Armin R Afshar1, Melike Pekmezci2, Michele M Bloomer3, Nicola J Cadenas4, Meredith Stevers5, Anuradha Banerjee6, Ritu Roy7, Adam B Olshen8, Jessica Van Ziffle9, Courtney Onodera9, W Patrick Devine9, James P Grenert9, Boris C Bastian10, David A Solomon11, Bertil E Damato12. 1. Department of Ophthalmology, University of California, San Francisco, San Francisco, California; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California. Electronic address: Armin.Afshar@ucsf.edu. 2. Department of Ophthalmology, University of California, San Francisco, San Francisco, California; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California; Department of Pathology, University of California, San Francisco, San Francisco, California. 3. Department of Ophthalmology, University of California, San Francisco, San Francisco, California; Department of Pathology, University of California, San Francisco, San Francisco, California. 4. Cancer Genetics and Prevention Program, University of California, San Francisco, San Francisco, California. 5. Department of Pathology, University of California, San Francisco, San Francisco, California. 6. Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California; Division of Hematology-Oncology, Department of Pediatrics, University of California, San Francisco, San Francisco, California. 7. Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California; Computational Biology and Informatics, University of California, San Francisco, San Francisco, California. 8. Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California; Computational Biology and Informatics, University of California, San Francisco, San Francisco, California; Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California. 9. Department of Pathology, University of California, San Francisco, San Francisco, California; Clinical Cancer Genomics Laboratory, University of California, San Francisco, San Francisco, California. 10. Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California; Department of Pathology, University of California, San Francisco, San Francisco, California; Clinical Cancer Genomics Laboratory, University of California, San Francisco, San Francisco, California; Department of Dermatology, University of California, San Francisco, San Francisco, California. 11. Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, California; Department of Pathology, University of California, San Francisco, San Francisco, California; Clinical Cancer Genomics Laboratory, University of California, San Francisco, San Francisco, California. 12. Department of Ophthalmology, University of California, San Francisco, San Francisco, California; Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, United Kingdom.
Abstract
PURPOSE: To determine the usefulness of a comprehensive, targeted-capture next-generation sequencing (NGS) assay for the clinical management of children undergoing enucleation for retinoblastoma. DESIGN: Cohort study. PARTICIPANTS: Thirty-two children with retinoblastoma. METHODS: We performed targeted NGS using the UCSF500 Cancer Panel (University of California, San Francisco, San Francisco, CA) on formalin-fixed, paraffin-embedded tumor tissue along with constitutional DNA isolated from peripheral blood, buccal swab, or uninvolved optic nerve. Peripheral blood samples were also sent to a commercial laboratory for germline RB1 mutation testing. MAIN OUTCOME MEASURES: Presence or absence of germline RB1 mutation or deletion, tumor genetic profile, and association of genetic alterations with clinicopathologic features. RESULTS: Germline mutation or deletion of the RB1 gene was identified in all children with bilateral retinoblastoma (n = 12), and these NGS results were 100% concordant with commercial germline RB1 mutation analysis. In tumor tissue tested with NGS, biallelic inactivation of RB1 was identified in 28 tumors and focal MYCN amplification was identified in 4 tumors (2 with wild-type RB1 and 2 with biallelic RB1 inactivation). Additional likely pathogenic alterations beyond RB1 were identified in 13 tumors (41%), several of which have not been reported previously in retinoblastoma. These included focal amplifications of MDM4 and RAF1, as well as damaging mutations involving BCOR, ARID1A, MGA, FAT1, and ATRX. The presence of additional likely pathogenetic mutations beyond RB1 inactivation was associated with aggressive histopathologic features, including higher histologic grade and anaplasia, and also with both unilateral and sporadic disease. CONCLUSIONS: Comprehensive NGS analysis reliably detects relevant mutations, amplifications, and chromosomal copy number changes in retinoblastoma. The presence of genetic alterations beyond RB1 inactivation correlates with aggressive histopathologic features.
PURPOSE: To determine the usefulness of a comprehensive, targeted-capture next-generation sequencing (NGS) assay for the clinical management of children undergoing enucleation for retinoblastoma. DESIGN: Cohort study. PARTICIPANTS: Thirty-two children with retinoblastoma. METHODS: We performed targeted NGS using the UCSF500 Cancer Panel (University of California, San Francisco, San Francisco, CA) on formalin-fixed, paraffin-embedded tumor tissue along with constitutional DNA isolated from peripheral blood, buccal swab, or uninvolved optic nerve. Peripheral blood samples were also sent to a commercial laboratory for germline RB1 mutation testing. MAIN OUTCOME MEASURES: Presence or absence of germline RB1 mutation or deletion, tumor genetic profile, and association of genetic alterations with clinicopathologic features. RESULTS: Germline mutation or deletion of the RB1 gene was identified in all children with bilateral retinoblastoma (n = 12), and these NGS results were 100% concordant with commercial germline RB1 mutation analysis. In tumor tissue tested with NGS, biallelic inactivation of RB1 was identified in 28 tumors and focal MYCN amplification was identified in 4 tumors (2 with wild-type RB1 and 2 with biallelic RB1 inactivation). Additional likely pathogenic alterations beyond RB1 were identified in 13 tumors (41%), several of which have not been reported previously in retinoblastoma. These included focal amplifications of MDM4 and RAF1, as well as damaging mutations involving BCOR, ARID1A, MGA, FAT1, and ATRX. The presence of additional likely pathogenetic mutations beyond RB1 inactivation was associated with aggressive histopathologic features, including higher histologic grade and anaplasia, and also with both unilateral and sporadic disease. CONCLUSIONS: Comprehensive NGS analysis reliably detects relevant mutations, amplifications, and chromosomal copy number changes in retinoblastoma. The presence of genetic alterations beyond RB1 inactivation correlates with aggressive histopathologic features.
Authors: Jeannette R Wong; Lindsay M Morton; Margaret A Tucker; David H Abramson; Johanna M Seddon; Joshua N Sampson; Ruth A Kleinerman Journal: J Clin Oncol Date: 2014-09-02 Impact factor: 44.544
Authors: Wenhui L Li; Jonathan Buckley; Pedro A Sanchez-Lara; Dennis T Maglinte; Lucy Viduetsky; Tatiana V Tatarinova; Jennifer G Aparicio; Jonathan W Kim; Margaret Au; Dejerianne Ostrow; Thomas C Lee; Maurice O'Gorman; Alexander Judkins; David Cobrinik; Timothy J Triche Journal: J Mol Diagn Date: 2016-05-04 Impact factor: 5.568
Authors: K C Sippel; R E Fraioli; G D Smith; M E Schalkoff; J Sutherland; B L Gallie; T P Dryja Journal: Am J Hum Genet Date: 1998-03 Impact factor: 11.025
Authors: Ella Bowles; Timothy W Corson; Jane Bayani; Jeremy A Squire; Nathalie Wong; Paul B-S Lai; Brenda L Gallie Journal: Genes Chromosomes Cancer Date: 2007-02 Impact factor: 5.006
Authors: Zhao Chen; Kimberly Moran; Jennifer Richards-Yutz; Erik Toorens; Daniel Gerhart; Tapan Ganguly; Carol L Shields; Arupa Ganguly Journal: Hum Mutat Date: 2013-12-20 Impact factor: 4.878
Authors: Irsan E Kooi; Berber M Mol; Maarten P G Massink; Marcus C de Jong; Pim de Graaf; Paul van der Valk; Hanne Meijers-Heijboer; Gertjan J L Kaspers; Annette C Moll; Hein Te Riele; Jacqueline Cloos; Josephine C Dorsman Journal: PLoS One Date: 2016-04-26 Impact factor: 3.240
Authors: Irsan E Kooi; Berber M Mol; Maarten P G Massink; Najim Ameziane; Hanne Meijers-Heijboer; Charlotte J Dommering; Saskia E van Mil; Yne de Vries; Annemarie H van der Hout; Gertjan J L Kaspers; Annette C Moll; Hein Te Riele; Jacqueline Cloos; Josephine C Dorsman Journal: Sci Rep Date: 2016-04-29 Impact factor: 4.379
Authors: Mary E Kim; Liya Xu; Rishvanth K Prabakar; Lishuang Shen; Chen-Ching Peng; Peter Kuhn; Xiaowu Gai; James Hicks; Jesse L Berry Journal: J Vis Exp Date: 2021-09-07 Impact factor: 1.424
Authors: Liya Xu; Lishuang Shen; Ashley Polski; Rishvanth K Prabakar; Rachana Shah; Rima Jubran; Jonathan W Kim; Jacklyn Biegel; Peter Kuhn; David Cobrinik; James Hicks; Xiaowu Gai; Jesse L Berry Journal: Ophthalmic Genet Date: 2020-08-17 Impact factor: 1.803
Authors: Jasmine H Francis; Allison L Richards; Diana L Mandelker; Michael F Berger; Michael F Walsh; Ira J Dunkel; Mark T A Donoghue; David H Abramson Journal: Cancers (Basel) Date: 2021-01-05 Impact factor: 6.639
Authors: Mary E Kim; Ashley Polski; Liya Xu; Rishvanth K Prabakar; Chen-Ching Peng; Mark W Reid; Rachana Shah; Peter Kuhn; David Cobrinik; James Hicks; Jesse L Berry Journal: Cancers (Basel) Date: 2021-07-03 Impact factor: 6.639