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Apostolides M, Li M, Arnoldo A, Ku M, Husić M, Ramani AK, Brudno M, Turinsky A, Hawkins C, Siddaway R. Clinical Implementation of MetaFusion for Accurate Cancer-Driving Fusion Detection from RNA Sequencing. J Mol Diagn 2023; 25:921-931. [PMID: 37748705 DOI: 10.1016/j.jmoldx.2023.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 08/15/2023] [Accepted: 09/07/2023] [Indexed: 09/27/2023] Open
Abstract
Oncogenic fusion genes may be identified from next-generation sequencing data, typically RNA-sequencing. However, in a clinical setting, identifying these alterations is challenging against a background of nonrelevant fusion calls that reduce workflow precision and specificity. Furthermore, although numerous algorithms have been developed to detect fusions in RNA-sequencing, there are variations in their individual sensitivities. Here this problem was addressed by introducing MetaFusion into clinical use. Its utility was illustrated when applied to both whole-transcriptome and targeted sequencing data sets. MetaFusion combines ensemble fusion calls from eight individual fusion-calling algorithms with practice-informed identification of gene fusions that are known to be clinically relevant. In doing so, it allows oncogenic fusions to be identified with near-perfect sensitivity and high precision and specificity, significantly outperforming the individual fusion callers it uses as well as existing clinical-grade software. MetaFusion enhances clinical yield over existing methods and is able to identify fusions that have patient relevance for the purposes of diagnosis, prognosis, and treatment.
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Affiliation(s)
- Michael Apostolides
- Centre for Computational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Michael Li
- Centre for Computational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Anthony Arnoldo
- Division of Pathology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Michelle Ku
- The Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario, Canada; Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Mia Husić
- Centre for Computational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Arun K Ramani
- Centre for Computational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Michael Brudno
- Centre for Computational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada; Department of Computer Science, University of Toronto, Toronto, Ontario, Canada; University Health Network, Toronto, Ontario, Canada
| | - Andrei Turinsky
- Centre for Computational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Cynthia Hawkins
- Division of Pathology, Hospital for Sick Children, Toronto, Ontario, Canada; The Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario, Canada; Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.
| | - Robert Siddaway
- Division of Pathology, Hospital for Sick Children, Toronto, Ontario, Canada; The Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario, Canada; Cell Biology Program, Hospital for Sick Children, Toronto, Ontario, Canada.
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4
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Vicente-Garcés C, Maynou J, Fernández G, Esperanza-Cebollada E, Torrebadell M, Català A, Rives S, Camós M, Vega-García N. Fusion InPipe, an integrative pipeline for gene fusion detection from RNA-seq data in acute pediatric leukemia. Front Mol Biosci 2023; 10:1141310. [PMID: 37363396 PMCID: PMC10288994 DOI: 10.3389/fmolb.2023.1141310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 05/30/2023] [Indexed: 06/28/2023] Open
Abstract
RNA sequencing (RNA-seq) is a reliable tool for detecting gene fusions in acute leukemia. Multiple bioinformatics pipelines have been developed to analyze RNA-seq data, but an agreed gold standard has not been established. This study aimed to compare the applicability of 5 fusion calling pipelines (Arriba, deFuse, CICERO, FusionCatcher, and STAR-Fusion), as well as to define and develop an integrative bioinformatics pipeline (Fusion InPipe) to detect clinically relevant gene fusions in acute pediatric leukemia. We analyzed RNA-seq data by each pipeline individually and by Fusion InPipe. Each algorithm individually called most of the fusions with similar sensitivity and precision. However, not all rearrangements were called, suggesting that choosing a single pipeline might cause missing important fusions. To improve this, we integrated the results of the five algorithms in just one pipeline, Fusion InPipe, comparing the output from the agreement of 5/5, 4/5, and 3/5 algorithms. The maximum sensitivity was achieved with the agreement of 3/5 algorithms, with a global sensitivity of 95%, achieving a 100% in patients' data. Furthermore, we showed the necessity of filtering steps to reduce the false positive detection rate. Here, we demonstrate that Fusion InPipe is an excellent tool for fusion detection in pediatric acute leukemia with the best performance when selecting those fusions called by at least 3/5 pipelines.
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Affiliation(s)
- Clara Vicente-Garcés
- Pediatric Cancer Center Barcelona (PCCB), Institut de Recerca Sant Joan de Déu, Leukemia and Pediatric Hematology Disorders, Developmental Tumors Biology Group, Esplugues de Llobregat, Spain
| | - Joan Maynou
- Hospital Sant Joan de Déu Barcelona, Genetics Medicine Section, Esplugues de Llobregat, Spain
- Institut de Recerca Hospital Sant Joan de Déu, Neurogenetics and Molecular Medicine, Esplugues de Llobregat, Spain
| | - Guerau Fernández
- Hospital Sant Joan de Déu Barcelona, Genetics Medicine Section, Esplugues de Llobregat, Spain
- Institut de Recerca Hospital Sant Joan de Déu, Neurogenetics and Molecular Medicine, Esplugues de Llobregat, Spain
| | - Elena Esperanza-Cebollada
- Pediatric Cancer Center Barcelona (PCCB), Institut de Recerca Sant Joan de Déu, Leukemia and Pediatric Hematology Disorders, Developmental Tumors Biology Group, Esplugues de Llobregat, Spain
| | - Montserrat Torrebadell
- Pediatric Cancer Center Barcelona (PCCB), Institut de Recerca Sant Joan de Déu, Leukemia and Pediatric Hematology Disorders, Developmental Tumors Biology Group, Esplugues de Llobregat, Spain
- Hospital Sant Joan de Déu Barcelona, Hematology Laboratory, Esplugues de Llobregat, Spain
- Instituto de Salud Carlos III, Centro de Investigación Biomédica en Red De Enfermedades Raras (CIBERER), Madrid, Spain
| | - Albert Català
- Pediatric Cancer Center Barcelona (PCCB), Institut de Recerca Sant Joan de Déu, Leukemia and Pediatric Hematology Disorders, Developmental Tumors Biology Group, Esplugues de Llobregat, Spain
- Instituto de Salud Carlos III, Centro de Investigación Biomédica en Red De Enfermedades Raras (CIBERER), Madrid, Spain
- Pediatric Cancer Center Barcelona (PCCB), Hospital Sant Joan De Déu Barcelona, Leukemia and Lymphoma Unit, Barcelona, Spain
| | - Susana Rives
- Pediatric Cancer Center Barcelona (PCCB), Institut de Recerca Sant Joan de Déu, Leukemia and Pediatric Hematology Disorders, Developmental Tumors Biology Group, Esplugues de Llobregat, Spain
- Instituto de Salud Carlos III, Centro de Investigación Biomédica en Red De Enfermedades Raras (CIBERER), Madrid, Spain
- Pediatric Cancer Center Barcelona (PCCB), Hospital Sant Joan De Déu Barcelona, Leukemia and Lymphoma Unit, Barcelona, Spain
| | - Mireia Camós
- Pediatric Cancer Center Barcelona (PCCB), Institut de Recerca Sant Joan de Déu, Leukemia and Pediatric Hematology Disorders, Developmental Tumors Biology Group, Esplugues de Llobregat, Spain
- Hospital Sant Joan de Déu Barcelona, Hematology Laboratory, Esplugues de Llobregat, Spain
- Instituto de Salud Carlos III, Centro de Investigación Biomédica en Red De Enfermedades Raras (CIBERER), Madrid, Spain
| | - Nerea Vega-García
- Pediatric Cancer Center Barcelona (PCCB), Institut de Recerca Sant Joan de Déu, Leukemia and Pediatric Hematology Disorders, Developmental Tumors Biology Group, Esplugues de Llobregat, Spain
- Hospital Sant Joan de Déu Barcelona, Hematology Laboratory, Esplugues de Llobregat, Spain
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6
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LaHaye S, Fitch JR, Voytovich KJ, Herman AC, Kelly BJ, Lammi GE, Arbesfeld JA, Wijeratne S, Franklin SJ, Schieffer KM, Bir N, McGrath SD, Miller AR, Wetzel A, Miller KE, Bedrosian TA, Leraas K, Varga EA, Lee K, Gupta A, Setty B, Boué DR, Leonard JR, Finlay JL, Abdelbaki MS, Osorio DS, Koo SC, Koboldt DC, Wagner AH, Eisfeld AK, Mrózek K, Magrini V, Cottrell CE, Mardis ER, Wilson RK, White P. Discovery of clinically relevant fusions in pediatric cancer. BMC Genomics 2021; 22:872. [PMID: 34863095 PMCID: PMC8642973 DOI: 10.1186/s12864-021-08094-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 10/15/2021] [Indexed: 12/13/2022] Open
Abstract
Background Pediatric cancers typically have a distinct genomic landscape when compared to adult cancers and frequently carry somatic gene fusion events that alter gene expression and drive tumorigenesis. Sensitive and specific detection of gene fusions through the analysis of next-generation-based RNA sequencing (RNA-Seq) data is computationally challenging and may be confounded by low tumor cellularity or underlying genomic complexity. Furthermore, numerous computational tools are available to identify fusions from supporting RNA-Seq reads, yet each algorithm demonstrates unique variability in sensitivity and precision, and no clearly superior approach currently exists. To overcome these challenges, we have developed an ensemble fusion calling approach to increase the accuracy of identifying fusions. Results Our Ensemble Fusion (EnFusion) approach utilizes seven fusion calling algorithms: Arriba, CICERO, FusionMap, FusionCatcher, JAFFA, MapSplice, and STAR-Fusion, which are packaged as a fully automated pipeline using Docker and Amazon Web Services (AWS) serverless technology. This method uses paired end RNA-Seq sequence reads as input, and the output from each algorithm is examined to identify fusions detected by a consensus of at least three algorithms. These consensus fusion results are filtered by comparison to an internal database to remove likely artifactual fusions occurring at high frequencies in our internal cohort, while a “known fusion list” prevents failure to report known pathogenic events. We have employed the EnFusion pipeline on RNA-Seq data from 229 patients with pediatric cancer or blood disorders studied under an IRB-approved protocol. The samples consist of 138 central nervous system tumors, 73 solid tumors, and 18 hematologic malignancies or disorders. The combination of an ensemble fusion-calling pipeline and a knowledge-based filtering strategy identified 67 clinically relevant fusions among our cohort (diagnostic yield of 29.3%), including RBPMS-MET, BCAN-NTRK1, and TRIM22-BRAF fusions. Following clinical confirmation and reporting in the patient’s medical record, both known and novel fusions provided medically meaningful information. Conclusions The EnFusion pipeline offers a streamlined approach to discover fusions in cancer, at higher levels of sensitivity and accuracy than single algorithm methods. Furthermore, this method accurately identifies driver fusions in pediatric cancer, providing clinical impact by contributing evidence to diagnosis and, when appropriate, indicating targeted therapies. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08094-z.
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Affiliation(s)
- Stephanie LaHaye
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - James R Fitch
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Kyle J Voytovich
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Adam C Herman
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Benjamin J Kelly
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Grant E Lammi
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Jeremy A Arbesfeld
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Saranga Wijeratne
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Samuel J Franklin
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Kathleen M Schieffer
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Natalie Bir
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Sean D McGrath
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Anthony R Miller
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Amy Wetzel
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Katherine E Miller
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Tracy A Bedrosian
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Kristen Leraas
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Elizabeth A Varga
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Kristy Lee
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Ajay Gupta
- Division of Hematology, Oncology, Blood and Marrow Transplant, Nationwide Children's Hospital, Columbus, OH, USA
| | - Bhuvana Setty
- Division of Hematology, Oncology, Blood and Marrow Transplant, Nationwide Children's Hospital, Columbus, OH, USA.,Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Daniel R Boué
- Department of Pathology, The Ohio State University, Columbus, OH, USA.,Department of Pathology, Nationwide Children's Hospital, Columbus, OH, USA
| | - Jeffrey R Leonard
- Department of Pediatrics, The Ohio State University, Columbus, OH, USA.,Section of Neurosurgery, Nationwide Children's Hospital, Columbus, OH, USA
| | - Jonathan L Finlay
- Division of Hematology, Oncology, Blood and Marrow Transplant, Nationwide Children's Hospital, Columbus, OH, USA.,Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Mohamed S Abdelbaki
- Division of Hematology, Oncology, Blood and Marrow Transplant, Nationwide Children's Hospital, Columbus, OH, USA.,Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Diana S Osorio
- Division of Hematology, Oncology, Blood and Marrow Transplant, Nationwide Children's Hospital, Columbus, OH, USA.,Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Selene C Koo
- Department of Pathology, The Ohio State University, Columbus, OH, USA.,Department of Pathology, Nationwide Children's Hospital, Columbus, OH, USA
| | - Daniel C Koboldt
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Alex H Wagner
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA.,Department of Pediatrics, The Ohio State University, Columbus, OH, USA.,Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Ann-Kathrin Eisfeld
- Division of Hematology, The Ohio State University, Columbus, OH, USA.,Clara D. Bloomfield Center for Leukemia Outcomes Research, The Ohio State University, Columbus, OH, USA.,The Ohio State Comprehensive Cancer Center, Columbus, OH, USA
| | - Krzysztof Mrózek
- Clara D. Bloomfield Center for Leukemia Outcomes Research, The Ohio State University, Columbus, OH, USA.,The Ohio State Comprehensive Cancer Center, Columbus, OH, USA
| | - Vincent Magrini
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA.,Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Catherine E Cottrell
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA.,Department of Pediatrics, The Ohio State University, Columbus, OH, USA.,Department of Pathology, The Ohio State University, Columbus, OH, USA
| | - Elaine R Mardis
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA.,Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Richard K Wilson
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA.,Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Peter White
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA. .,Department of Pediatrics, The Ohio State University, Columbus, OH, USA.
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