{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,26]],"date-time":"2025-10-26T21:18:32Z","timestamp":1761513512493},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"23","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":767,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: RNA-seq has become the method of choice to quantify genes and exons, discover novel transcripts and detect fusion genes. However, reliable variant identification from RNA-seq data remains challenging because of the complexities of the transcriptome, the challenges of accurately mapping exon boundary spanning reads and the bias introduced during the sequencing library preparation.<\/jats:p>\n               <jats:p>Method: We developed RVboost, a novel method specific for RNA variant prioritization. RVboost uses several attributes unique in the process of RNA library preparation, sequencing and RNA-seq data analyses. It uses a boosting method to train a model of \u2018good quality\u2019 variants using common variants from HapMap, and prioritizes and calls the RNA variants based on the trained model. We packaged RVboost in a comprehensive workflow, which integrates tools of variant calling, annotation and filtering.<\/jats:p>\n               <jats:p>Results: RVboost consistently outperforms the variant quality score recalibration from the Genome Analysis Tool Kit and the RNA-seq variant-calling pipeline SNPiR in 12 RNA-seq samples using ground-truth variants from paired exome sequencing data. Several RNA-seq\u2013specific attributes were identified as critical to differentiate true and false variants, including the distance of the variant positions to exon boundaries, and the percent of the reads supporting the variant in the first six base pairs. The latter identifies false variants introduced by the random hexamer priming during the library construction.<\/jats:p>\n               <jats:p>Availability and implementation: The RVboost package is implemented to readily run in Mac or Linux environments. The software and user manual are available at http:\/\/bioinformaticstools.mayo.edu\/research\/rvboost\/.<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu577","type":"journal-article","created":{"date-parts":[[2014,8,29]],"date-time":"2014-08-29T00:22:23Z","timestamp":1409271743000},"page":"3414-3416","source":"Crossref","is-referenced-by-count":39,"title":["RVboost: RNA-seq variants prioritization using a boosting method"],"prefix":"10.1093","volume":"30","author":[{"given":"Chen","family":"Wang","sequence":"first","affiliation":[{"name":"1 Division of Biomedical Statistics and Informatics, Mayo Clinic, 200 First Street SW, Rochester MN 55905, 2Department of Health Sciences Research, Mayo Clinic, 4500 San Pablo Road South, Jacksonville FL 32224, 3Department of Laboratory Medicine and Pathology, 4Division of Hematology, Department of Internal Medicine, 5Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, 200 First Street SW, Rochester MN 55905 and 6Department of Cancer Biology, Mayo Clinic, 4500 San Pablo Road South, Jacksonville FL 32224, USA"}]},{"given":"Jaime I.","family":"Davila","sequence":"additional","affiliation":[{"name":"1 Division of Biomedical Statistics and Informatics, Mayo Clinic, 200 First Street SW, Rochester MN 55905, 2Department of Health Sciences Research, Mayo Clinic, 4500 San Pablo Road South, Jacksonville FL 32224, 3Department of Laboratory Medicine and Pathology, 4Division of Hematology, Department of Internal Medicine, 5Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, 200 First Street SW, Rochester MN 55905 and 6Department of Cancer Biology, Mayo Clinic, 4500 San Pablo Road South, Jacksonville FL 32224, USA"}]},{"given":"Saurabh","family":"Baheti","sequence":"additional","affiliation":[{"name":"1 Division of Biomedical Statistics and Informatics, Mayo Clinic, 200 First Street SW, Rochester MN 55905, 2Department of Health Sciences Research, Mayo Clinic, 4500 San Pablo Road South, Jacksonville FL 32224, 3Department of Laboratory Medicine and Pathology, 4Division of Hematology, Department of Internal Medicine, 5Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, 200 First Street SW, Rochester MN 55905 and 6Department of Cancer Biology, Mayo Clinic, 4500 San Pablo Road South, Jacksonville FL 32224, USA"}]},{"given":"Aditya V.","family":"Bhagwate","sequence":"additional","affiliation":[{"name":"1 Division of Biomedical Statistics and Informatics, Mayo Clinic, 200 First Street SW, Rochester MN 55905, 2Department of Health Sciences Research, Mayo Clinic, 4500 San Pablo Road South, Jacksonville FL 32224, 3Department of Laboratory Medicine and Pathology, 4Division of Hematology, Department of Internal Medicine, 5Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, 200 First Street SW, Rochester MN 55905 and 6Department of Cancer Biology, Mayo Clinic, 4500 San Pablo Road South, Jacksonville FL 32224, USA"}]},{"given":"Xue","family":"Wang","sequence":"additional","affiliation":[{"name":"1 Division of Biomedical Statistics and Informatics, Mayo Clinic, 200 First Street SW, Rochester MN 55905, 2Department of Health Sciences Research, Mayo Clinic, 4500 San Pablo Road South, Jacksonville FL 32224, 3Department of Laboratory Medicine and Pathology, 4Division of Hematology, Department of Internal Medicine, 5Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, 200 First Street SW, Rochester MN 55905 and 6Department of Cancer Biology, Mayo Clinic, 4500 San Pablo Road South, Jacksonville FL 32224, USA"}]},{"given":"Jean-Pierre A.","family":"Kocher","sequence":"additional","affiliation":[{"name":"1 Division of Biomedical Statistics and Informatics, Mayo Clinic, 200 First Street SW, Rochester MN 55905, 2Department of Health Sciences Research, Mayo Clinic, 4500 San Pablo Road South, Jacksonville FL 32224, 3Department of Laboratory Medicine and Pathology, 4Division of Hematology, Department of Internal Medicine, 5Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, 200 First Street SW, Rochester MN 55905 and 6Department of Cancer Biology, Mayo Clinic, 4500 San Pablo Road South, Jacksonville FL 32224, USA"}]},{"given":"Susan L.","family":"Slager","sequence":"additional","affiliation":[{"name":"1 Division of Biomedical Statistics and Informatics, Mayo Clinic, 200 First Street SW, Rochester MN 55905, 2Department of Health Sciences Research, Mayo Clinic, 4500 San Pablo Road South, Jacksonville FL 32224, 3Department of Laboratory Medicine and Pathology, 4Division of Hematology, Department of Internal Medicine, 5Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, 200 First Street SW, Rochester MN 55905 and 6Department of Cancer Biology, Mayo Clinic, 4500 San Pablo Road South, Jacksonville FL 32224, USA"}]},{"given":"Andrew L.","family":"Feldman","sequence":"additional","affiliation":[{"name":"1 Division of Biomedical Statistics and Informatics, Mayo Clinic, 200 First Street SW, Rochester MN 55905, 2Department of Health Sciences Research, Mayo Clinic, 4500 San Pablo Road South, Jacksonville FL 32224, 3Department of Laboratory Medicine and Pathology, 4Division of Hematology, Department of Internal Medicine, 5Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, 200 First Street SW, Rochester MN 55905 and 6Department of Cancer Biology, Mayo Clinic, 4500 San Pablo Road South, Jacksonville FL 32224, USA"}]},{"given":"Anne J.","family":"Novak","sequence":"additional","affiliation":[{"name":"1 Division of Biomedical Statistics and Informatics, Mayo Clinic, 200 First Street SW, Rochester MN 55905, 2Department of Health Sciences Research, Mayo Clinic, 4500 San Pablo Road South, Jacksonville FL 32224, 3Department of Laboratory Medicine and Pathology, 4Division of Hematology, Department of Internal Medicine, 5Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, 200 First Street SW, Rochester MN 55905 and 6Department of Cancer Biology, Mayo Clinic, 4500 San Pablo Road South, Jacksonville FL 32224, USA"}]},{"given":"James R.","family":"Cerhan","sequence":"additional","affiliation":[{"name":"1 Division of Biomedical Statistics and Informatics, Mayo Clinic, 200 First Street SW, Rochester MN 55905, 2Department of Health Sciences Research, Mayo Clinic, 4500 San Pablo Road South, Jacksonville FL 32224, 3Department of Laboratory Medicine and Pathology, 4Division of Hematology, Department of Internal Medicine, 5Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, 200 First Street SW, Rochester MN 55905 and 6Department of Cancer Biology, Mayo Clinic, 4500 San Pablo Road South, Jacksonville FL 32224, USA"}]},{"given":"E. Aubrey","family":"Thompson","sequence":"additional","affiliation":[{"name":"1 Division of Biomedical Statistics and Informatics, Mayo Clinic, 200 First Street SW, Rochester MN 55905, 2Department of Health Sciences Research, Mayo Clinic, 4500 San Pablo Road South, Jacksonville FL 32224, 3Department of Laboratory Medicine and Pathology, 4Division of Hematology, Department of Internal Medicine, 5Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, 200 First Street SW, Rochester MN 55905 and 6Department of Cancer Biology, Mayo Clinic, 4500 San Pablo Road South, Jacksonville FL 32224, USA"}]},{"given":"Yan W.","family":"Asmann","sequence":"additional","affiliation":[{"name":"1 Division of Biomedical Statistics and Informatics, Mayo Clinic, 200 First Street SW, Rochester MN 55905, 2Department of Health Sciences Research, Mayo Clinic, 4500 San Pablo Road South, Jacksonville FL 32224, 3Department of Laboratory Medicine and Pathology, 4Division of Hematology, Department of Internal Medicine, 5Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, 200 First Street SW, Rochester MN 55905 and 6Department of Cancer Biology, Mayo Clinic, 4500 San Pablo Road South, Jacksonville FL 32224, USA"}]}],"member":"286","published-online":{"date-parts":[[2014,8,27]]},"reference":[{"key":"2023012712014128300_btu577-B1","doi-asserted-by":"crossref","first-page":"e100","DOI":"10.1093\/nar\/gkr362","article-title":"A novel bioinformatics pipeline for identification and characterization of fusion transcripts in breast cancer and normal cell lines","volume":"39","author":"Asmann","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2023012712014128300_btu577-B2","first-page":"477","article-title":"Boosting algorithms: regularization, prediction and model fitting","volume":"22","author":"B\u00fchlmann","year":"2007","journal-title":"Stat. 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