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SeekFusion - A Clinically Validated Fusion Transcript Detection Pipeline for PCR-Based Next-Generation Sequencing of RNA

Detecting gene fusions involving driver oncogenes is pivotal in clinical diagnosis and treatment of cancer patients. Recent developments in next-generation sequencing (NGS) technologies have enabled improved assays for bioinformatics-based gene fusions detection. In clinical applications, where a sm...

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Autores principales: Balan, Jagadheshwar, Jenkinson, Garrett, Nair, Asha, Saha, Neiladri, Koganti, Tejaswi, Voss, Jesse, Zysk, Christopher, Barr Fritcher, Emily G., Ross, Christian A., Giannini, Caterina, Raghunathan, Aditya, Kipp, Benjamin R., Jenkins, Robert, Ida, Cris, Halling, Kevin C., Blackburn, Patrick R., Dasari, Surendra, Oliver, Gavin R., Klee, Eric W.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8569241/
https://www.ncbi.nlm.nih.gov/pubmed/34745213
http://dx.doi.org/10.3389/fgene.2021.739054
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author Balan, Jagadheshwar
Jenkinson, Garrett
Nair, Asha
Saha, Neiladri
Koganti, Tejaswi
Voss, Jesse
Zysk, Christopher
Barr Fritcher, Emily G.
Ross, Christian A.
Giannini, Caterina
Raghunathan, Aditya
Kipp, Benjamin R.
Jenkins, Robert
Ida, Cris
Halling, Kevin C.
Blackburn, Patrick R.
Dasari, Surendra
Oliver, Gavin R.
Klee, Eric W.
author_facet Balan, Jagadheshwar
Jenkinson, Garrett
Nair, Asha
Saha, Neiladri
Koganti, Tejaswi
Voss, Jesse
Zysk, Christopher
Barr Fritcher, Emily G.
Ross, Christian A.
Giannini, Caterina
Raghunathan, Aditya
Kipp, Benjamin R.
Jenkins, Robert
Ida, Cris
Halling, Kevin C.
Blackburn, Patrick R.
Dasari, Surendra
Oliver, Gavin R.
Klee, Eric W.
author_sort Balan, Jagadheshwar
collection PubMed
description Detecting gene fusions involving driver oncogenes is pivotal in clinical diagnosis and treatment of cancer patients. Recent developments in next-generation sequencing (NGS) technologies have enabled improved assays for bioinformatics-based gene fusions detection. In clinical applications, where a small number of fusions are clinically actionable, targeted polymerase chain reaction (PCR)-based NGS chemistries, such as the QIAseq RNAscan assay, aim to improve accuracy compared to standard RNA sequencing. Existing informatics methods for gene fusion detection in NGS-based RNA sequencing assays traditionally use a transcriptome-based spliced alignment approach or a de-novo assembly approach. Transcriptome-based spliced alignment methods face challenges with short read mapping yielding low quality alignments. De-novo assembly-based methods yield longer contigs from short reads that can be more sensitive for genomic rearrangements, but face performance and scalability challenges. Consequently, there exists a need for a method to efficiently and accurately detect fusions in targeted PCR-based NGS chemistries. We describe SeekFusion, a highly accurate and computationally efficient pipeline enabling identification of gene fusions from PCR-based NGS chemistries. Utilizing biological samples processed with the QIAseq RNAscan assay and in-silico simulated data we demonstrate that SeekFusion gene fusion detection accuracy outperforms popular existing methods such as STAR-Fusion, TOPHAT-Fusion and JAFFA-hybrid. We also present results from 4,484 patient samples tested for neurological tumors and sarcoma, encompassing details on some novel fusions identified.
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spelling pubmed-85692412021-11-06 SeekFusion - A Clinically Validated Fusion Transcript Detection Pipeline for PCR-Based Next-Generation Sequencing of RNA Balan, Jagadheshwar Jenkinson, Garrett Nair, Asha Saha, Neiladri Koganti, Tejaswi Voss, Jesse Zysk, Christopher Barr Fritcher, Emily G. Ross, Christian A. Giannini, Caterina Raghunathan, Aditya Kipp, Benjamin R. Jenkins, Robert Ida, Cris Halling, Kevin C. Blackburn, Patrick R. Dasari, Surendra Oliver, Gavin R. Klee, Eric W. Front Genet Genetics Detecting gene fusions involving driver oncogenes is pivotal in clinical diagnosis and treatment of cancer patients. Recent developments in next-generation sequencing (NGS) technologies have enabled improved assays for bioinformatics-based gene fusions detection. In clinical applications, where a small number of fusions are clinically actionable, targeted polymerase chain reaction (PCR)-based NGS chemistries, such as the QIAseq RNAscan assay, aim to improve accuracy compared to standard RNA sequencing. Existing informatics methods for gene fusion detection in NGS-based RNA sequencing assays traditionally use a transcriptome-based spliced alignment approach or a de-novo assembly approach. Transcriptome-based spliced alignment methods face challenges with short read mapping yielding low quality alignments. De-novo assembly-based methods yield longer contigs from short reads that can be more sensitive for genomic rearrangements, but face performance and scalability challenges. Consequently, there exists a need for a method to efficiently and accurately detect fusions in targeted PCR-based NGS chemistries. We describe SeekFusion, a highly accurate and computationally efficient pipeline enabling identification of gene fusions from PCR-based NGS chemistries. Utilizing biological samples processed with the QIAseq RNAscan assay and in-silico simulated data we demonstrate that SeekFusion gene fusion detection accuracy outperforms popular existing methods such as STAR-Fusion, TOPHAT-Fusion and JAFFA-hybrid. We also present results from 4,484 patient samples tested for neurological tumors and sarcoma, encompassing details on some novel fusions identified. Frontiers Media S.A. 2021-10-22 /pmc/articles/PMC8569241/ /pubmed/34745213 http://dx.doi.org/10.3389/fgene.2021.739054 Text en Copyright © 2021 Balan, Jenkinson, Nair, Saha, Koganti, Voss, Zysk, Barr Fritcher, Ross, Giannini, Raghunathan, Kipp, Jenkins, Ida, Halling, Blackburn, Dasari, Oliver and Klee. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Balan, Jagadheshwar
Jenkinson, Garrett
Nair, Asha
Saha, Neiladri
Koganti, Tejaswi
Voss, Jesse
Zysk, Christopher
Barr Fritcher, Emily G.
Ross, Christian A.
Giannini, Caterina
Raghunathan, Aditya
Kipp, Benjamin R.
Jenkins, Robert
Ida, Cris
Halling, Kevin C.
Blackburn, Patrick R.
Dasari, Surendra
Oliver, Gavin R.
Klee, Eric W.
SeekFusion - A Clinically Validated Fusion Transcript Detection Pipeline for PCR-Based Next-Generation Sequencing of RNA
title SeekFusion - A Clinically Validated Fusion Transcript Detection Pipeline for PCR-Based Next-Generation Sequencing of RNA
title_full SeekFusion - A Clinically Validated Fusion Transcript Detection Pipeline for PCR-Based Next-Generation Sequencing of RNA
title_fullStr SeekFusion - A Clinically Validated Fusion Transcript Detection Pipeline for PCR-Based Next-Generation Sequencing of RNA
title_full_unstemmed SeekFusion - A Clinically Validated Fusion Transcript Detection Pipeline for PCR-Based Next-Generation Sequencing of RNA
title_short SeekFusion - A Clinically Validated Fusion Transcript Detection Pipeline for PCR-Based Next-Generation Sequencing of RNA
title_sort seekfusion - a clinically validated fusion transcript detection pipeline for pcr-based next-generation sequencing of rna
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8569241/
https://www.ncbi.nlm.nih.gov/pubmed/34745213
http://dx.doi.org/10.3389/fgene.2021.739054
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