1 line
No EOL
15 KiB
Text
1 line
No EOL
15 KiB
Text
{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2023,12,3]],"date-time":"2023-12-03T00:26:58Z","timestamp":1701563218855},"posted":{"date-parts":[[2022,12,6]]},"group-title":"Genomics","reference-count":44,"publisher":"Cold Spring Harbor Laboratory","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2023,4,5]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>The detection of circular RNA molecules (circRNAs) is typically based on short-read RNA sequencing data processed by computational detection tools. During the last decade, a plethora of such tools have been developed, but a systematic comparison with orthogonal validation is missing. Here, we set up a circRNA detection tool benchmarking study, in which 16 tools were used and detected over 315,000 unique circRNAs in three deeply sequenced human cell types. Next, 1,516 predicted circRNAs were empirically validated using three orthogonal methods. Generally, tool-specific precision values are high and similar (median of 98.8%, 96.3%, and 95.5% for qPCR, RNase R, and amplicon sequencing, respectively) whereas the sensitivity and number of predicted circRNAs (ranging from 1,372 to 58,032) are the most significant tool differentiators. Furthermore, we demonstrate the complementarity of tools through the increase in detection sensitivity by considering the union of highly-precise tool combinations while keeping the number of false discoveries low. Finally, based on the benchmarking results, recommendations are put forward for circRNA detection and validation.<\/jats:p>","DOI":"10.1101\/2022.12.06.519083","type":"posted-content","created":{"date-parts":[[2022,12,7]],"date-time":"2022-12-07T04:35:10Z","timestamp":1670387710000},"source":"Crossref","is-referenced-by-count":0,"title":["Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision"],"prefix":"10.1101","author":[{"ORCID":"http:\/\/orcid.org\/0000-0002-0163-0675","authenticated-orcid":false,"given":"Marieke","family":"Vromman","sequence":"first","affiliation":[]},{"given":"Jasper","family":"Anckaert","sequence":"additional","affiliation":[]},{"ORCID":"http:\/\/orcid.org\/0000-0001-8240-3070","authenticated-orcid":false,"given":"Stefania","family":"Bortoluzzi","sequence":"additional","affiliation":[]},{"given":"Alessia","family":"Buratin","sequence":"additional","affiliation":[]},{"given":"Chia-Ying","family":"Chen","sequence":"additional","affiliation":[]},{"given":"Qinjie","family":"Chu","sequence":"additional","affiliation":[]},{"given":"Trees-Juen","family":"Chuang","sequence":"additional","affiliation":[]},{"ORCID":"http:\/\/orcid.org\/0000-0001-7413-3437","authenticated-orcid":false,"given":"Roozbeh","family":"Dehghannasiri","sequence":"additional","affiliation":[]},{"given":"Christoph","family":"Dieterich","sequence":"additional","affiliation":[]},{"given":"Xin","family":"Dong","sequence":"additional","affiliation":[]},{"given":"Paul","family":"Flicek","sequence":"additional","affiliation":[]},{"ORCID":"http:\/\/orcid.org\/0000-0001-6338-7677","authenticated-orcid":false,"given":"Enrico","family":"Gaffo","sequence":"additional","affiliation":[]},{"ORCID":"http:\/\/orcid.org\/0000-0003-4501-0539","authenticated-orcid":false,"given":"Wanjun","family":"Gu","sequence":"additional","affiliation":[]},{"given":"Chunjiang","family":"He","sequence":"additional","affiliation":[]},{"given":"Steve","family":"Hoffmann","sequence":"additional","affiliation":[]},{"given":"Osagie","family":"Izuogu","sequence":"additional","affiliation":[]},{"given":"Michael S.","family":"Jackson","sequence":"additional","affiliation":[]},{"given":"Tobias","family":"Jakobi","sequence":"additional","affiliation":[]},{"ORCID":"http:\/\/orcid.org\/0000-0002-8432-5851","authenticated-orcid":false,"given":"Eric C.","family":"Lai","sequence":"additional","affiliation":[]},{"given":"Justine","family":"Nuytens","sequence":"additional","affiliation":[]},{"given":"Julia","family":"Salzman","sequence":"additional","affiliation":[]},{"given":"Mauro","family":"Santibanez-Koref","sequence":"additional","affiliation":[]},{"ORCID":"http:\/\/orcid.org\/0000-0002-5016-5191","authenticated-orcid":false,"given":"Peter","family":"Stadler","sequence":"additional","affiliation":[]},{"given":"Olivier","family":"Thas","sequence":"additional","affiliation":[]},{"given":"Eveline Vanden","family":"Eynde","sequence":"additional","affiliation":[]},{"given":"Kimberly","family":"Verniers","sequence":"additional","affiliation":[]},{"given":"Guoxia","family":"Wen","sequence":"additional","affiliation":[]},{"given":"Jakub","family":"Westholm","sequence":"additional","affiliation":[]},{"given":"Li","family":"Yang","sequence":"additional","affiliation":[]},{"given":"Chu-Yu","family":"Ye","sequence":"additional","affiliation":[]},{"given":"Nurten","family":"Yigit","sequence":"additional","affiliation":[]},{"given":"Guo-Hua","family":"Yuan","sequence":"additional","affiliation":[]},{"given":"Jinyang","family":"Zhang","sequence":"additional","affiliation":[]},{"given":"Fangqing","family":"Zhao","sequence":"additional","affiliation":[]},{"ORCID":"http:\/\/orcid.org\/0000-0001-6274-0184","authenticated-orcid":false,"given":"Jo","family":"Vandesompele","sequence":"additional","affiliation":[]},{"given":"Pieter-Jan","family":"Volders","sequence":"additional","affiliation":[]}],"member":"246","reference":[{"key":"2023040810301213000_2022.12.06.519083v2.1","doi-asserted-by":"publisher","DOI":"10.1038\/s41576-019-0158-7"},{"key":"2023040810301213000_2022.12.06.519083v2.2","doi-asserted-by":"crossref","unstructured":"Hulstaert, E. , Morlion, A. , Avila Cobos, F. , Verniers, K. , Nuytens, J. , vanden Eynde, E. , Yigit, N. , Anckaert, J. , Geerts, A. , Hindryckx, P. , et al. (2020) Charting Extracellular Transcriptomes in The Human Biofluid RNA Atlas. Cell Rep, 33.","DOI":"10.2139\/ssrn.3639616"},{"key":"2023040810301213000_2022.12.06.519083v2.3","doi-asserted-by":"publisher","DOI":"10.1186\/s12943-020-01305-3"},{"key":"2023040810301213000_2022.12.06.519083v2.4","doi-asserted-by":"crossref","first-page":"e181","DOI":"10.1002\/cpz1.181","article-title":"Validation of Circular RNAs Using RT-qPCR After Effective Removal of Linear RNAs by Ribonuclease R","volume":"1","year":"2021","journal-title":"Curr Protoc"},{"key":"2023040810301213000_2022.12.06.519083v2.5","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku643"},{"key":"2023040810301213000_2022.12.06.519083v2.6","doi-asserted-by":"publisher","DOI":"10.1038\/nrg.2016.114"},{"key":"2023040810301213000_2022.12.06.519083v2.7","doi-asserted-by":"crossref","first-page":"1208","DOI":"10.1038\/s41592-022-01487-2","article-title":"Best practice standards for circular RNA research","volume":"19","year":"2022","journal-title":"Nat Methods"},{"key":"2023040810301213000_2022.12.06.519083v2.8","doi-asserted-by":"publisher","DOI":"10.15252\/embr.202051851"},{"key":"2023040810301213000_2022.12.06.519083v2.9","first-page":"e1528","article-title":"Computational approaches for circular RNA analysis","volume":"2019","year":"2019","journal-title":"Wiley Interdiscip Rev RNA"},{"key":"2023040810301213000_2022.12.06.519083v2.10","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkv1458"},{"key":"2023040810301213000_2022.12.06.519083v2.11","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbab387"},{"key":"2023040810301213000_2022.12.06.519083v2.12","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.2890"},{"key":"2023040810301213000_2022.12.06.519083v2.13","doi-asserted-by":"crossref","unstructured":"Nguyen, D.T. , Trac, Q.T. , Nguyen, T.H. , Nguyen, H.N. , Ohad, N. , Pawitan, Y. and Vu, T.N. (2021) Circall: fast and accurate methodology for discovery of circular RNAs from paired-end RNA-sequencing data. BMC Bioinformatics, 22.","DOI":"10.1186\/s12859-021-04418-8"},{"key":"2023040810301213000_2022.12.06.519083v2.14","doi-asserted-by":"crossref","first-page":"e1005420","DOI":"10.1371\/journal.pcbi.1005420","article-title":"A comprehensive overview and evaluation of circular RNA detection tools","volume":"13","year":"2017","journal-title":"PLoS Comput Biol"},{"key":"2023040810301213000_2022.12.06.519083v2.15","doi-asserted-by":"crossref","unstructured":"Szabo, L. , Morey, R. , Palpant, N.J. , Wang, P.L. , Afari, N. , Jiang, C. , Parast, M.M. , Murry, C.E. , Laurent, L.C. and Salzman, J. (2015) Statistically based splicing detection reveals neural enrichment and tissue-specific induction of circular RNA during human fetal development. Genome Biol, 16.","DOI":"10.1186\/s13059-015-0690-5"},{"key":"2023040810301213000_2022.12.06.519083v2.16","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkv1289"},{"key":"2023040810301213000_2022.12.06.519083v2.17","first-page":"511","article-title":"CIRCexplorer3: A CLEAR Pipeline for Direct Comparison of Circular and Linear RNA Expression","volume":"17","year":"2020","journal-title":"Genomics Proteomics Bioinformatics"},{"key":"2023040810301213000_2022.12.06.519083v2.18","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2014.10.062"},{"key":"2023040810301213000_2022.12.06.519083v2.19","doi-asserted-by":"crossref","first-page":"1055","DOI":"10.1080\/15476286.2016.1245268","article-title":"Full-length sequence assembly reveals circular RNAs with diverse non-GT\/AG splicing signals in rice","volume":"14","year":"2017","journal-title":"RNA Biol"},{"key":"2023040810301213000_2022.12.06.519083v2.20","doi-asserted-by":"publisher","DOI":"10.1186\/s12943-018-0930-x"},{"key":"2023040810301213000_2022.12.06.519083v2.21","doi-asserted-by":"crossref","first-page":"2326","DOI":"10.1093\/bioinformatics\/bty948","article-title":"Circtools\u2014a one-stop software solution for circular RNA research","volume":"35","year":"2019","journal-title":"Bioinformatics"},{"key":"2023040810301213000_2022.12.06.519083v2.22","doi-asserted-by":"crossref","first-page":"803","DOI":"10.1093\/bib\/bbx014","article-title":"Circular RNA identification based on multiple seed matching","volume":"19","year":"2018","journal-title":"Brief Bioinform"},{"key":"2023040810301213000_2022.12.06.519083v2.23","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-019-13840-9"},{"key":"2023040810301213000_2022.12.06.519083v2.24","doi-asserted-by":"publisher","DOI":"10.1038\/nature11928"},{"key":"2023040810301213000_2022.12.06.519083v2.25","doi-asserted-by":"crossref","unstructured":"Chuang, T.J. , Wu, C.S. , Chen, C.Y. , Hung, L.Y. , Chiang, T.W. and Yang, M.Y. (2016) NCLscan: Accurate identification of non-co-linear transcripts (fusion, trans-splicing and circular RNA) with a good balance between sensitivity and precision. Nucleic Acids Res, 44.","DOI":"10.1093\/nar\/gkv1013"},{"key":"2023040810301213000_2022.12.06.519083v2.26","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-019-2669-9"},{"key":"2023040810301213000_2022.12.06.519083v2.27","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-017-4368-0"},{"key":"2023040810301213000_2022.12.06.519083v2.28","doi-asserted-by":"crossref","first-page":"2131","DOI":"10.1093\/bioinformatics\/btx129","article-title":"Quantifying circular RNA expression from RNA-seq data using model-based framework","volume":"33","year":"2017","journal-title":"In Bioinformatics"},{"key":"2023040810301213000_2022.12.06.519083v2.29","doi-asserted-by":"crossref","unstructured":"Hoffmann, S. , Otto, C. , Doose, G. , Tanzer, A. , Langenberger, D. , Christ, S. , Kunz, M. , Holdt, L.M. , Teupser, D. , Hackerm\u00fcller, J. , et al. (2014) A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection. Genome Biol, 15.","DOI":"10.1186\/gb-2014-15-2-r34"},{"key":"2023040810301213000_2022.12.06.519083v2.30","doi-asserted-by":"crossref","first-page":"288","DOI":"10.1093\/bib\/bbz175","article-title":"Closing the circle: current state and perspectives of circular RNA databases","volume":"22","year":"2021","journal-title":"Brief Bioinform"},{"key":"2023040810301213000_2022.12.06.519083v2.31","doi-asserted-by":"crossref","unstructured":"Vromman, M. , Anckaert, J. , Vandesompele, J. and Volders, P.-J. (2022) CIRCprimerXL: Convenient and High-Throughput PCR Primer Design for Circular RNA Quantification. Frontiers in Bioinformatics, 2.","DOI":"10.3389\/fbinf.2022.834655"},{"key":"2023040810301213000_2022.12.06.519083v2.32","doi-asserted-by":"crossref","first-page":"836","DOI":"10.1038\/s41587-021-00842-6","article-title":"Comprehensive profiling of circular RNAs with nanopore sequencing and CIRI-long","volume":"39","year":"2021","journal-title":"Nat Biotechnol"},{"key":"2023040810301213000_2022.12.06.519083v2.33","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-021-22785-x"},{"issue":"12","key":"2023040810301213000_2022.12.06.519083v2.34","first-page":"1","article-title":"isoCirc catalogs full-length circular RNA isoforms in human transcriptomes","volume":"2021","year":"2021","journal-title":"Nature Communications"},{"key":"2023040810301213000_2022.12.06.519083v2.35","doi-asserted-by":"publisher","DOI":"10.7554\/elife.69457"},{"key":"2023040810301213000_2022.12.06.519083v2.36","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkp829"},{"key":"2023040810301213000_2022.12.06.519083v2.37","doi-asserted-by":"publisher","DOI":"10.1093\/NAR\/GKAC318"},{"key":"2023040810301213000_2022.12.06.519083v2.38","unstructured":"R Core Team (2019) R: A language and environment for statistical computing."},{"key":"2023040810301213000_2022.12.06.519083v2.39","unstructured":"RStudio Team (2020) RStudio: Integrated Development for R. RStudio."},{"key":"2023040810301213000_2022.12.06.519083v2.40","unstructured":"van Rossum, G. and Drake, F.L. (2009) Python 3 Reference Manual."},{"issue":"9","key":"2023040810301213000_2022.12.06.519083v2.41","first-page":"357","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"2012","year":"2012","journal-title":"Nature Methods"},{"key":"2023040810301213000_2022.12.06.519083v2.42","doi-asserted-by":"crossref","unstructured":"Danecek, P. , Bonfield, J.K. , Liddle, J. , Marshall, J. , Ohan, V. , Pollard, M.O. , Whitwham, A. , Keane, T. , McCarthy, S.A. , Davies, R.M. , et al. (2021) Twelve years of SAMtools and BCFtools. Gigascience, 10.","DOI":"10.1093\/gigascience\/giab008"},{"key":"2023040810301213000_2022.12.06.519083v2.43","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btq033"},{"key":"2023040810301213000_2022.12.06.519083v2.44","doi-asserted-by":"publisher","DOI":"10.1093\/NAR\/GKAB1049"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1101\/2022.12.06.519083","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,12,2]],"date-time":"2023-12-02T15:50:52Z","timestamp":1701532252000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/2022.12.06.519083"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,12,6]]},"references-count":44,"URL":"http:\/\/dx.doi.org\/10.1101\/2022.12.06.519083","relation":{},"published":{"date-parts":[[2022,12,6]]},"subtype":"preprint"}} |