sunnyvale, CA
| | | | - Kyle Brothers
- Department of Pediatrics, University of Louisville, Louisville, KY
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY
| | - Michael H Gollob
- Division of Cardiology, Department of Physiology, University of Toronto, Toronto, ON, Canada
| | - Adam S Gordon
- Department of Pharmacology, Center for Genetic Medicine, Northwestern University, Chicago, IL
| | | | - Ray E Hershberger
- Divisions of Human Genetics and Cardiovascular Medicine, Department of Internal Medicine, The Ohio State University, Columbus, OH
| | - Teri E Klein
- Departments of Biomedical Data Science and Medicine, Stanford University, Stanford, CA
| | - C Sue Richards
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR
| | - Douglas R Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD
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18
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Shapiro JA, Gaonkar KS, Spielman SJ, Savonen CL, Bethell CJ, Jin R, Rathi KS, Zhu Y, Egolf LE, Farrow BK, Miller DP, Yang Y, Koganti T, Noureen N, Koptyra MP, Duong N, Santi M, Kim J, Robins S, Storm PB, Mack SC, Lilly JV, Xie HM, Jain P, Raman P, Rood BR, Lulla RR, Nazarian J, Kraya AA, Vaksman Z, Heath AP, Kline C, Scolaro L, Viaene AN, Huang X, Way GP, Foltz SM, Zhang B, Poetsch AR, Mueller S, Ennis BM, Prados M, Diskin SJ, Zheng S, Guo Y, Kannan S, Waanders AJ, Margol AS, Kim MC, Hanson D, Van Kuren N, Wong J, Kaufman RS, Coleman N, Blackden C, Cole KA, Mason JL, Madsen PJ, Koschmann CJ, Stewart DR, Wafula E, Brown MA, Resnick AC, Greene CS, Rokita JL, Taroni JN. OpenPBTA: The Open Pediatric Brain Tumor Atlas. Cell Genom 2023; 3:100340. [PMID: 37492101 PMCID: PMC10363844 DOI: 10.1016/j.xgen.2023.100340] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 02/28/2023] [Accepted: 05/04/2023] [Indexed: 07/27/2023]
Abstract
Pediatric brain and spinal cancers are collectively the leading disease-related cause of death in children; thus, we urgently need curative therapeutic strategies for these tumors. To accelerate such discoveries, the Children's Brain Tumor Network (CBTN) and Pacific Pediatric Neuro-Oncology Consortium (PNOC) created a systematic process for tumor biobanking, model generation, and sequencing with immediate access to harmonized data. We leverage these data to establish OpenPBTA, an open collaborative project with over 40 scalable analysis modules that genomically characterize 1,074 pediatric brain tumors. Transcriptomic classification reveals universal TP53 dysregulation in mismatch repair-deficient hypermutant high-grade gliomas and TP53 loss as a significant marker for poor overall survival in ependymomas and H3 K28-mutant diffuse midline gliomas. Already being actively applied to other pediatric cancers and PNOC molecular tumor board decision-making, OpenPBTA is an invaluable resource to the pediatric oncology community.
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Affiliation(s)
- Joshua A. Shapiro
- Childhood Cancer Data Lab, Alex’s Lemonade Stand Foundation, Bala Cynwyd, PA 19004, USA
| | - Krutika S. Gaonkar
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Bioinformatics and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Stephanie J. Spielman
- Childhood Cancer Data Lab, Alex’s Lemonade Stand Foundation, Bala Cynwyd, PA 19004, USA
- Rowan University, Glassboro, NJ 08028, USA
| | - Candace L. Savonen
- Childhood Cancer Data Lab, Alex’s Lemonade Stand Foundation, Bala Cynwyd, PA 19004, USA
| | - Chante J. Bethell
- Childhood Cancer Data Lab, Alex’s Lemonade Stand Foundation, Bala Cynwyd, PA 19004, USA
| | - Run Jin
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Komal S. Rathi
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Bioinformatics and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Yuankun Zhu
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Laura E. Egolf
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Bailey K. Farrow
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Daniel P. Miller
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Yang Yang
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL 60637, USA
| | - Tejaswi Koganti
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Nighat Noureen
- Greehey Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229, USA
| | - Mateusz P. Koptyra
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Nhat Duong
- Department of Bioinformatics and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Mariarita Santi
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Jung Kim
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20850, USA
| | - Shannon Robins
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Phillip B. Storm
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Stephen C. Mack
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Jena V. Lilly
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Hongbo M. Xie
- Department of Bioinformatics and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Payal Jain
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Pichai Raman
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Bioinformatics and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Brian R. Rood
- Children’s National Research Institute, Washington, DC 20012, USA
- George Washington University School of Medicine and Health Sciences, Washington, DC 20052, USA
| | - Rishi R. Lulla
- Division of Hematology/Oncology, Hasbro Children’s Hospital, Providence, RI 02903, USA
- Department of Pediatrics, The Warren Alpert School of Brown University, Providence, RI 02912, USA
| | - Javad Nazarian
- Children’s National Research Institute, Washington, DC 20012, USA
- George Washington University School of Medicine and Health Sciences, Washington, DC 20052, USA
- Department of Pediatrics, University of Zurich, Zurich, Switzerland
| | - Adam A. Kraya
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Zalman Vaksman
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Allison P. Heath
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Cassie Kline
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Laura Scolaro
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Angela N. Viaene
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Xiaoyan Huang
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Gregory P. Way
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Steven M. Foltz
- Childhood Cancer Data Lab, Alex’s Lemonade Stand Foundation, Bala Cynwyd, PA 19004, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Bo Zhang
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Anna R. Poetsch
- Biotechnology Center, Technical University Dresden, Dresden, Germany
- National Center for Tumor Diseases, Dresden, Germany
| | - Sabine Mueller
- Department of Neurology, Neurosurgery and Pediatrics, University of California, San Francisco, San Francisco, CA 94115, USA
| | - Brian M. Ennis
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Michael Prados
- University of California, San Francisco, San Francisco, CA 94115, USA
| | - Sharon J. Diskin
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Siyuan Zheng
- Greehey Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229, USA
| | - Yiran Guo
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Shrivats Kannan
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Angela J. Waanders
- Division of Hematology, Oncology, Neuro-Oncology, and Stem Cell Transplant, Ann & Robert H Lurie Children’s Hospital of Chicago, Chicago, IL 60611, USA
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Ashley S. Margol
- Division of Hematology and Oncology, Children’s Hospital of Los Angeles, Los Angeles, CA 90027, USA
- Department of Pediatrics, Keck School of Medicine of University of Southern California, Los Angeles, CA 90033, USA
| | - Meen Chul Kim
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Derek Hanson
- Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA
- Hackensack University Medical Center, Hackensack, NJ 07601, USA
| | - Nicholas Van Kuren
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jessica Wong
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Rebecca S. Kaufman
- Department of Bioinformatics and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Noel Coleman
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Christopher Blackden
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Kristina A. Cole
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jennifer L. Mason
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Peter J. Madsen
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Carl J. Koschmann
- Department of Pediatrics, University of Michigan Health, Ann Arbor, MI 48105, USA
- Pediatric Hematology Oncology, Mott Children’s Hospital, Ann Arbor, MI 48109, USA
| | - Douglas R. Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20850, USA
| | - Eric Wafula
- Department of Bioinformatics and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Miguel A. Brown
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Adam C. Resnick
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Casey S. Greene
- Childhood Cancer Data Lab, Alex’s Lemonade Stand Foundation, Bala Cynwyd, PA 19004, USA
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jo Lynne Rokita
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Bioinformatics and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Jaclyn N. Taroni
- Childhood Cancer Data Lab, Alex’s Lemonade Stand Foundation, Bala Cynwyd, PA 19004, USA
| | - Children’s Brain Tumor Network
- Childhood Cancer Data Lab, Alex’s Lemonade Stand Foundation, Bala Cynwyd, PA 19004, USA
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Bioinformatics and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Rowan University, Glassboro, NJ 08028, USA
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL 60637, USA
- Greehey Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229, USA
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20850, USA
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Children’s National Research Institute, Washington, DC 20012, USA
- George Washington University School of Medicine and Health Sciences, Washington, DC 20052, USA
- Division of Hematology/Oncology, Hasbro Children’s Hospital, Providence, RI 02903, USA
- Department of Pediatrics, The Warren Alpert School of Brown University, Providence, RI 02912, USA
- Department of Pediatrics, University of Zurich, Zurich, Switzerland
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA
- Biotechnology Center, Technical University Dresden, Dresden, Germany
- National Center for Tumor Diseases, Dresden, Germany
- Department of Neurology, Neurosurgery and Pediatrics, University of California, San Francisco, San Francisco, CA 94115, USA
- University of California, San Francisco, San Francisco, CA 94115, USA
- Department of Pediatrics, University of Pennsylvania, Philadelphia, PA 19104, USA
- Division of Hematology, Oncology, Neuro-Oncology, and Stem Cell Transplant, Ann & Robert H Lurie Children’s Hospital of Chicago, Chicago, IL 60611, USA
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Division of Hematology and Oncology, Children’s Hospital of Los Angeles, Los Angeles, CA 90027, USA
- Department of Pediatrics, Keck School of Medicine of University of Southern California, Los Angeles, CA 90033, USA
- Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA
- Hackensack University Medical Center, Hackensack, NJ 07601, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Pediatrics, University of Michigan Health, Ann Arbor, MI 48105, USA
- Pediatric Hematology Oncology, Mott Children’s Hospital, Ann Arbor, MI 48109, USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Pacific Pediatric Neuro-Oncology Consortium
- Childhood Cancer Data Lab, Alex’s Lemonade Stand Foundation, Bala Cynwyd, PA 19004, USA
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Bioinformatics and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Rowan University, Glassboro, NJ 08028, USA
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL 60637, USA
- Greehey Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229, USA
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20850, USA
- Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
- Children’s National Research Institute, Washington, DC 20012, USA
- George Washington University School of Medicine and Health Sciences, Washington, DC 20052, USA
- Division of Hematology/Oncology, Hasbro Children’s Hospital, Providence, RI 02903, USA
- Department of Pediatrics, The Warren Alpert School of Brown University, Providence, RI 02912, USA
- Department of Pediatrics, University of Zurich, Zurich, Switzerland
- Department of Biomedical Informatics, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA 19104, USA
- Biotechnology Center, Technical University Dresden, Dresden, Germany
- National Center for Tumor Diseases, Dresden, Germany
- Department of Neurology, Neurosurgery and Pediatrics, University of California, San Francisco, San Francisco, CA 94115, USA
- University of California, San Francisco, San Francisco, CA 94115, USA
- Department of Pediatrics, University of Pennsylvania, Philadelphia, PA 19104, USA
- Division of Hematology, Oncology, Neuro-Oncology, and Stem Cell Transplant, Ann & Robert H Lurie Children’s Hospital of Chicago, Chicago, IL 60611, USA
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Division of Hematology and Oncology, Children’s Hospital of Los Angeles, Los Angeles, CA 90027, USA
- Department of Pediatrics, Keck School of Medicine of University of Southern California, Los Angeles, CA 90033, USA
- Hackensack Meridian School of Medicine, Nutley, NJ 07110, USA
- Hackensack University Medical Center, Hackensack, NJ 07601, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Pediatrics, University of Michigan Health, Ann Arbor, MI 48105, USA
- Pediatric Hematology Oncology, Mott Children’s Hospital, Ann Arbor, MI 48109, USA
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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19
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Stundon JL, Ijaz H, Gaonkar KS, Kaufman RS, Jin R, Karras A, Vaksman Z, Kim J, Corbett RJ, Lueder MR, Miller DP, Guo Y, Santi M, Li M, Lopez G, Storm PB, Resnick AC, Waanders AJ, MacFarland SP, Stewart DR, Diskin SJ, Rokita JL, Cole KA. Alternative lengthening of telomeres (ALT) in pediatric high-grade gliomas can occur without ATRX mutation and is enriched in patients with pathogenic germline mismatch repair (MMR) variants. Neuro Oncol 2023; 25:1331-1342. [PMID: 36541551 PMCID: PMC10326481 DOI: 10.1093/neuonc/noac278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND To achieve replicative immortality, most cancers develop a telomere maintenance mechanism, such as reactivation of telomerase or alternative lengthening of telomeres (ALT). There are limited data on the prevalence and clinical significance of ALT in pediatric brain tumors, and ALT-directed therapy is not available. METHODS We performed C-circle analysis (CCA) on 579 pediatric brain tumors that had corresponding tumor/normal whole genome sequencing through the Open Pediatric Brain Tumor Atlas (OpenPBTA). We detected ALT in 6.9% (n = 40/579) of these tumors and completed additional validation by ultrabright telomeric foci in situ on a subset of these tumors. We used CCA to validate TelomereHunter for computational prediction of ALT status and focus subsequent analyses on pediatric high-grade gliomas (pHGGs) Finally, we examined whether ALT is associated with recurrent somatic or germline alterations. RESULTS ALT is common in pHGGs (n = 24/63, 38.1%), but occurs infrequently in other pediatric brain tumors (<3%). Somatic ATRX mutations occur in 50% of ALT+ pHGGs and in 30% of ALT- pHGGs. Rare pathogenic germline variants in mismatch repair (MMR) genes are significantly associated with an increased occurrence of ALT. CONCLUSIONS We demonstrate that ATRX is mutated in only a subset of ALT+ pHGGs, suggesting other mechanisms of ATRX loss of function or alterations in other genes may be associated with the development of ALT in these patients. We show that germline variants in MMR are associated with the development of ALT in patients with pHGG.
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Affiliation(s)
- Jennifer L Stundon
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Department of Pediatrics, University of Pennsylvania, Philadelphia, Pennsylvania,USA
| | - Heba Ijaz
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania,USA
| | - Krutika S Gaonkar
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Department of Bioinformatics and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
| | - Rebecca S Kaufman
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Department of Bioinformatics and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
| | - Run Jin
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
| | - Anastasios Karras
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
| | - Zalman Vaksman
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Department of Bioinformatics and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
| | - Jung Kim
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland,USA
| | - Ryan J Corbett
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
| | - Matthew R Lueder
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
| | - Daniel P Miller
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
| | - Yiran Guo
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
| | - Mariarita Santi
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
| | - Marilyn Li
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
| | - Gonzalo Lopez
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
| | - Phillip B Storm
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
| | - Adam C Resnick
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
| | - Angela J Waanders
- Division of Hematology, Oncology, NeuroOncology, and Stem Cell Transplant, Ann & Robert H Lurie Children’s Hospital of Chicago, Illinois,USA
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois,USA
| | - Suzanne P MacFarland
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Department of Pediatrics, University of Pennsylvania, Philadelphia, Pennsylvania,USA
| | - Douglas R Stewart
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland,USA
| | - Sharon J Diskin
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Department of Pediatrics, University of Pennsylvania, Philadelphia, Pennsylvania,USA
- Department of Bioinformatics and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania,USA
| | - Jo Lynne Rokita
- Center for Data-Driven Discovery in Biomedicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Department of Bioinformatics and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Division of Neurosurgery, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
| | - Kristina A Cole
- Division of Oncology, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania,USA
- Department of Pediatrics, University of Pennsylvania, Philadelphia, Pennsylvania,USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania,USA
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20
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Katki HA, Berndt SI, Machiela MJ, Stewart DR, Garcia-Closas M, Kim J, Shi J, Yu K, Rothman N. Increase in power by obtaining 10 or more controls per case when type-1 error is small in large-scale association studies. BMC Med Res Methodol 2023; 23:153. [PMID: 37386403 PMCID: PMC10308790 DOI: 10.1186/s12874-023-01973-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 06/10/2023] [Indexed: 07/01/2023] Open
Abstract
BACKGROUND The rule of thumb that there is little gain in statistical power by obtaining more than 4 controls per case, is based on type-1 error α = 0.05. However, association studies that evaluate thousands or millions of associations use smaller α and may have access to plentiful controls. We investigate power gains, and reductions in p-values, when increasing well beyond 4 controls per case, for small α. METHODS We calculate the power, the median expected p-value, and the minimum detectable odds-ratio (OR), as a function of the number of controls/case, as α decreases. RESULTS As α decreases, at each ratio of controls per case, the increase in power is larger than for α = 0.05. For α between 10-6 and 10-9 (typical for thousands or millions of associations), increasing from 4 controls per case to 10-50 controls per case increases power. For example, a study with power = 0.2 (α = 5 × 10-8) with 1 control/case has power = 0.65 with 4 controls/case, but with 10 controls/case has power = 0.78, and with 50 controls/case has power = 0.84. For situations where obtaining more than 4 controls per case provides small increases in power beyond 0.9 (at small α), the expected p-value can decrease by orders-of-magnitude below α. Increasing from 1 to 4 controls/case reduces the minimum detectable OR toward the null by 20.9%, and from 4 to 50 controls/case reduces by an additional 9.7%, a result which applies regardless of α and hence also applies to "regular" α = 0.05 epidemiology. CONCLUSIONS At small α, versus 4 controls/case, recruiting 10 or more controls/cases can increase power, reduce the expected p-value by 1-2 orders of magnitude, and meaningfully reduce the minimum detectable OR. These benefits of increasing the controls/case ratio increase as the number of cases increases, although the amount of benefit depends on exposure frequencies and true OR. Provided that controls are comparable to cases, our findings suggest greater sharing of comparable controls in large-scale association studies.
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Affiliation(s)
- Hormuzd A Katki
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Douglas R Stewart
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Montserrat Garcia-Closas
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jung Kim
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, Department of Health and Human Services, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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21
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Astiazaran-Symonds E, Ney GM, Higgs C, Oba L, Srivastava R, Livinski AA, Rosenberg PS, Stewart DR. Cancer in Costello syndrome: a systematic review and meta-analysis. Br J Cancer 2023; 128:2089-2096. [PMID: 36966234 PMCID: PMC10205753 DOI: 10.1038/s41416-023-02229-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 02/22/2023] [Accepted: 03/02/2023] [Indexed: 03/27/2023] Open
Abstract
BACKGROUND Costello syndrome (CS) is a cancer-predisposition disorder caused by germline pathogenic variants in HRAS. We conducted a systematic review using case reports and case series to characterise cancer risk in CS. METHODS We conducted a systematic review to identify CS cases to create a retrospective cohort. We tested genotype-phenotype correlations and calculated cumulative incidence and hazard rates (HR) for cancer and cancer-free death, standardised incidence rates (SIR) and survival after cancer. RESULTS This study includes 234 publications reporting 621 patients from 35 countries. Over nine percent had cancer, including rhabdomyosarcoma, bladder, and neuroblastoma. The rate of cancer and death associated with p.Gly12Ser were lower when compared to all other variants (P < 0.05). Higher mortality for p.Gly12Cys, p.Gly12Asp, p.Gly12Val and p.Gly60Val and higher malignancy rate for p.Gly12Ala were confirmed (P < 0.05). Cumulative incidence by age 20 was 13% (cancer) and 11% (cancer-free death). HR (death) was 3-4% until age 3. Statistically significant SIRs were found for rhabdomyosarcoma (SIR = 1240), bladder (SIR = 1971), and neuroblastoma (SIR = 60). Survival after cancer appeared reduced. CONCLUSIONS This is the largest investigation of cancer in CS to date. The high incidence and SIR values found to highlight the need for rigorous surveillance and evidence-based guidelines for this high-risk population.
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Affiliation(s)
- Esteban Astiazaran-Symonds
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
- Department of Medicine, College of Medicine-Tucson, University of Arizona, Tucson, AZ, USA
| | - Gina M Ney
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Cecilia Higgs
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Leatrisse Oba
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Radhika Srivastava
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Alicia A Livinski
- NIH Library, Office of Research Services, Office of the Director, National Institutes of Health, Bethesda, MD, USA
| | - Philip S Rosenberg
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA
| | - Douglas R Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD, USA.
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22
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Nelson AT, Dybvik A, Mallinger P, McQuaid SW, Watson D, Harney LA, Stewart DR, Dehner LP, Messinger YH, Kunin-Batson A, Schultz KAP. Health-related quality of life in children and adolescents with pleuropulmonary blastoma: A report from the International PPB/DICER1 Registry. Pediatr Blood Cancer 2023; 70:e30077. [PMID: 36424733 PMCID: PMC9974753 DOI: 10.1002/pbc.30077] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 10/07/2022] [Accepted: 10/09/2022] [Indexed: 11/26/2022]
Abstract
PURPOSE Pleuropulmonary blastoma (PPB) is the most common lung cancer of infancy and early childhood and is associated with germline DICER1 variants. Type I and Ir PPB are cystic lesions treated surgically, with a subset of children with type I receiving chemotherapy. Type II and III are more aggressive lesions, treated with surgery, intensive chemotherapy and potentially radiation. We sought to assess health-related quality of life (HRQoL) in children with PPB and known germline DICER1 variants. METHODS Children with a diagnosis of PPB or germline DICER1 pathogenic variant without history of PPB or other DICER1-related neoplasm (DICER1+ only) were enrolled in the International PPB/DICER1 Registry. Parent reports for participants aged 2-17 years for the PedsQL v.4 and PedsQL Multidimensional Fatigue Scale v.3 were collected. Fatigue, physical, and psychosocial function scores were compared. RESULTS Analysis included 84 participants (PPB type Ir = 20, type I = 15, type II/III = 27, DICER1+ only = 22). Total fatigue scores of participants with type I and II/III PPB were lower compared to DICER1+ only, with effect size larger in type II/III (-0.82 vs. -0.40). Total psychosocial and physical functioning scores were lower in participants with type I and type II/III PPB compared to DICER1+ only, with larger effects noted in type II/III. Female sex was suggestive of worse HRQoL for both type I/Ir and type II/III cohorts. CONCLUSIONS These data demonstrate the importance of regular HRQoL assessment in patients with a history of PPB as well as the importance and feasibility of studying HRQoL in children with rare tumors.
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Affiliation(s)
- Alexander T. Nelson
- International Pleuropulmonary Blastoma/DICER1 Registry, Children’s Minnesota, Minneapolis, MN;,International Ovarian and Testicular Stromal Tumor Registry, Children’s Minnesota, Minneapolis, MN;,Cancer and Blood Disorders, Children’s Minnesota, Minneapolis, MN;,University of Minnesota Medical School, Minneapolis, MN
| | - Anna Dybvik
- International Pleuropulmonary Blastoma/DICER1 Registry, Children’s Minnesota, Minneapolis, MN;,International Ovarian and Testicular Stromal Tumor Registry, Children’s Minnesota, Minneapolis, MN;,Cancer and Blood Disorders, Children’s Minnesota, Minneapolis, MN
| | - Paige Mallinger
- International Pleuropulmonary Blastoma/DICER1 Registry, Children’s Minnesota, Minneapolis, MN;,International Ovarian and Testicular Stromal Tumor Registry, Children’s Minnesota, Minneapolis, MN;,Cancer and Blood Disorders, Children’s Minnesota, Minneapolis, MN
| | - Shelly Weiss McQuaid
- Department of Genetics, Birth Defects & Metabolism, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, IL
| | - Dave Watson
- Research Institute, Children’s Minnesota, Minneapolis, MN
| | | | - Douglas R. Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD
| | - Louis P. Dehner
- Lauren V. Ackerman Laboratory of Surgical Pathology, Department of Pathology and Immunology, Washington University Medical Center, St. Louis, MO
| | - Yoav H. Messinger
- International Pleuropulmonary Blastoma/DICER1 Registry, Children’s Minnesota, Minneapolis, MN;,International Ovarian and Testicular Stromal Tumor Registry, Children’s Minnesota, Minneapolis, MN;,Cancer and Blood Disorders, Children’s Minnesota, Minneapolis, MN
| | - Alicia Kunin-Batson
- Department of Pediatrics, University of Minnesota Medical School, Minneapolis, MN
| | - Kris Ann P. Schultz
- International Pleuropulmonary Blastoma/DICER1 Registry, Children’s Minnesota, Minneapolis, MN;,International Ovarian and Testicular Stromal Tumor Registry, Children’s Minnesota, Minneapolis, MN;,Cancer and Blood Disorders, Children’s Minnesota, Minneapolis, MN
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23
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Hatton JN, Frone MN, Cox HC, Crowley SB, Hiraki S, Yokoyama NN, Abul-Husn NS, Amatruda JF, Anderson MJ, Bofill-De Ros X, Carr AG, Chao EC, Chen KS, Gu S, Higgs C, Machado J, Ritter D, Schultz KA, Soper ER, Wu MK, Mester JL, Kim J, Foulkes WD, Witkowski L, Stewart DR. Specifications of the ACMG/AMP Variant Classification Guidelines for Germline DICER1 Variant Curation. Hum Mutat 2023; 2023:9537832. [PMID: 38084291 PMCID: PMC10713350 DOI: 10.1155/2023/9537832] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Germline pathogenic variants in DICER1 predispose individuals to develop a variety of benign and malignant tumors. Accurate variant curation and classification is essential for reliable diagnosis of DICER1-related tumor predisposition and identification of individuals who may benefit from surveillance. Since 2015, most labs have followed the American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP) sequence variant classification guidelines for DICER1 germline variant curation. However, these general guidelines lack gene-specific nuances and leave room for subjectivity. Consequently, a group of DICER1 experts joined ClinGen to form the DICER1 and miRNA-Processing Genes Variant Curation Expert Panel (VCEP), to create DICER1- specific ACMG/AMP guidelines for germline variant curation. The VCEP followed the FDA-approved ClinGen protocol for adapting and piloting these guidelines. A diverse set of 40 DICER1 variants were selected for piloting, including 14 known Pathogenic/Likely Pathogenic (P/LP) variants, 12 known Benign/Likely Benign (B/LB) variants, and 14 variants classified as variants of uncertain significance (VUS) or with conflicting interpretations in ClinVar. Clinically meaningful classifications (i.e., P, LP, LB, or B) were achieved for 82.5% (33/40) of the pilot variants, with 100% concordance among the known P/LP and known B/LB variants. Half of the VUS or conflicting variants were resolved with four variants classified as LB and three as LP. These results demonstrate that the DICER1-specific guidelines for germline variant curation effectively classify known pathogenic and benign variants while reducing the frequency of uncertain classifications. Individuals and labs curating DICER1 variants should consider adopting this classification framework to encourage consistency and improve objectivity.
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Affiliation(s)
- Jessica N Hatton
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | - Megan N Frone
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | - Hannah C Cox
- PreventionGenetics LLC, Marshfield, Wisconsin, USA
| | | | | | | | - Noura S Abul-Husn
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - James F Amatruda
- Cancer and Blood Disease Institute, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | | | - Xavier Bofill-De Ros
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | | | - Elizabeth C Chao
- Ambry Genetics, Aliso Viejo, California, USA
- Division of Genetics and Genomics, Department of Pediatrics, University of California, Irvine, California, USA
| | - Kenneth S Chen
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Shuo Gu
- RNA Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Cecilia Higgs
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | - Jerry Machado
- Exact Sciences Laboratories, Madison, Wisconsin, USA
| | | | - Kris Ann Schultz
- Cancer and Blood Disorders, Children's Minnesota, International Pleuropulmonary Blastoma/DICER1 Registry, Minneapolis, Minnesota, USA
| | - Emily R Soper
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Mona K Wu
- Cancer and Blood Disease Institute, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | | | - Jung Kim
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | - William D Foulkes
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Leora Witkowski
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Douglas R Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
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24
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Tayeh MK, Chen M, Fullerton SM, Gonzales PR, Huang SJ, Massingham LJ, O'Daniel JM, Stewart DR, Stiles AR, Evans BJ. The designated record set for clinical genetic and genomic testing: A points to consider statement of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2023; 25:100342. [PMID: 36547466 DOI: 10.1016/j.gim.2022.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 12/24/2022] Open
Affiliation(s)
| | - Margaret Chen
- Western Michigan University Homer Stryker M.D. School of Medicine, Kalamazoo, MI; GeneDx, Gaithersburg, MD
| | - Stephanie M Fullerton
- Division of Medical Genetics, Department of Medicine, University of Washington School of Medicine, Seattle, WA; Department of Bioethics & Humanities, University of Washington School of Medicine, Seattle, WA
| | - Patrick R Gonzales
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Lenexa, KS
| | - Samuel J Huang
- Division of Medical Genetics, Marshfield Clinic, Marshfield, WI
| | - Lauren J Massingham
- Division of Medical Genetics, Department of Pediatrics, Hasbro Children's Hospital, Providence, RI; The Warren Alpert School of Medicine at Brown University, Providence, RI
| | - Julianne M O'Daniel
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Douglas R Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD
| | - Ashlee R Stiles
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical Center, Durham, NC
| | - Barbara J Evans
- Levin College of Law, University of Florida, Gainesville, FL; Herbert Wertheim College of Engineering, University of Florida, Gainesville, FL
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- American College of Medical Genetics and Genomics, Bethesda, MD
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25
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Ricarte-Filho JC, Casado-Medrano V, Reichenberger E, Spangler Z, Scheerer M, Isaza A, Baran J, Patel T, MacFarland SP, Brodeur GM, Stewart DR, Baloch Z, Bauer AJ, Wasserman JD, Franco AT. DICER1 RNase IIIb domain mutations trigger widespread miRNA dysregulation and MAPK activation in pediatric thyroid cancer. Front Endocrinol (Lausanne) 2023; 14:1083382. [PMID: 36896180 PMCID: PMC9990750 DOI: 10.3389/fendo.2023.1083382] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 02/01/2023] [Indexed: 02/25/2023] Open
Abstract
DICER1 is a highly conserved RNase III endoribonuclease essential for the biogenesis of single-stranded mature microRNAs (miRNAs) from stem-loop precursor miRNAs. Somatic mutations in the RNase IIIb domain of DICER1 impair its ability to generate mature 5p miRNAs and are believed to drive tumorigenesis in DICER1 syndrome-associated and sporadic thyroid tumors. However, the DICER1-driven specific changes in miRNAs and resulting changes in gene expression are poorly understood in thyroid tissue. In this study, we profiled the miRNA (n=2,083) and mRNA (n=2,559) transcriptomes of 20 non-neoplastic, 8 adenomatous and 60 pediatric thyroid cancers (13 follicular thyroid cancers [FTC] and 47 papillary thyroid cancers [PTC]) of which 8 had DICER1 RNase IIIb mutations. All DICER1-mutant differentiated thyroid cancers (DTC) were follicular patterned (six follicular variant PTC and two FTC), none had lymph node metastasis. We demonstrate that DICER1 pathogenic somatic mutations were associated with a global reduction of 5p-derived miRNAs, including those particularly abundant in the non-neoplastic thyroid tissue such as let-7 and mir-30 families, known for their tumor suppressor function. There was also an unexpected increase of 3p miRNAs, possibly associated with DICER1 mRNA expression increase in tumors harboring RNase IIIb mutations. These abnormally expressed 3p miRNAs, which are otherwise low or absent in DICER1-wt DTC and non-neoplastic thyroid tissues, make up exceptional markers for malignant thyroid tumors harboring DICER1 RNase IIIb mutations. The extensive disarray in the miRNA transcriptome results in gene expression changes, which were indicative of positive regulation of cell-cycle. Moreover, differentially expressed genes point to increased MAPK signaling output and loss of thyroid differentiation comparable to the RAS-like subgroup of PTC (as coined by The Cancer Genome Atlas), which is reflective of the more indolent clinical behavior of these tumors.
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Affiliation(s)
- Julio C. Ricarte-Filho
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
| | - Victoria Casado-Medrano
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
| | - Erin Reichenberger
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Zachary Spangler
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
| | - Michele Scheerer
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
| | - Amber Isaza
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
| | - Julia Baran
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
| | - Tasleema Patel
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
| | - Suzanne P. MacFarland
- Division of Oncology, Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
- Cancer Predisposition Program, Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
| | - Garrett M. Brodeur
- Division of Oncology, Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
- Cancer Predisposition Program, Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, United States
| | - Douglas R. Stewart
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, United States
| | - Zubair Baloch
- Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
| | - Andrew J. Bauer
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
- Cancer Predisposition Program, Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
| | | | - Aime T. Franco
- Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
- Cancer Predisposition Program, Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, United States
- Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, United States
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26
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Nelson AT, Harris AK, Watson D, Miniati D, Finch M, Kamihara J, Mitchell SG, Wilson DB, Gettinger K, Rangaswami AA, Campos JM, Lederman S, Feltis BA, Vasta LM, Harney LA, Stewart DR, Dehner LP, Messinger YH, Hill DA, Schultz KAP. Type I and Ir pleuropulmonary blastoma (PPB): A report from the International PPB/DICER1 Registry. Cancer 2023; 129:600-613. [PMID: 36541021 DOI: 10.1002/cncr.34593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 10/14/2022] [Accepted: 11/03/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND Pleuropulmonary blastoma (PPB) is the most common lung cancer of infancy and early childhood. Type I PPB is a purely cystic lesion that has a microscopic population of primitive small cells with or without rhabdomyoblastic features and may progress to type II or III PPB, whereas type Ir lacks primitive small cells. METHODS Children with suspected PPB were enrolled in the International PPB/DICER1 Registry. Pathology was centrally reviewed, and follow-up was ascertained annually. RESULTS Between 2006 and 2022, 205 children had centrally reviewed type I or Ir PPB; 39% of children with type I and 5% of children with type Ir PPB received chemotherapy. Outcomes were favorable, although 11 children (nine with type I and two with type Ir PPB) experienced progression to type II/III (n = 8) or regrowth of type I PPB at the surgical site (n = 3), none of whom received chemotherapy before progression. Age and cyst size in combination were more suitable than either factor alone in predicting whether a particular lesion was type I or Ir PPB. CONCLUSIONS For young children with type I PPB, outcomes are favorable, but complete resection is indicated because of the risk for progression. Chemotherapy may be useful in a subset of children at increased risk for recurrence/progression. Efforts to risk stratify children with type I PPB to optimize outcomes while reducing treatment-related side effects are underway.
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Affiliation(s)
- Alexander T Nelson
- International Pleuropulmonary Blastoma/DICER1 Registry, Children's Minnesota, Minneapolis, Minnesota, USA.,International Ovarian and Testicular Stromal Tumor Registry, Children's Minnesota, Minneapolis, Minnesota, USA.,Cancer and Blood Disorders, Children's Minnesota, Minneapolis, Minnesota, USA.,University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Anne K Harris
- International Pleuropulmonary Blastoma/DICER1 Registry, Children's Minnesota, Minneapolis, Minnesota, USA.,International Ovarian and Testicular Stromal Tumor Registry, Children's Minnesota, Minneapolis, Minnesota, USA.,Cancer and Blood Disorders, Children's Minnesota, Minneapolis, Minnesota, USA
| | - Dave Watson
- Research and Sponsored Programs, Children's Minnesota, Minneapolis, Minnesota, USA
| | - Doug Miniati
- Division of Pediatric Surgery, Kaiser Permanente Northern California, Roseville, California, USA
| | - Mike Finch
- Research and Sponsored Programs, Children's Minnesota, Minneapolis, Minnesota, USA
| | - Junne Kamihara
- Pediatric Oncology, Boston Children's Hospital/Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Sarah G Mitchell
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Emory University School of Medicine, Atlanta, Georgia, USA
| | - David B Wilson
- Department of Pediatrics, Washington University School of Medicine, St Louis Children's Hospital, St Louis, MO, USA
| | - Katie Gettinger
- Department of Pediatrics, Washington University School of Medicine, St Louis Children's Hospital, St Louis, MO, USA
| | - Arun A Rangaswami
- Division of Pediatric Hematology and Oncology, University of California San Francisco, San Francisco, California, USA
| | - José M Campos
- Division of Pediatric Surgery, Hospital Sotero del Rio, Santiago, Chile
| | - Sara Lederman
- International Pleuropulmonary Blastoma/DICER1 Registry, Children's Minnesota, Minneapolis, Minnesota, USA.,International Ovarian and Testicular Stromal Tumor Registry, Children's Minnesota, Minneapolis, Minnesota, USA.,Cancer and Blood Disorders, Children's Minnesota, Minneapolis, Minnesota, USA.,University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Brad A Feltis
- Division of Pediatric Surgery, East Tennessee State University, Johnson City, Tennessee, USA
| | - Lauren M Vasta
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | | | - Douglas R Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, USA
| | - Louis P Dehner
- Lauren V. Ackerman Laboratory of Surgical Pathology, Department of Pathology and Immunology, Washington University Medical Center, St Louis, Missouri, USA
| | - Yoav H Messinger
- International Pleuropulmonary Blastoma/DICER1 Registry, Children's Minnesota, Minneapolis, Minnesota, USA.,International Ovarian and Testicular Stromal Tumor Registry, Children's Minnesota, Minneapolis, Minnesota, USA.,Cancer and Blood Disorders, Children's Minnesota, Minneapolis, Minnesota, USA
| | - D Ashley Hill
- Department of Pathology and Laboratory Medicine, Children's National Medical Center, Washington, District of Columbia, USA.,ResourcePath LLC, Sterling, Virginia, USA
| | - Kris Ann P Schultz
- International Pleuropulmonary Blastoma/DICER1 Registry, Children's Minnesota, Minneapolis, Minnesota, USA.,International Ovarian and Testicular Stromal Tumor Registry, Children's Minnesota, Minneapolis, Minnesota, USA.,Cancer and Blood Disorders, Children's Minnesota, Minneapolis, Minnesota, USA
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27
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Schultz KAP, Harris AK, Nelson AT, Watson D, Lucas JT, Miniati D, Stewart DR, Hagedorn KN, Mize W, Kamihara J, Mitchell SG, Wilson DB, Gettinger K, Rangaswami AA, Harney LA, Rodriguez Galindo C, Bisogno G, Dehner LP, Hill DA, Messinger YH. Outcomes for Children With Type II and Type III Pleuropulmonary Blastoma Following Chemotherapy: A Report From the International PPB/ DICER1 Registry. J Clin Oncol 2023; 41:778-789. [PMID: 36137255 PMCID: PMC9901992 DOI: 10.1200/jco.21.02925] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 05/11/2022] [Accepted: 08/08/2022] [Indexed: 02/03/2023] Open
Abstract
PURPOSE Pleuropulmonary blastoma (PPB) is the most common primary lung neoplasm of infancy and early childhood. Type II and type III PPB have historically been associated with a poor prognosis. METHODS Patients with known or suspected PPB were enrolled in the International PPB/DICER1 Registry. Medical records were abstracted with follow-up ascertained annually. All PPB diagnoses were confirmed by central pathology review. Beginning in 2007, the IVADo regimen (ifosfamide, vincristine, actinomycin-D, and doxorubicin) was recommended as a potential treatment regimen for children with type II and type III PPB. This regimen was compared with a historical control cohort. RESULTS From 1987 to 2021, 314 children with centrally confirmed type II and type III PPB who received upfront chemotherapy were enrolled; 132 children (75 with type II and 57 with type III) received IVADo chemotherapy. Adjusted analyses suggest improved overall survival for children treated with IVADo in comparison with historical controls with an estimated hazard ratio of 0.65 (95% CI, 0.39 to 1.08). Compared with localized disease, distant metastasis at diagnosis was associated with worse PPB event-free survival and overall survival with hazard ratio of 4.23 (95% CI, 2.42 to 7.38) and 4.69 (95% CI, 2.50 to 8.80), respectively. CONCLUSION The use of IVADo in children with type II and type III PPB resulted in similar-to-improved outcomes compared with historical controls. Inferior outcomes with metastatic disease suggest the need for novel therapies. This large cohort of uniformly treated children with advanced PPB serves as a benchmark for future multicenter therapeutic studies for this rare pediatric tumor.
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Affiliation(s)
- Kris Ann P. Schultz
- International Pleuropulmonary Blastoma/DICER1 Registry, Children's Minnesota, Minneapolis, MN
- International Ovarian and Testicular Stromal Tumor Registry, Children's Minnesota, Minneapolis, MN
- Cancer and Blood Disorders, Children's Minnesota, Minneapolis, MN
| | - Anne K. Harris
- International Pleuropulmonary Blastoma/DICER1 Registry, Children's Minnesota, Minneapolis, MN
- International Ovarian and Testicular Stromal Tumor Registry, Children's Minnesota, Minneapolis, MN
- Cancer and Blood Disorders, Children's Minnesota, Minneapolis, MN
| | - Alexander T. Nelson
- International Pleuropulmonary Blastoma/DICER1 Registry, Children's Minnesota, Minneapolis, MN
- International Ovarian and Testicular Stromal Tumor Registry, Children's Minnesota, Minneapolis, MN
- Cancer and Blood Disorders, Children's Minnesota, Minneapolis, MN
- University of Minnesota Medical School, Minneapolis, MN
| | - Dave Watson
- Research Institute, Children's Minnesota, Minneapolis, MN
| | - John T. Lucas
- Department of Radiation Oncology, St Jude Children's Research Hospital, Memphis, TN
| | - Doug Miniati
- Division of Pediatric Surgery, Kaiser Permanente Northern California, Roseville, CA
| | - Douglas R. Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD
| | | | - William Mize
- Department of Radiology, Children's Minnesota, Minneapolis, MN
| | - Junne Kamihara
- Pediatric Oncology, Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA
| | - Sarah G. Mitchell
- Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA
| | - David B. Wilson
- Department of Pediatrics, Washington University School of Medicine, St Louis Children's Hospital, St Louis, MO
| | - Katie Gettinger
- Department of Pediatrics, Washington University School of Medicine, St Louis Children's Hospital, St Louis, MO
| | - Arun A. Rangaswami
- Division of Pediatric Hematology and Oncology, University of California San Francisco, San Francisco, CA
| | | | | | - Gianni Bisogno
- Hematology, Oncology and Stem Cell Transplant Division, Department of Women's and Children's Health, University of Padova, Padova, Italy
| | - Louis P. Dehner
- Lauren V. Ackerman Laboratory of Surgical Pathology, Department of Pathology and Immunology, Washington University School of Medicine, St Louis, MO
| | - D. Ashley Hill
- Division of Pathology, Children's National Medical Center, George Washington University School of Medicine and Health Sciences, Washington, DC
- ResourcePath LLC, Sterling, VA
| | - Yoav H. Messinger
- International Pleuropulmonary Blastoma/DICER1 Registry, Children's Minnesota, Minneapolis, MN
- International Ovarian and Testicular Stromal Tumor Registry, Children's Minnesota, Minneapolis, MN
- Cancer and Blood Disorders, Children's Minnesota, Minneapolis, MN
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28
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Kim J, Karyadi DM, Hartley SW, Zhu B, Wang M, Wu D, Song L, Armstrong GT, Bhatia S, Robison LL, Yasui Y, Carter B, Sampson JN, Freedman ND, Goldstein AM, Mirabello L, Chanock SJ, Morton LM, Savage SA, Stewart DR. Inflated expectations: Rare-variant association analysis using public controls. PLoS One 2023; 18:e0280951. [PMID: 36696392 PMCID: PMC9876209 DOI: 10.1371/journal.pone.0280951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 01/12/2023] [Indexed: 01/26/2023] Open
Abstract
The use of publicly available sequencing datasets as controls (hereafter, "public controls") in studies of rare variant disease associations has great promise but can increase the risk of false-positive discovery. The specific factors that could contribute to inflated distribution of test statistics have not been systematically examined. Here, we leveraged both public controls, gnomAD v2.1 and several datasets sequenced in our laboratory to systematically investigate factors that could contribute to the false-positive discovery, as measured by λΔ95, a measure to quantify the degree of inflation in statistical significance. Analyses of datasets in this investigation found that 1) the significantly inflated distribution of test statistics decreased substantially when the same variant caller and filtering pipelines were employed, 2) differences in library prep kits and sequencers did not affect the false-positive discovery rate and, 3) joint vs. separate variant-calling of cases and controls did not contribute to the inflation of test statistics. Currently available methods do not adequately adjust for the high false-positive discovery. These results, especially if replicated, emphasize the risks of using public controls for rare-variant association tests in which individual-level data and the computational pipeline are not readily accessible, which prevents the use of the same variant-calling and filtering pipelines on both cases and controls. A plausible solution exists with the emergence of cloud-based computing, which can make it possible to bring containerized analytical pipelines to the data (rather than the data to the pipeline) and could avert or minimize these issues. It is suggested that future reports account for this issue and provide this as a limitation in reporting new findings based on studies that cannot practically analyze all data on a single pipeline.
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Affiliation(s)
- Jung Kim
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, United States of America
| | - Danielle M. Karyadi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, United States of America
| | - Stephen W. Hartley
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, United States of America
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, United States of America
| | - Mingyi Wang
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, United States of America
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Dongjing Wu
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, United States of America
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, United States of America
| | - Lei Song
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, United States of America
| | - Gregory T. Armstrong
- Department of Epidemiology and Cancer Control, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Smita Bhatia
- Institute for Cancer Outcomes and Survivorship, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Leslie L. Robison
- Department of Epidemiology and Cancer Control, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Yutaka Yasui
- Department of Epidemiology and Cancer Control, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Brian Carter
- Department of Population Science, American Cancer Society, Atlanta, Georgia, United States of America
| | - Joshua N. Sampson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, United States of America
| | - Neal D. Freedman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, United States of America
| | - Alisa M. Goldstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, United States of America
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, United States of America
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, United States of America
| | - Lindsay M. Morton
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, United States of America
| | - Sharon A. Savage
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, United States of America
| | - Douglas R. Stewart
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland, United States of America
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29
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Kim J, Vaksman Z, Egolf LE, Kaufman R, Evans JP, Conkrite KL, Danesh A, Lopez G, Randall MP, Dent MH, Farra LM, Menghani N, Dymek M, Desai H, Hausler R, Auvil JG, Gerhard DS, Hakonarson H, Maxwell KN, Cole KA, Pugh TJ, Bosse KR, Khan J, Wei JS, Maris JM, Stewart DR, Diskin SJ. Germline pathogenic variants in 786 neuroblastoma patients. medRxiv 2023:2023.01.23.23284864. [PMID: 36747619 PMCID: PMC9901064 DOI: 10.1101/2023.01.23.23284864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Importance Neuroblastoma accounts for 12% of childhood cancer deaths. The genetic contribution of rare pathogenic germline variation in patients without a family history remains unclear. Objective To define the prevalence, spectrum, and clinical significance of pathogenic germline variation in cancer predisposition genes (CPGs) in neuroblastoma patients. Design Setting and Participants Germline DNA sequencing was performed on the peripheral blood from 786 neuroblastoma patients unselected for family history. Rare variants mapping to CPGs were evaluated for pathogenicity and the percentage of cases harboring pathogenic (P) or likely pathogenic (LP) variants was quantified. The frequency of CPG P-LP variants in neuroblastoma cases was compared to two distinct cancer-free control cohorts to assess enrichment. Matched tumor DNA sequencing was evaluated for "second hits" at CPGs and germline DNA array data from 5,585 neuroblastoma cases and 23,505 cancer-free control children was analyzed to identify rare germline copy number variants (CNVs) affecting genes with an excess burden of P-LP variants in neuroblastoma. Neuroblastoma patients with germline P-LP variants were compared to those without P-LP variants to test for association with clinical characteristics, tumor features, and patient survival. Main Outcomes and Measures Rare variant prevalence, pathogenicity, enrichment, and association with clinical characteristics, tumor features, and patient survival. Results We observed 116 P-LP variants in CPGs involving 13.9% (109/786) of patients, representing a significant excess burden of P-LP variants compared to controls (9.1%; P = 5.14 × 10-5, Odds Ratio: 1.60, 95% confidence interval: 1.27-2.00). BARD1 harbored the most significant burden of P-LP variants compared to controls (1.0% vs. 0.03%; P = 8.18 × 10-7; Odds Ratio: 32.30, 95% confidence interval: 6.44-310.35). Rare germline CNVs disrupting BARD1 were also identified in neuroblastoma patients (0.05%) but absent in controls (P = 7.08 × 10-3; Odds Ratio: 29.47, 95% confidence interval: 1.52 - 570.70). Overall, P-LP variants in DNA repair genes in this study were enriched in cases compared to controls (8.1% vs. 5.7%; P = 0.01; Odds Ratio: 1.45, 95% confidence interval: 1.08-1.92). Neuroblastoma patients harboring a germline P-LP variant had a worse overall survival when compared to patients without P-LP variants (P = 8.6 × 10-3), and this remained significant in a multivariate Cox proportional-hazards model (P = 0.01). Conclusions and Relevance Neuroblastoma patients harboring germline P-LP variants in CPGs have worse overall survival and BARD1 is an important predisposition gene affected by both common and rare pathogenic variation. Germline sequencing should be performed for all neuroblastoma patients at diagnosis to inform genetic counseling and support future longitudinal and mechanistic studies. Patients with a germline P-LP variant should be closely monitored, regardless of risk group assignment.
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Affiliation(s)
- Jung Kim
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, USA
| | - Zalman Vaksman
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Laura E. Egolf
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Rebecca Kaufman
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - J. Perry Evans
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Karina L. Conkrite
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Arnavaz Danesh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, ON, M5S Canada
| | - Gonzalo Lopez
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Michael P. Randall
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Maiah H. Dent
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Lance M. Farra
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Neil Menghani
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Malwina Dymek
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Heena Desai
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ryan Hausler
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Penn Medicine BioBank
- Penn Medicine BioBank, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | | | | | - Hakon Hakonarson
- Center for Applied Genomics, Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kara N. Maxwell
- Division of Hematology/Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Kristina A. Cole
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Trevor J. Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, ON, M5S Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, ON, M5S Canada
| | - Kristopher R. Bosse
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Javed Khan
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Jun S. Wei
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - John M. Maris
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Douglas R. Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, USA
| | - Sharon J. Diskin
- Department of Biomedical and Health Informatics, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Division of Oncology and Center for Childhood Cancer Research, Children’s Hospital of Philadelphia, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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30
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Beck DB, Bodian DL, Shah V, Mirshahi UL, Kim J, Ding Y, Magaziner SJ, Strande NT, Cantor A, Haley JS, Cook A, Hill W, Schwartz AL, Grayson PC, Ferrada MA, Kastner DL, Carey DJ, Stewart DR. Estimated Prevalence and Clinical Manifestations of UBA1 Variants Associated With VEXAS Syndrome in a Clinical Population. JAMA 2023; 329:318-324. [PMID: 36692560 PMCID: PMC10408261 DOI: 10.1001/jama.2022.24836] [Citation(s) in RCA: 54] [Impact Index Per Article: 54.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 12/26/2022] [Indexed: 01/25/2023]
Abstract
IMPORTANCE VEXAS (vacuoles, E1-ubiquitin-activating enzyme, X-linked, autoinflammatory, somatic) syndrome is a disease with rheumatologic and hematologic features caused by somatic variants in UBA1. Pathogenic variants are associated with a broad spectrum of clinical manifestations. Knowledge of prevalence, penetrance, and clinical characteristics of this disease have been limited by ascertainment biases based on known phenotypes. OBJECTIVE To determine the prevalence of pathogenic variants in UBA1 and associated clinical manifestations in an unselected population using a genomic ascertainment approach. DESIGN, SETTING, AND PARTICIPANTS This retrospective observational study evaluated UBA1 variants in exome data from 163 096 participants within the Geisinger MyCode Community Health Initiative. Clinical phenotypes were determined from Geisinger electronic health record data from January 1, 1996, to January 1, 2022. EXPOSURES Exome sequencing was performed. MAIN OUTCOMES AND MEASURES Outcome measures included prevalence of somatic UBA1 variation; presence of rheumatologic, hematologic, pulmonary, dermatologic, and other findings in individuals with somatic UBA1 variation on review of the electronic health record; review of laboratory data; bone marrow biopsy pathology analysis; and in vitro enzymatic assays. RESULTS In 163 096 participants (mean age, 52.8 years; 94% White; 61% women), 11 individuals harbored likely somatic variants at known pathogenic UBA1 positions, with 11 of 11 (100%) having clinical manifestations consistent with VEXAS syndrome (9 male, 2 female). A total of 5 of 11 individuals (45%) did not meet criteria for rheumatologic and/or hematologic diagnoses previously associated with VEXAS syndrome; however, all individuals had anemia (hemoglobin: mean, 7.8 g/dL; median, 7.5 g/dL), which was mostly macrocytic (10/11 [91%]) with concomitant thrombocytopenia (10/11 [91%]). Among the 11 patients identified, there was a pathogenic variant in 1 male participant prior to onset of VEXAS-related signs or symptoms and 2 female participants had disease with heterozygous variants. A previously unreported UBA1 variant (c.1861A>T; p.Ser621Cys) was found in a symptomatic patient, with in vitro data supporting a catalytic defect and pathogenicity. Together, disease-causing UBA1 variants were found in 1 in 13 591 unrelated individuals (95% CI, 1:7775-1:23 758), 1 in 4269 men older than 50 years (95% CI, 1:2319-1:7859), and 1 in 26 238 women older than 50 years (95% CI, 1:7196-1:147 669). CONCLUSIONS AND RELEVANCE This study provides an estimate of the prevalence and a description of the clinical manifestations of UBA1 variants associated with VEXAS syndrome within a single regional health system in the US. Additional studies are needed in unselected and genetically diverse populations to better define general population prevalence and phenotypic spectrum.
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Affiliation(s)
- David B. Beck
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
- Center for Human Genetics and Genomics, New York University School of Medicine
- Division of Rheumatology, Department of Medicine, New York University School of Medicine
| | | | - Vandan Shah
- Department of Molecular and Functional Genomics, Geisinger, Danville, Pennsylvania
| | - Uyenlinh L. Mirshahi
- Department of Molecular and Functional Genomics, Geisinger, Danville, Pennsylvania
| | - Jung Kim
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland
| | - Yi Ding
- Department of Laboratory Medicine, Geisinger, Danville, Pennsylvania
| | - Samuel J. Magaziner
- Center for Human Genetics and Genomics, New York University School of Medicine
| | - Natasha T. Strande
- Department of Molecular and Functional Genomics, Geisinger, Danville, Pennsylvania
| | - Anna Cantor
- Center for Human Genetics and Genomics, New York University School of Medicine
- Division of Rheumatology, Department of Medicine, New York University School of Medicine
| | - Jeremy S. Haley
- Department of Molecular and Functional Genomics, Geisinger, Danville, Pennsylvania
| | - Adam Cook
- Department of Molecular and Functional Genomics, Geisinger, Danville, Pennsylvania
| | - Wesley Hill
- Department of Molecular and Functional Genomics, Geisinger, Danville, Pennsylvania
| | - Alan L. Schwartz
- Department of Pediatrics, Washington University in St Louis, Missouri
| | - Peter C. Grayson
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland
| | - Marcela A. Ferrada
- National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland
| | - Daniel L. Kastner
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - David J. Carey
- Department of Molecular and Functional Genomics, Geisinger, Danville, Pennsylvania
| | - Douglas R. Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland
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31
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Ney G, Gross A, Livinski A, Kratz CP, Stewart DR. Cancer incidence and surveillance strategies in individuals with RASopathies. Am J Med Genet C Semin Med Genet 2022; 190:530-540. [PMID: 36533693 PMCID: PMC9825668 DOI: 10.1002/ajmg.c.32018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/15/2022] [Accepted: 11/20/2022] [Indexed: 12/24/2022]
Abstract
RASopathies are a set of clinical syndromes that have molecular and clinical overlap. Genetically, these syndromes are defined by germline pathogenic variants in RAS/MAPK pathway genes resulting in activation of this pathway. Clinically, their common molecular signature leads to comparable phenotypes, including cardiac anomalies, neurologic disorders and notably, elevated cancer risk. Cancer risk in individuals with RASopathies has been estimated from retrospective reviews and cohort studies. For example, in Costello syndrome, cancer incidence is significantly elevated over the general population, largely due to solid tumors. In some forms of Noonan syndrome, cancer risk is also elevated over the general population and is enriched for hematologic malignancies. Thus, cancer surveillance guidelines have been developed to monitor for the occurrence of such cancers in individuals with some RASopathies. These include abdominal ultrasound and urinalyses for individuals with Costello syndrome, while complete blood counts and splenic examination are recommended in Noonan syndrome. Improved cancer risk estimates and refinement of surveillance recommendations will improve the care of individuals with RASopathies.
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Affiliation(s)
- Gina Ney
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, Maryland, USA
| | - Andrea Gross
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Alicia Livinski
- National Institutes of Health Library, National Institutes of Health, Bethesda, Maryland, USA
| | - Christian P Kratz
- Department of Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Douglas R Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, Maryland, USA
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32
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Astiazaran-Symonds E, Graham C, Kim J, Tucker MA, Ingvar C, Helgadottir H, Pastorino L, van Doorn R, Sampson JN, Zhu B, Bruno W, Queirolo P, Fornarini G, Sciallero S, Carter B, Hicks B, Hutchinson A, Jones K, Stewart DR, Chanock SJ, Freedman ND, Landi MT, Höiom V, Puig S, Gruis N, Yang XR, Ghiorzo P, Goldstein AM. Gene-Level Associations in Patients With and Without Pathogenic Germline Variants in CDKN2A and Pancreatic Cancer. JCO Precis Oncol 2022; 6:e2200145. [PMID: 36409970 PMCID: PMC10166474 DOI: 10.1200/po.22.00145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/28/2022] [Accepted: 10/03/2022] [Indexed: 11/22/2022] Open
Abstract
PURPOSE Pancreatic ductal adenocarcinoma (PDAC) is a component of familial melanoma due to germline pathogenic variants (GPVs) in CDKN2A. However, it is unclear what role this gene or other genes play in its etiology. MATERIALS AND METHODS We analyzed 189 cancer predisposition genes using parametric rare-variant association (RVA) tests and nonparametric permutation tests to identify gene-level associations in PDAC for patients with (CDKN2A+) and without (CDKN2A-) GPV. Exome sequencing was performed on 84 patients with PDAC, 47 CDKN2A+ and 37 CDKN2A-. After variant filtering, various RVA tests and permutation tests were run separately by CDKN2A status. Genes with the strongest nominal associations were evaluated in patients with PDAC from The Cancer Genome Atlas and the UK Biobank (UKB). A secondary analysis including only GPV from UKB was also performed. RESULTS In RVA tests, ERCC4 and RET showed the most compelling evidence as plausible PDAC candidate genes for CDKN2A+ patients. In contrast, the findings in CDKN2A- patients provided evidence for HMBS, EPCAM, and MRE11 as potential new candidate genes and confirmed ATM, BRCA2, and PALB2 as PDAC genes, consistent with findings in The Cancer Genome Atlas and the UKB. As expected, CDKN2A- patients were more likely to harbor GPVs from the 189 genes investigated. When including only GPVs from UKB, significant associations with PDAC were seen for ATM, BRCA2, and CDKN2A. CONCLUSION These results suggest that variants in other genes likely play a role in PDAC in all patients and that PDAC in CDKN2A+ patients has a distinct etiology from PDAC in CDKN2A- patients.
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Affiliation(s)
- Esteban Astiazaran-Symonds
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, MD
- National Human Genome Research Institute, NIH, Bethesda, MD
- Department of Medicine, College of Medicine-Tucson, University of Arizona, Tucson, AZ
| | - Cole Graham
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, MD
| | - Jung Kim
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, MD
| | | | | | - Hildur Helgadottir
- Department of Oncology Pathology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Lorenza Pastorino
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
- Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
| | - Remco van Doorn
- Department of Dermatology, Leiden University Medical Center, Leiden, the Netherlands
| | - Joshua N. Sampson
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, MD
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, MD
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - William Bruno
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
- Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
| | - Paola Queirolo
- Melanoma Sarcoma and Rare Tumors, IEO European Institute of Oncology, Milano, Italy
| | - Giuseppe Fornarini
- Medical Oncology Unit 1, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | - Stefania Sciallero
- Medical Oncology Unit 1, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
| | | | - Belynda Hicks
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, MD
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, MD
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Kristine Jones
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, MD
- Cancer Genomics Research Laboratory, Leidos Biomedical Research Inc, Frederick National Laboratory for Cancer Research, Frederick, MD
| | | | | | - Neal D. Freedman
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, MD
| | | | - Veronica Höiom
- Department of Oncology Pathology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Susana Puig
- Melanoma Unit, Hospital Clínic de Barcelona, IDIBAPS, Universitat de Barcelona and CIBERER, Barcelona, Spain
| | - Nelleke Gruis
- Department of Dermatology, Leiden University Medical Center, Leiden, the Netherlands
| | - Xiaohong R. Yang
- Division of Cancer Epidemiology and Genetics, NCI, NIH, Bethesda, MD
| | - Paola Ghiorzo
- Genetics of Rare Cancers, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
- Department of Internal Medicine and Medical Specialties, University of Genoa, Genoa, Italy
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33
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Miller DT, Lee K, Abul-Husn NS, Amendola LM, Brothers K, Chung WK, Gollob MH, Gordon AS, Harrison SM, Hershberger RE, Klein TE, Richards CS, Stewart DR, Martin CL. ACMG SF v3.1 list for reporting of secondary findings in clinical exome and genome sequencing: A policy statement of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2022; 24:1407-1414. [DOI: 10.1016/j.gim.2022.04.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 04/01/2022] [Indexed: 11/25/2022] Open
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34
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Golmard L, Vasta LM, Duflos V, Corsini C, d’Enghien CD, McMaster ML, Harney LA, Carr AG, Ling A, Dijoud F, Gauthier A, Miettinen M, Cost NG, Gauthier-Villars M, Orbach D, Irtan S, Haouy S, Schultz KAP, Stoppa-Lyonnet D, Coupier I, Stewart DR, Sirvent N. Testicular Sertoli cell tumour and potentially testicular Leydig cell tumour are features of DICER1 syndrome. J Med Genet 2022; 59:346-350. [PMID: 33782093 PMCID: PMC9743800 DOI: 10.1136/jmedgenet-2020-107434] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 12/19/2020] [Accepted: 01/10/2021] [Indexed: 12/14/2022]
Abstract
DICER1 syndrome is a rare paediatric autosomal dominant inherited disorder predisposing to various benign and malignant tumours. It is caused by a germline pathogenic variant in DICER1, and the second hit for tumour development is usually a missense hotspot pathogenic variant in the DICER1 ribonuclease IIIb domain. While DICER1 predisposing variants account for about 60% of ovarian Sertoli-Leydig cell tumours, no DICER1-related testicular stromal tumours have been described. Here we report the first two cases of testicular stromal tumours in children carrying a DICER1 germline pathogenic variant: a case of Sertoli cell tumour and a case of Leydig cell tumour diagnosed at 2 and 12 years of age, respectively. A somatic DICER1 hotspot pathogenic variant was detected in the Sertoli cell tumour. This report extends the spectrum of DICER1-related tumours to include testicular Sertoli cell tumour and potentially testicular Leydig cell tumour. Diagnosis of a testicular Sertoli cell tumour should prompt DICER1 genetic testing so that patients with a DICER1 germline pathogenic variant can benefit from established surveillance guidelines. DICER1 genetic evaluation may be considered for testicular Leydig cell tumour. Our findings suggest that miRNA dysregulation underlies the aetiology of some testicular stromal tumours.
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Affiliation(s)
- Lisa Golmard
- Department of Genetics, Institut Curie, PSL Research University, Paris, France
| | - Lauren M. Vasta
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA,National Capital Consortium, Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Valérie Duflos
- Department of Pediatric oncology, Montpellier University Hospital, Montpellier, France
| | - Carole Corsini
- Department of Oncogenetics, Montpellier University Hospital, Montpellier, France
| | | | - Mary L. McMaster
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | | | | | | | | | - Arnaud Gauthier
- Department of Pathology, Institut Curie, PSL Research University, Paris, France
| | - Markku Miettinen
- National Cancer Institute Laboratory of Pathology, Bethesda, MD, USA
| | - Nicholas G. Cost
- Department of Surgery, Division of Urology, Pediatric Urology and Urologic Oncology, Department of Pediatrics, Section of Hematology and Oncology, Pediatric Oncology, University of Colorado School of Medicine
| | | | - Daniel Orbach
- SIREDO Oncology Center (Care, Innovation and Research for Children and AYA with Cancer), PSL Research University, Institut Curie, Paris, France
| | - Sabine Irtan
- Department of Pediatric surgery, Trousseau hospital, AP-HP, Paris, France
| | - Stéphanie Haouy
- Department of Pediatric oncology, Montpellier University Hospital, Montpellier, France
| | - Kris Ann P. Schultz
- International Pleuropulmonary Blastoma/DICER1 Registry, Children’s Minnesota, Minneapolis, MN, USA,Cancer and Blood Disorders, Children’s Minnesota, Minneapolis, MN, USA,International Ovarian and Testicular Stromal Tumor Registry, Children’s Minnesota, Minneapolis, MN, USA
| | - Dominique Stoppa-Lyonnet
- Department of Genetics, Institut Curie, PSL Research University, Paris, France,Paris University, Paris, France
| | - Isabelle Coupier
- Department of Oncogenetics, Montpellier University Hospital, Montpellier, France
| | - Douglas R. Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Nicolas Sirvent
- Department of Pediatric oncology, Montpellier University Hospital, Montpellier, France
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González IA, Stewart DR, Schultz KAP, Field AP, Hill DA, Dehner LP. DICER1 tumor predisposition syndrome: an evolving story initiated with the pleuropulmonary blastoma. Mod Pathol 2022; 35:4-22. [PMID: 34599283 PMCID: PMC8695383 DOI: 10.1038/s41379-021-00905-8] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 08/09/2021] [Accepted: 08/09/2021] [Indexed: 02/06/2023]
Abstract
DICER1 syndrome (OMIM 606241, 601200) is a rare autosomal dominant familial tumor predisposition disorder with a heterozygous DICER1 germline mutation. The most common tumor seen clinically is the pleuropulmonary blastoma (PPB), a lung neoplasm of early childhood which is classified on its morphologic features into four types (IR, I, II and III) with tumor progression over time within the first 4-5 years of life from the prognostically favorable cystic type I to the unfavorable solid type III. Following the initial report of PPB, its association with other cystic neoplasms was demonstrated in family studies. The detection of the germline mutation in DICER1 provided the opportunity to identify and continue to recognize a number seemingly unrelated extrapulmonary neoplasms: Sertoli-Leydig cell tumor, gynandroblastoma, embryonal rhabdomyosarcomas of the cervix and other sites, multinodular goiter, differentiated and poorly differentiated thyroid carcinoma, cervical-thyroid teratoma, cystic nephroma-anaplastic sarcoma of kidney, nasal chondromesenchymal hamartoma, intestinal juvenile-like hamartomatous polyp, ciliary body medulloepithelioma, pituitary blastoma, pineoblastoma, primary central nervous system sarcoma, embryonal tumor with multilayered rosettes-like cerebellar tumor, PPB-like peritoneal sarcoma, DICER1-associated presacral malignant teratoid neoplasm and other non-neoplastic associations. Each of these neoplasms is characterized by a second somatic mutation in DICER1. In this review, we have summarized the salient clinicopathologic aspects of these tumors whose histopathologic features have several overlapping morphologic attributes particularly the primitive mesenchyme often with rhabdomyoblastic and chondroid differentiation and an uncommitted spindle cell pattern. Several of these tumors have an initial cystic stage from which there is progression to a high grade, complex patterned neoplasm. These pathologic findings in the appropriate clinical setting should serve to alert the pathologist to the possibility of a DICER1-associated neoplasm and initiate appropriate testing on the neoplasm and to alert the clinician about the concern for a DICER1 mutation.
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Affiliation(s)
- Iván A. González
- grid.239552.a0000 0001 0680 8770Department of Pathology and Laboratory Medicine, Children’s Hospital of Philadelphia, Philadelphia, PA USA
| | - Douglas R. Stewart
- grid.48336.3a0000 0004 1936 8075Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD USA
| | - Kris Ann P. Schultz
- International Pleuropulmonary Blastoma/DICER1 Registry, Children’s Minnesota, Minneapolis, MN USA ,Cancer and Blood Disorders, Children’s Minnesota, Minneapolis, MN USA
| | | | - D. Ashley Hill
- International Pleuropulmonary Blastoma/DICER1 Registry, Children’s Minnesota, Minneapolis, MN USA ,ResourcePath LLC, Sterling, VA USA ,grid.253615.60000 0004 1936 9510Division of Pathology, Children’s National Medical Center, George Washington University School of Medicine and Health Sciences, Washington, DC USA
| | - Louis P. Dehner
- International Pleuropulmonary Blastoma/DICER1 Registry, Children’s Minnesota, Minneapolis, MN USA ,grid.411019.cThe Lauren V. Ackerman Laboratory of Surgical Pathology, Barnes-Jewish and St. Louis Children’s Hospitals, Washington University Medical Center, St. Louis, MO USA
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36
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Pemov A, Wegman-Ostrosky T, Kim J, Koutros S, Douthitt B, Jones K, Zhu B, Baris D, Schwenn M, Johnson A, Karagas MR, Carter BD, McCullough ML, Landi MT, Freedman ND, Albanes D, Silverman DT, Rothman N, Caporaso NE, Greene MH, Fraumeni JF, Stewart DR. Identification of Genetic Risk Factors for Familial Urinary Bladder Cancer: An Exome Sequencing Study. JCO Precis Oncol 2021; 5:PO.21.00115. [PMID: 34964002 PMCID: PMC8710334 DOI: 10.1200/po.21.00115] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 09/21/2021] [Accepted: 11/03/2021] [Indexed: 12/19/2022] Open
Abstract
PURPOSE Previous studies have shown an approximately two-fold elevation in the relative risk of urinary bladder cancer (UBC) among people with a family history that could not be entirely explained by shared environmental exposures, thus suggesting a genetic component in its predisposition. Multiple genome-wide association studies and recent gene panel sequencing studies identified several genetic loci that are associated with UBC risk; however, the list of UBC-associated variants and genes is incomplete. MATERIALS AND METHODS We exome sequenced eight patients from three multiplex UBC pedigrees and a group of 77 unrelated familial UBC cases matched to 241 cancer-free controls. In addition, we examined pathogenic germline variation in 444 candidate genes in 392 The Cancer Genome Atlas UBC cases. RESULTS In the pedigrees, segregating variants were family-specific although the identified genes clustered in common pathways, most notably DNA repair (MLH1 and MSH2) and cellular metabolism (IDH1 and ME1). In the familial UBC group, the proportion of pathogenic and likely pathogenic variants was significantly higher in cases compared with controls (P = .003). Pathogenic and likely pathogenic variant load was also significantly increased in genes involved in cilia biogenesis (P = .001). In addition, a pathogenic variant in CHEK2 (NM_007194.4:c.1100del; p.T367Mfs*15) was over-represented in cases (variant frequency = 2.6%; 95% CI, 0.71 to 6.52) compared with controls (variant frequency = 0.21%; 95% CI, 0.01 to 1.15), but was not statistically significant. CONCLUSION These results point to a complex polygenic predisposition to UBC. Despite heterogeneity, the genes cluster in several biologically relevant pathways and processes, for example, DNA repair, cilia biogenesis, and cellular metabolism. Larger studies are required to determine the importance of CHEK2 in UBC etiology.
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Affiliation(s)
- Alexander Pemov
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - Talia Wegman-Ostrosky
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - Jung Kim
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - Stella Koutros
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - Brenna Douthitt
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - Kristine Jones
- Frederick National Laboratory for Cancer Research, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD
| | - Bin Zhu
- Frederick National Laboratory for Cancer Research, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD
| | - Dalsu Baris
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | | | | | - Margaret R. Karagas
- Department of Epidemiology, Geisel School of Medicine at Dartmouth, Hanover, NH
| | - Brian D. Carter
- Department of Population Science, American Cancer Society, Atlanta, GA
| | | | - Maria Teresa Landi
- Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - Neal D. Freedman
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - Demetrius Albanes
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - Debra T. Silverman
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - Nathaniel Rothman
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - Neil E. Caporaso
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - Mark H. Greene
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - Joseph F. Fraumeni
- Office of the Director, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - Douglas R. Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
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Stewart DR. Insights Into Immune-Mediated Disease and Cancer Risk-Delivering on the Promise of UK Biobank Big Data. JAMA Oncol 2021; 8:219-220. [PMID: 34854873 DOI: 10.1001/jamaoncol.2021.5572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Douglas R Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, Maryland
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38
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Frone MN, Stewart DR, Savage SA, Khincha PP. Quantification of Discordant Variant Interpretations in a Large Family-Based Study of Li-Fraumeni Syndrome. JCO Precis Oncol 2021; 5:PO.21.00320. [PMID: 34805717 PMCID: PMC8594664 DOI: 10.1200/po.21.00320] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 09/22/2021] [Accepted: 10/06/2021] [Indexed: 12/26/2022] Open
Abstract
PURPOSE The use of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology guidelines has improved germline variant classification concordance, but discrepancies persist, sometimes directly affecting medical management. We evaluated variant discordance between and within families with germline TP53 variants in the National Cancer Institute's Li-Fraumeni syndrome longitudinal cohort study. MATERIALS AND METHODS Germline TP53 genetic testing results were obtained from 421 individuals in 140 families. A discordant test result was defined as a report of pathogenicity that differed between two clinical testing laboratories, between a testing laboratory and the ClinVar database, or between either the laboratory or ClinVar database and variant classification by internal study review. RESULTS There were 141 variants in 140 families (one family had two different TP53 variants). Fifty-four families had discordant interpretations (54 of 140, 39%). Sixteen families had discordant classifications leading to clinically important differences in medical management (16 of 140, 11%). Interfamilial discordance was observed between four families (two different variants). Intrafamilial discordance was observed within six families. One family experienced both intrafamilial and interfamilial discordance. CONCLUSION This large single-gene study found discordant germline TP53 variant interpretations in 39% of families studied; 11% had a variant with the potential to significantly affect medical management. This finding is especially concerning in patients with Li-Fraumeni syndrome because of their exceedingly high risks of multiple cancers and intensive cancer screening and risk-reducing recommendations. Centralized data sharing, gene-specific variant curation guidelines, and provider education for consistent variant interpretation are essential for optimal patient care.
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Affiliation(s)
- Megan N Frone
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Douglas R Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Sharon A Savage
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Payal P Khincha
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD
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Zhang T, Joubert P, Ansari-Pour N, Zhao W, Hoang PH, Lokanga R, Moye AL, Rosenbaum J, Gonzalez-Perez A, Martínez-Jiménez F, Castro A, Muscarella LA, Hofman P, Consonni D, Pesatori AC, Kebede M, Li M, Gould Rothberg BE, Peneva I, Schabath MB, Poeta ML, Costantini M, Hirsch D, Heselmeyer-Haddad K, Hutchinson A, Olanich M, Lawrence SM, Lenz P, Duggan M, Bhawsar PMS, Sang J, Kim J, Mendoza L, Saini N, Klimczak LJ, Islam SMA, Otlu B, Khandekar A, Cole N, Stewart DR, Choi J, Brown KM, Caporaso NE, Wilson SH, Pommier Y, Lan Q, Rothman N, Almeida JS, Carter H, Ried T, Kim CF, Lopez-Bigas N, Garcia-Closas M, Shi J, Bossé Y, Zhu B, Gordenin DA, Alexandrov LB, Chanock SJ, Wedge DC, Landi MT. Genomic and evolutionary classification of lung cancer in never smokers. Nat Genet 2021; 53:1348-1359. [PMID: 34493867 PMCID: PMC8432745 DOI: 10.1038/s41588-021-00920-0] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 07/15/2021] [Indexed: 12/26/2022]
Abstract
Lung cancer in never smokers (LCINS) is a common cause of cancer mortality but its genomic landscape is poorly characterized. Here high-coverage whole-genome sequencing of 232 LCINS showed 3 subtypes defined by copy number aberrations. The dominant subtype (piano), which is rare in lung cancer in smokers, features somatic UBA1 mutations, germline AR variants and stem cell-like properties, including low mutational burden, high intratumor heterogeneity, long telomeres, frequent KRAS mutations and slow growth, as suggested by the occurrence of cancer drivers' progenitor cells many years before tumor diagnosis. The other subtypes are characterized by specific amplifications and EGFR mutations (mezzo-forte) and whole-genome doubling (forte). No strong tobacco smoking signatures were detected, even in cases with exposure to secondhand tobacco smoke. Genes within the receptor tyrosine kinase-Ras pathway had distinct impacts on survival; five genomic alterations independently doubled mortality. These findings create avenues for personalized treatment in LCINS.
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Affiliation(s)
- Tongwu Zhang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Philippe Joubert
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Laval University, Quebec City, Quebec, Canada
| | - Naser Ansari-Pour
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Wei Zhao
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Phuc H Hoang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Rachel Lokanga
- Cancer Genomics Section, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Aaron L Moye
- Stem Cell Program and Divisions of Hematology/Oncology and Pulmonary Medicine, Boston Children's Hospital, Boston, MA, USA
| | | | - Abel Gonzalez-Perez
- Institute for Research in Biomedicine Barcelona, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Francisco Martínez-Jiménez
- Institute for Research in Biomedicine Barcelona, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Andrea Castro
- Department of Medicine, Division of Medical Genetics, University of California San Diego, San Diego, CA, USA
| | - Lucia Anna Muscarella
- Laboratory of Oncology, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Paul Hofman
- Laboratory of Clinical and Experimental Pathology, University Hospital Federation OncoAge, Nice Hospital, University Côte d'Azur, Nice, France
| | - Dario Consonni
- Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Angela C Pesatori
- Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Clinical Sciences and Community Health, University of Milan, Milan, Italy
| | - Michael Kebede
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Mengying Li
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Bonnie E Gould Rothberg
- Smilow Cancer Hospital, Yale-New Haven Health, New Haven, CT, USA
- Yale Comprehensive Cancer Center, New Haven, CT, USA
| | - Iliana Peneva
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
- National Institute for Health Research Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford, UK
| | - Matthew B Schabath
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL, USA
| | - Maria Luana Poeta
- Department of Bioscience, Biotechnology and Biopharmaceutics, University of Bari, Bari, Italy
| | - Manuela Costantini
- Department of Urology, Istituto di Ricovero e Cura a Carattere Scientifico Regina Elena National Cancer Institute, Rome, Italy
| | - Daniela Hirsch
- Cancer Genomics Section, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | | | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Mary Olanich
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Scott M Lawrence
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Petra Lenz
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Maire Duggan
- Department of Pathology and Laboratory Medicine, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Praphulla M S Bhawsar
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jian Sang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jung Kim
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Laura Mendoza
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Natalie Saini
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle, NC, USA
| | - Leszek J Klimczak
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, Research Triangle, NC, USA
| | - S M Ashiqul Islam
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California San Diego, San Diego, CA, USA
| | - Burcak Otlu
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California San Diego, San Diego, CA, USA
| | - Azhar Khandekar
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California San Diego, San Diego, CA, USA
| | - Nathan Cole
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Douglas R Stewart
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jiyeon Choi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Kevin M Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Neil E Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Samuel H Wilson
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle, NC, USA
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Qing Lan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Nathaniel Rothman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Jonas S Almeida
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Hannah Carter
- Department of Medicine, Division of Medical Genetics, University of California San Diego, San Diego, CA, USA
| | - Thomas Ried
- Cancer Genomics Section, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Carla F Kim
- Stem Cell Program and Divisions of Hematology/Oncology and Pulmonary Medicine, Boston Children's Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Nuria Lopez-Bigas
- Institute for Research in Biomedicine Barcelona, The Barcelona Institute of Science and Technology, Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | | | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Yohan Bossé
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, Laval University, Quebec City, Quebec, Canada
- Department of Molecular Medicine, Laval University, Quebec City, Quebec, Canada
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Dmitry A Gordenin
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle, NC, USA
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California San Diego, San Diego, CA, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - David C Wedge
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Manchester Cancer Research Centre, The University of Manchester, Manchester, UK
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA.
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40
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Ney GM, Stewart DR. Another Weak Link in the Electron Transport Chain: Variants in SUCLG2 and Risk for Pheochromocytoma and Paraganglioma. J Natl Cancer Inst 2021; 114:7-8. [PMID: 34415349 DOI: 10.1093/jnci/djab160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 08/11/2021] [Indexed: 11/14/2022] Open
Affiliation(s)
- Gina M Ney
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Douglas R Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
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Miller DT, Lee K, Chung WK, Gordon AS, Herman GE, Klein TE, Stewart DR, Amendola LM, Adelman K, Bale SJ, Gollob MH, Harrison SM, Hershberger RE, McKelvey K, Richards CS, Vlangos CN, Watson MS, Martin CL. Correction to: ACMG SF v3.0 list for reporting of secondary findings in clinical exome and genome sequencing: a policy statement of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2021; 23:1582-1584. [PMID: 34345026 PMCID: PMC10764012 DOI: 10.1038/s41436-021-01278-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- David T Miller
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Kristy Lee
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY, USA
| | - Adam S Gordon
- Department of Pharmacology & Center for Genetic Medicine, Northwestern University, Chicago, IL, USA
| | - Gail E Herman
- Professor Emeritus, Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Teri E Klein
- Departments of Biomedical Data Science & Medicine, Stanford University, Stanford, CA, USA
| | - Douglas R Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Laura M Amendola
- Division of Medical Genetics, University of Washington, Seattle, WA, USA
| | | | | | - Michael H Gollob
- Division of Cardiology and Department of Physiology, University of Toronto, Toronto, ON, Canada
| | | | - Ray E Hershberger
- Divisions of Human Genetics and Cardiovascular Medicine, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Kent McKelvey
- Departments of Genetics and Family Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - C Sue Richards
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA
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42
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Dehner LP, Hill DA, Stewart DR, Schultz KAP. Reply: pleuropulmonary blastoma-like peritoneal sarcoma and DICER1-associated sarcomas: toward a unified nomenclature. Mod Pathol 2021; 34:1229-1230. [PMID: 33875804 PMCID: PMC9191827 DOI: 10.1038/s41379-021-00810-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 03/16/2021] [Accepted: 03/16/2021] [Indexed: 11/09/2022]
Affiliation(s)
- Louis P. Dehner
- Department of Pathology and Immunology, Washington
University in St. Louis School of Medicine, St. Louis, Missouri
| | - D. Ashley Hill
- Department of Pathology, Center for Cancer and Immunology
Research, Children’s National Medical Center, Washington D.C
| | - Douglas R. Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology
and Genetics, National Cancer Institute, Rockville, Maryland
| | - Kris Ann P. Schultz
- International Pleuropulmonary
Blastoma/DICER1 Registry, Children’s Minnesota,
Minneapolis, Minnesota,Cancer and Blood Disorders Program, Children’s
Minnesota, Minneapolis, Minnesota
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43
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Miller DT, Lee K, Chung WK, Gordon AS, Herman GE, Klein TE, Stewart DR, Amendola LM, Adelman K, Bale SJ, Gollob MH, Harrison SM, Hershberger RE, McKelvey K, Richards CS, Vlangos CN, Watson MS, Martin CL. ACMG SF v3.0 list for reporting of secondary findings in clinical exome and genome sequencing: a policy statement of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2021; 23:1381-1390. [PMID: 34012068 DOI: 10.1038/s41436-021-01172-3] [Citation(s) in RCA: 268] [Impact Index Per Article: 89.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 03/26/2021] [Accepted: 03/26/2021] [Indexed: 01/17/2023] Open
Affiliation(s)
- David T Miller
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Kristy Lee
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY, USA
| | - Adam S Gordon
- Department of Pharmacology & Center for Genetic Medicine, Northwestern University, Chicago, IL, USA
| | - Gail E Herman
- Professor Emeritus, Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Teri E Klein
- Departments of Biomedical Data Science & Medicine, Stanford University, Stanford, CA, USA
| | - Douglas R Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Laura M Amendola
- Division of Medical Genetics, University of Washington, Seattle, WA, USA
| | | | | | - Michael H Gollob
- Division of Cardiology and Department of Physiology, University of Toronto, Toronto, ON, Canada
| | | | - Ray E Hershberger
- Divisions of Human Genetics and Cardiovascular Medicine, Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Kent McKelvey
- Departments of Genetics and Family Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - C Sue Richards
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA
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Nelson A, Harris A, Watson D, Pyper SR, Hall N, Kamihara J, Stewart DR, Dehner LP, Hill DA, Messinger YH, Frazier LL, Billmire DF, Schneider DT, Schultz KAP. Stage I Sertoli-Leydig cell tumors: An interim report from the International PPB/ DICER1 & OTST Registry. J Clin Oncol 2021. [DOI: 10.1200/jco.2021.39.15_suppl.5547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
5547 Background: Sertoli-Leydig cell tumors (SLCT) are rare ovarian sex cord-stromal tumors which occur primarily in adolescents and young adults and are associated with DICER1 pathogenic variants. Methods: Informed consent for participation in the International PPB/ DICER1 or OTST Registry was obtained. When available, pathology was centrally reviewed. Staging was evaluated by Registry review using the International Federation of Gynecology and Obstetrics (FIGO) classification system. Results: Eighty-three patients with stage I SLCT were enrolled. Median age at diagnosis was 15 (range 1-60) years. Most (57/83) patients had germline DICER1 testing; 35/57 (61%) had germline pathogenic variants. Fifty-six patients had Ia and 27 had Ic SLCT. The distribution of patients receiving chemo based on histology and stage is displayed in Table. One patient with poorly differentiated stage Ia SLCT with sarcomatous elements and no chemo at diagnosis recurred 6 months after surgery and died of disease. Three patients with local diagnosis of stage Ia SLCT, with data unavailable for Registry confirmation of stage, developed a subsequent SLCT 33 to 74 months after diagnosis; of these, 2 died, and 1 remains in treatment for recurrence. Available records and molecular testing in these 3 cases have not provided a distinction between recurrent and metachronous disease. Excluding the latter 3 patients, 3-year overall survival was 97.3% for stage Ia SLCT. Six patients with stage Ic SLCT recurred (Stage Ic1=5 and Stage Ic2=1) with a median time to recurrence of 25 (range 3-53) months. In stage Ic1, 18% (2/11) recurred after upfront chemo compared to 33% (3/9) after surgery alone. Of the 5 patients with stage Ic1 disease that recurred, 4 had intermediate and 1 had poorly differentiated SLCT. One patient had sarcomatous elements and 2 received upfront chemo. Two of the 5 patients are alive, neither received upfront chemo. One patient with poorly differentiated stage Ic2 SLCT with sarcomatous elements and no upfront chemo recurred and died of disease. Three-year event free and overall survival were 86.9 and 88.6% for stage Ic SLCT. Four patients had metachronous SLCT in the contralateral ovary confirmed by clinical review or somatic testing at a median time from diagnosis of 33 (range 28-104) months. All 4 have germline pathogenic variants and no evidence of disease at last follow-up. Conclusions: Individuals with early stage SLCT generally fare well, however, ongoing surveillance for recurrence and metachronous disease is indicated. Novel therapies are needed to address recurrent SLCT.[Table: see text]
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Affiliation(s)
| | - Anne Harris
- Children's Hospitals and Clinics of Minnesota, Minneapolis, MN
| | - Dave Watson
- Children's Hospital and Clinics of Minnesota, Minneapolis, MN
| | | | | | - Junne Kamihara
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Boston, MA
| | - Douglas R Stewart
- National Institutes of Health/National Cancer Institute, Rockville, MD
| | | | - D. Ashley Hill
- ResourcePath Laboratory, Sterling, VA and Center for Cancer and Immunology Research, Children's National Health System, Washington, DC
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Tischkowitz M, Balmaña J, Foulkes WD, James P, Ngeow J, Schmutzler R, Voian N, Wick MJ, Stewart DR, Pal T. Management of individuals with germline variants in PALB2: a clinical practice resource of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2021; 23:1416-1423. [PMID: 33976419 DOI: 10.1038/s41436-021-01151-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/04/2021] [Accepted: 03/08/2021] [Indexed: 12/16/2022] Open
Abstract
PURPOSE PALB2 germline pathogenic variants are associated with increased breast cancer risk and smaller increased risk of pancreatic and likely ovarian cancer. Resources for health-care professionals managing PALB2 heterozygotes are currently limited. METHODS A workgroup of experts sought to outline management of PALB2 heterozygotes based on current evidence. Peer-reviewed publications from PubMed were identified to guide recommendations, which arose by consensus and the collective expertise of the authors. RESULTS PALB2 heterozygotes should be offered BRCA1/2-equivalent breast surveillance. Risk-reducing mastectomy can be considered guided by personalized risk estimates. Pancreatic cancer surveillance should be considered, but ideally as part of a clinical trial. Typically, ovarian cancer surveillance is not recommended, and risk-reducing salpingo-oophorectomy should only rarely be considered before the age of 50. Given the mechanistic similarities, PALB2 heterozygotes should be considered for therapeutic regimens and trials as those for BRCA1/2. CONCLUSION This guidance is similar to those for BRCA1/2. While the range of the cancer risk estimates overlap with BRCA1/2, point estimates are lower in PALB2 so individualized estimates are important for management decisions. Systematic prospective data collection is needed to determine as yet unanswered questions such as the risk of contralateral breast cancer and survival after cancer diagnosis.
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Affiliation(s)
- Marc Tischkowitz
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - Judith Balmaña
- Hereditary Cancer Genetics Group, Vall d'Hebron Institute of Oncology (VHIO) and 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
| | - Joanne Ngeow
- Genomic Medicine, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore.,Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre, Singapore, Singapore
| | - Rita Schmutzler
- Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany.,University Hospital of Cologne, Center of Integrated Oncology, CIO and Center of Familial Breast and Ovarian Cancer, Cologne, Germany
| | - Nicoleta Voian
- Genetic Risk Clinic, Providence Cancer Institute, Portland, OR, USA
| | - Myra J Wick
- Departments of Obstetrics and Gynecology and Clinical Genomics, Mayo Clinic, Rochester, MN, USA
| | - Douglas R Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Tuya Pal
- Department of Medicine, Vanderbilt University Medical Center/Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
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Pemov A, Hansen NF, Sindiri S, Patidar R, Higham CS, Dombi E, Miettinen MM, Fetsch P, Brems H, Chandrasekharappa SC, Jones K, Zhu B, Wei JS, Mullikin JC, Wallace MR, Khan J, Legius E, Widemann BC, Stewart DR. Low mutation burden and frequent loss of CDKN2A/B and SMARCA2, but not PRC2, define premalignant neurofibromatosis type 1-associated atypical neurofibromas. Neuro Oncol 2021; 21:981-992. [PMID: 30722027 DOI: 10.1093/neuonc/noz028] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Neurofibromatosis type 1 (NF1) is a tumor-predisposition disorder caused by germline mutations in NF1. NF1 patients have an 8-16% lifetime risk of developing a malignant peripheral nerve sheath tumor (MPNST), a highly aggressive soft-tissue sarcoma, often arising from preexisting benign plexiform neurofibromas (PNs) and atypical neurofibromas (ANFs). ANFs are distinct from both PN and MPNST, representing an intermediate step in malignant transformation. METHODS In the first comprehensive genomic analysis of ANF originating from multiple patients, we performed tumor/normal whole-exome sequencing (WES) of 16 ANFs. In addition, we conducted WES of 3 MPNSTs, copy-number meta-analysis of 26 ANFs and 28 MPNSTs, and whole transcriptome sequencing analysis of 5 ANFs and 5 MPNSTs. RESULTS We identified a low number of mutations (median 1, range 0-5) in the exomes of ANFs (only NF1 somatic mutations were recurrent), and frequent deletions of CDKN2A/B (69%) and SMARCA2 (42%). We determined that polycomb repressor complex 2 (PRC2) genes EED and SUZ12 were frequently mutated, deleted, or downregulated in MPNSTs but not in ANFs. Our pilot gene expression study revealed upregulated NRAS, MDM2, CCND1/2/3, and CDK4/6 in ANFs and MPNSTs, and overexpression of EZH2 in MPNSTs only. CONCLUSIONS The PN-ANF transition is primarily driven by the deletion of CDKN2A/B. Further progression from ANF to MPNST likely involves broad chromosomal rearrangements and frequent inactivation of the PRC2 genes, loss of the DNA repair genes, and copy-number increase of signal transduction and cell-cycle and pluripotency self-renewal genes.
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Affiliation(s)
- Alexander Pemov
- Clinical Genetics Branch, DCEG, NCI, National Institutes of Health (NIH), Rockville, Maryland, USA
| | - Nancy F Hansen
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, NIH, Rockville, Maryland, USA
| | - Sivasish Sindiri
- Genetics Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, USA
| | - Rajesh Patidar
- Genetics Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, USA.,Molecular Characterization & Clinical Assay Development Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, Maryland, USA
| | - Christine S Higham
- Children's National Medical Center, Washington, DC, USA.,Pediatric Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, USA
| | - Eva Dombi
- Pediatric Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, USA
| | | | | | - Hilde Brems
- Department of Human Genetics, Catholic University Leuven, Leuven, Belgium
| | - Settara C Chandrasekharappa
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, NIH, Rockville, Maryland, USA
| | - Kristine Jones
- Cancer Genomics Research Laboratory, DCEG, NIH, Rockville, Maryland, USA
| | - Bin Zhu
- Cancer Genomics Research Laboratory, DCEG, NIH, Rockville, Maryland, USA
| | - Jun S Wei
- Genetics Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, USA
| | | | | | - James C Mullikin
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, NIH, Rockville, Maryland, USA.,NISC, National Human Genome Research Institute, NIH, Rockville, Maryland, USA
| | - Margaret R Wallace
- Department of Molecular Genetics and Microbiology, UF Genetics Institute, UF Health Cancer Center, University of Florida, Gainesville, Florida, USA
| | - Javed Khan
- Genetics Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, USA
| | - Eric Legius
- Department of Human Genetics, Catholic University Leuven, Leuven, Belgium
| | - Brigitte C Widemann
- Pediatric Oncology Branch, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, USA
| | - Douglas R Stewart
- Clinical Genetics Branch, DCEG, NCI, National Institutes of Health (NIH), Rockville, Maryland, USA
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47
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Bhala S, Stewart DR, Kennerley V, Petkov VI, Rosenberg PS, Best AF. Incidence of Benign Meningiomas in the United States: Current and Future Trends. JNCI Cancer Spectr 2021; 5:pkab035. [PMID: 34250440 DOI: 10.1093/jncics/pkab035] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/16/2021] [Accepted: 03/17/2021] [Indexed: 12/13/2022] Open
Abstract
Background Benign meningiomas are the most frequently reported central nervous system tumors in the United States, with increasing incidence in past decades. However, the future trajectory of this neoplasm remains unclear. Methods We analyzed benign meningioma incidence of cases identified by any means (eg, radiographically with or without microscopic confirmation) in US Surveillance, Epidemiology, and End Results cancer registries among groups aged 35 to 84 years during 2004-2017 by sex and race and ethnicity using age-period-cohort models. We employed age-period-cohort forecasting models to glean insights regarding the etiology, distribution, and anticipated future (2018-2027) public health impact of this neoplasm. Results In all groups, meningioma incidence overall increased through 2010, then stabilized. Temporal declines were statistically significant overall and in most groups. JoinPoint analysis of cohort rate-ratios identified substantial acceleration in White men born after 1963 (from 1.1% to 3.2% per birth year); cohort rate-ratios were stable or increasing in all groups and all birth cohorts. We forecast that meningioma incidence through 2027 will remain stable or decrease among groups aged 55-84 years but remain similar to current levels among groups aged 35-54 years. The case count of total meningioma burden in 2027 is expected to be approximately 30 470, similar to the expected case count of 27 830 in 2018. Conclusions Between 2004 and 2017, overall incidence of benign meningioma increased and then stabilized or declined. For 2018-2027, our forecast is incidence will remain generally stable in younger age groups but decrease in older age groups. Nonetheless, the total future burden will remain similar to current levels because the population is aging.
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Affiliation(s)
- Sonia Bhala
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, USA
| | - Douglas R Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, USA
| | - Victoria Kennerley
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, USA
| | - Valentina I Petkov
- Surveillance Research Program, Division of Cancer Control and Population Sciences, National Cancer Institute, NIH, Rockville, MD, USA
| | - Philip S Rosenberg
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD, USA
| | - Ana F Best
- Biostatistics Branch, Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, NIH, Rockville, MD, USA
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48
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Kim J, Gianferante M, Karyadi DM, Hartley SW, Frone MN, Luo W, Robison LL, Armstrong GT, Bhatia S, Dean M, Yeager M, Zhu B, Song L, Sampson JN, Yasui Y, Leisenring WM, Brodie SA, de Andrade KC, Fortes FP, Goldstein AM, Khincha PP, Machiela MJ, McMaster ML, Nickerson ML, Oba L, Pemov A, Pinheiro M, Rotunno M, Santiago K, Wegman-Ostrosky T, Diver WR, Teras L, Freedman ND, Hicks BD, Zhu B, Wang M, Jones K, Hutchinson AA, Dagnall C, Savage SA, Tucker MA, Chanock SJ, Morton LM, Stewart DR, Mirabello L. Frequency of Pathogenic Germline Variants in Cancer-Susceptibility Genes in the Childhood Cancer Survivor Study. JNCI Cancer Spectr 2021; 5:pkab007. [PMID: 34308104 PMCID: PMC8023430 DOI: 10.1093/jncics/pkab007] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 12/01/2020] [Accepted: 12/22/2020] [Indexed: 11/13/2022] Open
Abstract
Background Pediatric cancers are the leading cause of death by disease in children despite improved survival rates overall. The contribution of germline genetic susceptibility to pediatric cancer survivors has not been extensively characterized. We assessed the frequency of pathogenic or likely pathogenic (P/LP) variants in 5451 long-term pediatric cancer survivors from the Childhood Cancer Survivor Study. Methods Exome sequencing was conducted on germline DNA from 5451 pediatric cancer survivors (cases who survived ≥5 years from diagnosis; n = 5105 European) and 597 European cancer-free adults (controls). Analyses focused on comparing the frequency of rare P/LP variants in 237 cancer-susceptibility genes and a subset of 60 autosomal dominant high-to-moderate penetrance genes, for both case-case and case-control comparisons. Results Of European cases, 4.1% harbored a P/LP variant in high-to-moderate penetrance autosomal dominant genes compared with 1.3% in controls (2-sided P = 3 × 10-4). The highest frequency of P/LP variants was in genes typically associated with adult onset rather than pediatric cancers, including BRCA1/2, FH, PALB2, PMS2, and CDKN2A. A statistically significant excess of P/LP variants, after correction for multiple tests, was detected in patients with central nervous system cancers (NF1, SUFU, TSC1, PTCH2), Wilms tumor (WT1, REST), non-Hodgkin lymphoma (PMS2), and soft tissue sarcomas (SDHB, DICER1, TP53, ERCC4, FGFR3) compared with other pediatric cancers. Conclusion In long-term pediatric cancer survivors, we identified P/LP variants in cancer-susceptibility genes not previously associated with pediatric cancer as well as confirmed known associations. Further characterization of variants in these genes in pediatric cancer will be important to provide optimal genetic counseling for patients and their families.
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Affiliation(s)
- Jung Kim
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Matthew Gianferante
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Danielle M Karyadi
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Stephen W Hartley
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Megan N Frone
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Wen Luo
- Cancer Genomics Research Laboratory, Frederick
National Laboratory for Cancer Research, Frederick, MD, USA
| | - Leslie L Robison
- Department of Epidemiology and Cancer Control, St.
Jude Children’s Research Hospital, Memphis, TN, USA
| | - Gregory T Armstrong
- Department of Epidemiology and Cancer Control, St.
Jude Children’s Research Hospital, Memphis, TN, USA
| | - Smita Bhatia
- Institute for Cancer Outcomes and Survivorship,
University of Alabama at Birmingham, Birmingham, AL, USA
| | - Michael Dean
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick
National Laboratory for Cancer Research, Frederick, MD, USA
| | - Meredith Yeager
- Cancer Genomics Research Laboratory, Frederick
National Laboratory for Cancer Research, Frederick, MD, USA
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Lei Song
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Joshua N Sampson
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Yutaka Yasui
- Department of Epidemiology and Cancer Control, St.
Jude Children’s Research Hospital, Memphis, TN, USA
| | - Wendy M Leisenring
- Cancer Prevention and Clinical Statistics Programs,
Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Seth A Brodie
- Cancer Genomics Research Laboratory, Frederick
National Laboratory for Cancer Research, Frederick, MD, USA
| | - Kelvin C de Andrade
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Fernanda P Fortes
- International Research Center, A.C. Camargo Cancer
Center, São Paulo, Brazil
| | - Alisa M Goldstein
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Payal P Khincha
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Mary L McMaster
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Michael L Nickerson
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Leatrisse Oba
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Alexander Pemov
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Maisa Pinheiro
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Melissa Rotunno
- Division of Cancer Control and Population Sciences,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Karina Santiago
- International Research Center, A.C. Camargo Cancer
Center, São Paulo, Brazil
| | - Talia Wegman-Ostrosky
- Basic Research Subdirection, Instituto Nacional de
Cancerología (INCan), Mexico City, Mexico
| | - W Ryan Diver
- Epidemiology Research Program, American Cancer
Society, Atlanta, GA, USA
| | - Lauren Teras
- Epidemiology Research Program, American Cancer
Society, Atlanta, GA, USA
| | - Neal D Freedman
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Belynda D Hicks
- Cancer Genomics Research Laboratory, Frederick
National Laboratory for Cancer Research, Frederick, MD, USA
| | - Bin Zhu
- Cancer Genomics Research Laboratory, Frederick
National Laboratory for Cancer Research, Frederick, MD, USA
| | - Mingyi Wang
- Cancer Genomics Research Laboratory, Frederick
National Laboratory for Cancer Research, Frederick, MD, USA
| | - Kristine Jones
- Cancer Genomics Research Laboratory, Frederick
National Laboratory for Cancer Research, Frederick, MD, USA
| | - Amy A Hutchinson
- Cancer Genomics Research Laboratory, Frederick
National Laboratory for Cancer Research, Frederick, MD, USA
| | - Casey Dagnall
- Cancer Genomics Research Laboratory, Frederick
National Laboratory for Cancer Research, Frederick, MD, USA
| | - Sharon A Savage
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Margaret A Tucker
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Lindsay M Morton
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Douglas R Stewart
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
| | - Lisa Mirabello
- Division of Cancer Epidemiology and Genetics,
National Cancer Institute, National Institutes of Health,
Bethesda, MD, USA
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49
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Mirshahi UL, Kim J, Best AF, Chen ZE, Hu Y, Haley JS, Golden A, Stahl R, Manickam K, Carr AG, Harney LA, Field A, Hatton J, Schultz KAP, Bauer AJ, Hill DA, Rosenberg PS, Murray MF, Carey DJ, Stewart DR. A Genome-First Approach to Characterize DICER1 Pathogenic Variant Prevalence, Penetrance, and Phenotype. JAMA Netw Open 2021; 4:e210112. [PMID: 33630087 PMCID: PMC7907958 DOI: 10.1001/jamanetworkopen.2021.0112] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
IMPORTANCE Genetic disorders are historically defined through phenotype-first approaches. However, risk estimates derived from phenotype-linked ascertainment may overestimate severity and penetrance. Pathogenic variants in DICER1 are associated with increased risks of rare and common neoplasms and thyroid disease in adults and children. This study explored how effectively a genome-first approach could characterize the clinical traits associated with germline DICER1 putative loss-of-function (pLOF) variants in an unselected clinical cohort. OBJECTIVE To examine the prevalence, penetrance, and phenotypic characteristics of carriers of germline DICER1 pLOF variants via genome-first ascertainment. DESIGN, SETTING, AND PARTICIPANTS This cohort study classifies DICER1 variants in germline exome sequence data from 92 296 participants of the Geisinger MyCode Community Health Initiative. Data for each MyCode participant were used from the start of the Geisinger electronic health record to February 1, 2018. MAIN OUTCOMES AND MEASURES Prevalence of germline DICER1 variation; penetrance of malignant tumors and thyroid disease in carriers of germline DICER1 variation; structured, manual review of electronic health records; and DICER1 sequencing of available tumors from an associated cancer registry. RESULTS A total of 92 296 adults (mean [SD] age, 59 [18] years; 98% white; 60% female) participated in the study. Germline DICER1 pLOF variants were observed in 1 in 3700 to 1 in 4600 participants, more than double the expected prevalence. Malignant tumors (primarily thyroid carcinoma) were observed in 4 of 25 participants (16%) with DICER1 pLOF variants, which is comparable (by 50 years of age) to the frequency of neoplasms in the largest registry- and clinic-based (phenotype-first) DICER1 studies published to date. DICER1 pLOF variants were significantly associated with risks of thyroidectomy (odds ratio [OR], 6.0; 95% CI, 2.2-16.3; P = .007) and thyroid cancer (OR, 9.2; 95% CI, 2.1-34.7; P = .02) compared with controls, but there was not a significant increase in the risk of goiter (OR, 1.8; 95% CI, 0.7-4.9). A female patient in her 80s who was a carrier of a germline DICER1 hotspot variant was apparently healthy on electronic health record review. The term DICER1 did not appear in any of the medical records of the 25 participants with a pLOF DICER1 variant, even in those affected with a known DICER1-associated tumor or thyroid phenotype. CONCLUSIONS AND RELEVANCE This cohort study was able to ascertain individuals with germline DICER1 variants based on a genome-first approach rather than through a previously established DICER1-related phenotype. Use of the genome-first approach may complement more traditional approaches to syndrome delineation and may be an efficient approach for risk estimation.
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Affiliation(s)
| | - Jung Kim
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
| | - Ana F. Best
- Biostatistics Branch, Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Rockville, Maryland
| | - Zongming E. Chen
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota
| | - Ying Hu
- Geisinger Clinic, Geisinger Health System, Danville, Pennsylvania
- Department of Endocrinology, Main Line Health System, Wynnewood, Pennsylvania
| | - Jeremy S. Haley
- Geisinger Clinic, Geisinger Health System, Danville, Pennsylvania
| | - Alicia Golden
- Geisinger Clinic, Geisinger Health System, Danville, Pennsylvania
| | - Richard Stahl
- Geisinger Clinic, Geisinger Health System, Danville, Pennsylvania
| | - Kandamurugu Manickam
- Division of Genetic and Genomic Medicine, Nationwide Children’s Hospital, Columbus, Ohio
| | | | | | | | - Jessica Hatton
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
| | - Kris Ann P. Schultz
- Cancer and Blood Disorders, Children’s Minnesota, Minneapolis
- International Pleuropulmonary Blastoma/DICER1 Registry, Minneapolis, Minnesota
- International Ovarian and Testicular Stromal Tumor Registry, Minneapolis, Minnesota
| | - Andrew J. Bauer
- The Thyroid Center, Division of Endocrinology and Diabetes, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - D. Ashley Hill
- ResourcePath, Sterling, Virginia
- Division of Pathology and Center for Cancer and Immunology Research, Children's National Health System, Washington, DC
- Department of Integrative Systems Biology, George Washington University School of Medicine and Health Sciences, Washington, DC
| | - Philip S. Rosenberg
- Biostatistics Branch, Biometric Research Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, National Institutes of Health, Rockville, Maryland
| | - Michael F. Murray
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut
| | - David J. Carey
- Geisinger Clinic, Geisinger Health System, Danville, Pennsylvania
| | - Douglas R. Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
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Kim J, Light N, Subasri V, Young EL, Wegman-Ostrosky T, Barkauskas DA, Hall D, Lupo PJ, Patidar R, Maese LD, Jones K, Wang M, Tavtigian SV, Wu D, Shlien A, Telfer F, Goldenberg A, Skapek SX, Wei JS, Wen X, Catchpoole D, Hawkins DS, Schiffman JD, Khan J, Malkin D, Stewart DR. Pathogenic Germline Variants in Cancer Susceptibility Genes in Children and Young Adults With Rhabdomyosarcoma. JCO Precis Oncol 2021; 5:PO.20.00218. [PMID: 34095712 PMCID: PMC8169077 DOI: 10.1200/po.20.00218] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/10/2020] [Accepted: 11/06/2020] [Indexed: 12/30/2022] Open
Abstract
Rhabdomyosarcoma (RMS) is the most common pediatric soft-tissue sarcoma and accounts for 3% of all pediatric cancer. In this study, we investigated germline sequence and structural variation in a broad set of genes in two large, independent RMS cohorts. MATERIALS AND METHODS Genome sequencing of the discovery cohort (n = 273) and exome sequencing of the secondary cohort (n = 121) were conducted on germline DNA. Analyses were performed on 130 cancer susceptibility genes (CSG). Pathogenic or likely pathogenic (P/LP) variants were predicted using the American College of Medical Genetics and Genomics (ACMG) criteria. Structural variation and survival analyses were performed on the discovery cohort. RESULTS We found that 6.6%-7.7% of patients with RMS harbored P/LP variants in dominant-acting CSG. An additional approximately 1% have structural variants (ATM, CDKN1C) in CSGs. CSG variants did not influence survival, although there was a significant correlation with an earlier age of tumor onset. There was a nonsignificant excess of P/LP variants in dominant inheritance genes in the patients with FOXO1 fusion-negative RMS patients versus the patients with FOXO1 fusion-positive RMS. We identified pathogenic germline variants in CSGs previously (TP53, NF1, DICER1, mismatch repair genes), rarely (BRCA2, CBL, CHEK2, SMARCA4), or never (FGFR4) reported in RMS. Numerous genes (TP53, BRCA2, mismatch repair) were on the ACMG Secondary Findings 2.0 list. CONCLUSION In two cohorts of patients with RMS, we identified pathogenic germline variants for which gene-specific therapies and surveillance guidelines may be beneficial. In families with a proband with an RMS-risk P/LP variant, genetic counseling and cascade testing should be considered, especially for ACMG Secondary Findings genes and/or with gene-specific surveillance guidelines.
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Affiliation(s)
- Jung Kim
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD
| | - Nicholas Light
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Vallijah Subasri
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, ON, Canada
- Vector Institute of Artificial Intelligence, Toronto, ON, Canada
| | - Erin L. Young
- Department of Pediatrics, University of Utah, Salt Lake City, UT
| | - Talia Wegman-Ostrosky
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD
- Basic Research Subdirection, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
| | - Donald A. Barkauskas
- QuadW-COG Childhood Sarcoma Biostatistics and Annotation Office, Children's Oncology Group, Monrovia, CA
- Department of Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, CA
| | - David Hall
- QuadW-COG Childhood Sarcoma Biostatistics and Annotation Office, Children's Oncology Group, Monrovia, CA
| | - Philip J. Lupo
- Department of Pediatrics, Hematology-Oncology Section, Baylor College of Medicine, Houston, TX
| | - Rajesh Patidar
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Luke D. Maese
- Department of Pediatrics, University of Utah, Salt Lake City, UT
| | - Kristine Jones
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Mingyi Wang
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Sean V. Tavtigian
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT
| | - Dongjing Wu
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Adam Shlien
- Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathology, University of Toronto, Toronto, ON, Canada
| | - Frank Telfer
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, ON, Canada
| | - Anna Goldenberg
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Vector Institute of Artificial Intelligence, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | | | - Jun S. Wei
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Xinyu Wen
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Daniel Catchpoole
- The Tumour Bank, Children's Cancer Research Unit, Kids Research Institute, The Children's Hospital at Westmead, Westmead, NSW, Australia
| | - Douglas S. Hawkins
- Division of Hematology/Oncology, Seattle Children's Hospital, University of Washington, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Joshua D. Schiffman
- Department of Pediatrics, University of Utah, Salt Lake City, UT
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT
| | - Javed Khan
- Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - David Malkin
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, ON, Canada
- Division of Hematology-Oncology, The Hospital for Sick Children, Department of Pediatrics, University of Toronto, Toronto, ON, Canada
| | - Douglas R. Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD
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