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      Current recommendations for clinical surveillance and genetic testing in rhabdoid tumor predisposition: a report from the SIOPE Host Genome Working Group

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          Abstract

          The rhabdoid tumor (RT) predisposition syndromes 1 and 2 (RTPS1 and 2) are rare genetic conditions rendering young children vulnerable to an increased risk of RT, malignant neoplasms affecting the kidney, miscellaneous soft-part tissues, the liver and the central nervous system (Atypical Teratoid Rhabdoid Tumors, ATRT). Both, RTPS1&2 are due to pathogenic variants (PV) in genes encoding constituents of the BAF chromatin remodeling complex, i.e. SMARCB1 (RTPS1) and SMARCA4 (RTPS2). In contrast to other genetic disorders related to PVs in SMARCB1 and SMARCA4 such as Coffin-Siris Syndrome, RTPS1&2 are characterized by a predominance of truncating PVs, terminating transcription thus explaining a specific cancer risk. The penetrance of RTPS1 early in life is high and associated with a poor survival. However, few unaffected carriers may be encountered. Beyond RT, the tumor spectrum may be larger than initially suspected, and cancer surveillance offered to unaffected carriers (siblings or parents) and long-term survivors of RT is still a matter of discussion. RTPS2 exposes female carriers to an ill-defined risk of small cell carcinoma of the ovaries, hypercalcemic type (SCCOHT), which may appear in prepubertal females. RT surveillance protocols for these rare families have not been established. To address unresolved issues in the care of individuals with RTPS and to propose appropriate surveillance guidelines in childhood, the SIOPe Host Genome working group invited pediatric oncologists and geneticists to contribute to an expert meeting. The current manuscript summarizes conclusions of the panel discussion, including consented statements as well as non-evidence-based proposals for validation in the future.

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          Standards and Guidelines for the Interpretation of Sequence Variants: A Joint Consensus Recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology

          The American College of Medical Genetics and Genomics (ACMG) previously developed guidance for the interpretation of sequence variants. 1 In the past decade, sequencing technology has evolved rapidly with the advent of high-throughput next generation sequencing. By adopting and leveraging next generation sequencing, clinical laboratories are now performing an ever increasing catalogue of genetic testing spanning genotyping, single genes, gene panels, exomes, genomes, transcriptomes and epigenetic assays for genetic disorders. By virtue of increased complexity, this paradigm shift in genetic testing has been accompanied by new challenges in sequence interpretation. In this context, the ACMG convened a workgroup in 2013 comprised of representatives from the ACMG, the Association for Molecular Pathology (AMP) and the College of American Pathologists (CAP) to revisit and revise the standards and guidelines for the interpretation of sequence variants. The group consisted of clinical laboratory directors and clinicians. This report represents expert opinion of the workgroup with input from ACMG, AMP and CAP stakeholders. These recommendations primarily apply to the breadth of genetic tests used in clinical laboratories including genotyping, single genes, panels, exomes and genomes. This report recommends the use of specific standard terminology: ‘pathogenic’, ‘likely pathogenic’, ‘uncertain significance’, ‘likely benign’, and ‘benign’ to describe variants identified in Mendelian disorders. Moreover, this recommendation describes a process for classification of variants into these five categories based on criteria using typical types of variant evidence (e.g. population data, computational data, functional data, segregation data, etc.). Because of the increased complexity of analysis and interpretation of clinical genetic testing described in this report, the ACMG strongly recommends that clinical molecular genetic testing should be performed in a CLIA-approved laboratory with results interpreted by a board-certified clinical molecular geneticist or molecular genetic pathologist or equivalent.
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            Atypical Teratoid/Rhabdoid Tumors Are Comprised of Three Epigenetic Subgroups with Distinct Enhancer Landscapes.

            Atypical teratoid/rhabdoid tumor (ATRT) is one of the most common brain tumors in infants. Although the prognosis of ATRT patients is poor, some patients respond favorably to current treatments, suggesting molecular inter-tumor heterogeneity. To investigate this further, we genetically and epigenetically analyzed 192 ATRTs. Three distinct molecular subgroups of ATRTs, associated with differences in demographics, tumor location, and type of SMARCB1 alterations, were identified. Whole-genome DNA and RNA sequencing found no recurrent mutations in addition to SMARCB1 that would explain the differences between subgroups. Whole-genome bisulfite sequencing and H3K27Ac chromatin-immunoprecipitation sequencing of primary tumors, however, revealed clear differences, leading to the identification of subgroup-specific regulatory networks and potential therapeutic targets.
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              Recurrent SMARCA4 mutations in small cell carcinoma of the ovary.

              Small cell carcinoma of the ovary, hypercalcemic type (SCCOHT) is a rare, highly aggressive form of ovarian cancer primarily diagnosed in young women. We identified inactivating biallelic SMARCA4 mutations in 100% of the 12 SCCOHT tumors examined. Protein studies confirmed loss of SMARCA4 expression, suggesting a key role for the SWI/SNF chromatin-remodeling complex in SCCOHT.
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                Author and article information

                Contributors
                michael.fruehwald@uk-augsburg.de
                franck.bourdeaut@curie.net
                Journal
                Fam Cancer
                Fam Cancer
                Familial Cancer
                Springer Netherlands (Dordrecht )
                1389-9600
                1573-7292
                3 February 2021
                3 February 2021
                2021
                : 20
                : 4
                : 305-316
                Affiliations
                [1 ]Paediatric and Adolescent Medicine, Swabian Children’s Cancer Center, University Medical Center Augsburg, Stenglinstraße 2, 86156 Augsburg, Germany
                [2 ]GRID grid.22937.3d, ISNI 0000 0000 9259 8492, St. Anna Children’s Hospital and Children’s Cancer Research Institute, Department of Pediatrics, , Medical University of Vienna, ; Vienna, Austria
                [3 ]GRID grid.7692.a, ISNI 0000000090126352, Department of Genetics, , University Medical Center Utrecht, ; Utrecht, The Netherlands
                [4 ]GRID grid.5379.8, ISNI 0000000121662407, Manchester Centre for Genomic Medicine, Division of Evolution and Genomic Sciences, MAHSC, St Mary’s Hospital, Manchester University Hospitals NHS Foundation Trust, , University of Manchester, ; Manchester, UK
                [5 ]GRID grid.416003.0, ISNI 0000 0004 6086 6623, Department of Pediatrics, Division of Hematology/Oncology, , LAU Medical Center-Rizk Hospital, ; Ashrafieh, Beirut, Lebanon
                [6 ]GRID grid.5216.0, ISNI 0000 0001 2155 0800, Pediatric Hematology-Oncology Unit, First Department of Pediatrics, National and Kapodistrian University of Athens, , “Aghia Sofia” Children’s Hospital, ; Athens, Greece
                [7 ]GRID grid.451052.7, ISNI 0000 0004 0581 2008, Great Ormond Street Hospital for Children, , NHS Foundation Trust, ; London, WC1N 3JH UK
                [8 ]GRID grid.5253.1, ISNI 0000 0001 0328 4908, Institute of Human Genetics, , Heidelberg University Hospital, ; Heidelberg, Germany
                [9 ]GRID grid.510964.f, Hopp Children’s Cancer Center Heidelberg (KiTZ), ; Heidelberg, Germany
                [10 ]GRID grid.7737.4, ISNI 0000 0004 0410 2071, Children’s Hospital, , University of Helsinki and Helsinki University Hospital, ; Helsinki, Finland
                [11 ]GRID grid.413795.d, ISNI 0000 0001 2107 2845, Department of Pediatric Hematology-Oncology, The Edmond and Lily Safra Children’s Hospital, , Chaim Sheba Medical Center, ; 52621 Tel-Hashomer, Israel
                [12 ]GRID grid.16149.3b, ISNI 0000 0004 0551 4246, Department of Pediatric Hematology and Oncology, , University Children’s Hospital Münster, ; Albert-Schweitzer-Campus 1, 48149 Münster, Germany
                [13 ]GRID grid.10423.34, ISNI 0000 0000 9529 9877, Pediatric Hematology and Oncology, , Hannover Medical School, ; Hannover, Germany
                [14 ]GRID grid.7497.d, ISNI 0000 0004 0492 0584, Division of Pediatric Neurooncology, , German Cancer Research Center (DKFZ) and German Cancer Consortium (DKTK), ; Heidelberg, Germany
                [15 ]GRID grid.5253.1, ISNI 0000 0001 0328 4908, Department of Pediatric Oncology, Hematology, and Immunology, , University Hospital Heidelberg, ; Heidelberg, Germany
                [16 ]GRID grid.13648.38, ISNI 0000 0001 2180 3484, Department of Pediatric Hematology and Oncology, , University Medical Center Hamburg Eppendorf, ; Hamburg, Germany
                [17 ]Department of Pediatric Oncology and Haematology, Mitera Children’s Hospital, Athens, Greece
                [18 ]GRID grid.412341.1, ISNI 0000 0001 0726 4330, Department of Oncology, , University Children’s Hospital, ; Zurich, Switzerland
                [19 ]GRID grid.440907.e, ISNI 0000 0004 1784 3645, Institut Curie, SIREDO Pediatric Cancer Center, INSERM U830, Laboratory of Translational Research in Pediatric Oncology, , Paris Sciences Lettres Research University, ; Paris, France
                Author information
                http://orcid.org/0000-0002-8237-1854
                http://orcid.org/0000-0002-8482-5784
                https://orcid.org/0000-0002-6392-1590
                http://orcid.org/0000-0002-9217-052X
                http://orcid.org/0000-0001-8558-2561
                http://orcid.org/0000-0002-4920-0930
                http://orcid.org/0000-0003-4806-345X
                http://orcid.org/0000-0002-5676-8102
                http://orcid.org/0000-0003-4120-5873
                http://orcid.org/0000-0002-3562-6121
                http://orcid.org/0000-0001-6375-2320
                http://orcid.org/0000-0001-8658-4702
                http://orcid.org/0000-0001-9489-6781
                Article
                229
                10.1007/s10689-021-00229-1
                8484234
                33532948
                a0bdeb10-fb9e-40ae-82e4-f7f5e5d8fa06
                © The Author(s) 2021

                Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 27 September 2020
                : 6 January 2021
                Funding
                Funded by: Projekt DEAL
                Categories
                Original Article
                Custom metadata
                © Springer Nature B.V. 2021

                Oncology & Radiotherapy
                rhabdoid,atrt,smarcb1,predisposition,germline,surveillance
                Oncology & Radiotherapy
                rhabdoid, atrt, smarcb1, predisposition, germline, surveillance

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