{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,3]],"date-time":"2025-12-03T17:48:06Z","timestamp":1764784086869},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"19","license":[{"start":{"date-parts":[[2018,5,3]],"date-time":"2018-05-03T00:00:00Z","timestamp":1525305600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"GENMED Laboratory of Excellence on Medical Genomics","award":["ANR-10-LABX-0013"],"award-info":[{"award-number":["ANR-10-LABX-0013"]}]},{"name":"France Genomique National Infrastructure","award":["ANR- 10-INBS-0009"],"award-info":[{"award-number":["ANR- 10-INBS-0009"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,10,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Predicted deleteriousness of coding variants is a frequently used criterion to filter out variants detected in next-generation sequencing projects and to select candidates impacting on the risk of human diseases. Most available dedicated tools implement a base-to-base annotation approach that could be biased in presence of several variants in the same genetic codon. We here proposed the MACARON program that, from a standard VCF file, identifies, re-annotates and predicts the amino acid change resulting from multiple single nucleotide variants (SNVs) within the same genetic codon. Applied to the whole exome dataset of 573 individuals, MACARON identifies 114 situations where multiple SNVs within a genetic codon induce an amino acid change that is different from those predicted by standard single SNV annotation tool. Such events are not uncommon and deserve to be studied in sequencing projects with inconclusive findings.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>MACARON is written in python with codes available on the GENMED website (www.genmed.fr).<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty382","type":"journal-article","created":{"date-parts":[[2018,5,2]],"date-time":"2018-05-02T11:10:47Z","timestamp":1525259447000},"page":"3396-3398","source":"Crossref","is-referenced-by-count":7,"title":["MACARON: a python framework to identify and re-annotate multi-base affected codons in whole genome\/exome sequence data"],"prefix":"10.1093","volume":"34","author":[{"given":"Waqasuddin","family":"Khan","sequence":"first","affiliation":[{"name":"Sorbonne Universit\u00e9s, UPMC Universit\u00e9 Paris 06, INSERM UMR_S 1166, Paris, France"},{"name":"ICAN Institute for Cardiometabolism and Nutrition, Paris, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ganapathi","family":"Varma Saripella","sequence":"additional","affiliation":[{"name":"Sorbonne Universit\u00e9s, UPMC Universit\u00e9 Paris 06, INSERM UMR_S 1166, Paris, France"},{"name":"ICAN Institute for Cardiometabolism and Nutrition, Paris, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thomas","family":"Ludwig","sequence":"additional","affiliation":[{"name":"INSERM U1078, G\u00e9n\u00e9tique, G\u00e9nomique Fonctionnelle et Biotechnologies, Universit\u00e9 de Bretagne Occidentale, CHU Brest, Brest, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tania","family":"Cuppens","sequence":"additional","affiliation":[{"name":"INSERM U1078, G\u00e9n\u00e9tique, G\u00e9nomique Fonctionnelle et Biotechnologies, Universit\u00e9 de Bretagne Occidentale, CHU Brest, Brest, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Florian","family":"Thibord","sequence":"additional","affiliation":[{"name":"Sorbonne Universit\u00e9s, UPMC Universit\u00e9 Paris 06, INSERM UMR_S 1166, Paris, France"},{"name":"ICAN Institute for Cardiometabolism and Nutrition, Paris, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Emmanuelle","family":"G\u00e9nin","sequence":"additional","affiliation":[{"name":"INSERM U1078, G\u00e9n\u00e9tique, G\u00e9nomique Fonctionnelle et Biotechnologies, Universit\u00e9 de Bretagne Occidentale, CHU Brest, Brest, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jean-Francois","family":"Deleuze","sequence":"additional","affiliation":[{"name":"Centre National de Recherche en G\u00e9nomique Humaine (CNRGH), Direction de la Recherche Fondamentale, CEA, Institut de Biologie Fran\u00e7ois Jacob, Evry, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David-Alexandre","family":"Tr\u00e9gou\u00ebt","sequence":"additional","affiliation":[{"name":"Sorbonne Universit\u00e9s, UPMC Universit\u00e9 Paris 06, INSERM UMR_S 1166, Paris, France"},{"name":"ICAN Institute for Cardiometabolism and Nutrition, Paris, France"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2018,5,3]]},"reference":[{"key":"2023012712483811300_bty382-B1","doi-asserted-by":"crossref","first-page":"80","DOI":"10.4161\/fly.19695","article-title":"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: sNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3","volume":"6","author":"Cingolani","year":"2012","journal-title":"Fly"},{"key":"2023012712483811300_bty382-B2","doi-asserted-by":"crossref","first-page":"556","DOI":"10.1038\/nrg3767","article-title":"Expanding the computational toolbox for mining cancer genomes","volume":"15","author":"Ding","year":"2014","journal-title":"Nat. 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Epidemiol"},{"key":"2023012712483811300_bty382-B4","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1038\/nature19057","article-title":"Analysis of protein-coding genetic variation in 60, 706 humans","volume":"536","author":"Lek","year":"2016","journal-title":"Nature"},{"key":"2023012712483811300_bty382-B5","doi-asserted-by":"crossref","first-page":"1297","DOI":"10.1101\/gr.107524.110","article-title":"The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data","volume":"20","author":"McKenna","year":"2010","journal-title":"Genome Res"},{"key":"2023012712483811300_bty382-B6","doi-asserted-by":"crossref","first-page":"122.","DOI":"10.1186\/s13059-016-0974-4","article-title":"The ensembl variant effect predictor","volume":"17","author":"McLaren","year":"2016","journal-title":"Genome Biol"},{"key":"2023012712483811300_bty382-B7","doi-asserted-by":"crossref","first-page":"3812","DOI":"10.1093\/nar\/gkg509","article-title":"SIFT: predicting amino acid changes that affect protein function","volume":"31","author":"Ng","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"2023012712483811300_bty382-B8","doi-asserted-by":"crossref","first-page":"11.10. 1","DOI":"10.1002\/0471250953.bi1110s43","article-title":"From FastQ data to high confidence variant calls: the genome analysis toolkit best practices pipeline","volume":"43","author":"Van der Auwera","year":"2013","journal-title":"Curr. 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Protoc"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/19\/3396\/48918944\/bioinformatics_34_19_3396.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/34\/19\/3396\/48918944\/bioinformatics_34_19_3396.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,27]],"date-time":"2023-01-27T13:41:25Z","timestamp":1674826885000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/34\/19\/3396\/4992149"}},"subtitle":[],"editor":[{"given":"John","family":"Hancock","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2018,5,3]]},"references-count":10,"journal-issue":{"issue":"19","published-print":{"date-parts":[[2018,10,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty382","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2018,10,1]]},"published":{"date-parts":[[2018,5,3]]}}}