VISMapper: Ultra-fast exhaustive cartography of viral insertion sites for gene therapy

SOFTWARE Open Access VISMappe : ul a- as exhaus i e ca og aphy o i al inse ion si es o gene he apy José M. Juanes 1,2† , Asunción Gallego 3,4† , Joaquín Tá aga 2,5 , Felipe J. Cha es 6,7 , Pablo Ma ín-Ga cia 6,8 , Ignacio Medina 5 , Vicen e A nau 1,2,8 and Joaquín Dopazo 3,9,10* Abs ac Backg ound: The possibili y o in eg a ing i al ec o s o become a pe sis en pa o he hos genome makes hem a c ucial elemen o clinical gene he apy. Howe e , i al in eg a ion has associa ed isks, such as he unin en ional ac i a ion o oncogenes ha can esul in cance . The e o e, he analysis o in eg a ion si es o e o i al ec o s is a c ucial s ep in de eloping sa e ec o s o he apeu ic use. Resul s: He e we p esen VISMappe , a ec o in eg a ion si e analysis web se e , o analyze nex -gene a ion sequencing da a o e o i al ec o in eg a ion si es. VISMappe can be ound a : h p:// ismappe .babelomics.o g. Conclusions: Because i uses no el mapping algo i hms VISMappe is ema kably as e han p e ious a ailable p og ams. I also p o ides a use ul g aphical in e ace o analyze he in eg a ion si es ound in he genomic con ex . Keywo ds: Gene he apy, Vi al inse ion, Vi al in eg a ion, Sequence mapping, Genome iewe Backg ound The s able, long- e m co ec ion o diseases by in eg a - ing i al ec o s ca ying heal hy copies de ec i e genes in he pa ien ’s genome has become mains eam p oced- u e in clinical gene he apy [1, 2]. Howe e , despi e i s success ul applica ion, i al in eg a ion based he apies a e no exemp o isks, such as he acciden al ac i a ion o oncogenes ha can cause malignan ans o ma ion o he cells [3, 4]. Vec o loca ions in he hos genome con- s i u e molecula ma ke s ha help moni o ing he a e o a ec ed cells. Analysis o ec o inse ion si es (ISs) is ca ied ou by he ampli ica ion (cu en ly using Nex Gene a ion Sequencing –NGS- echnologies) o se- quences om e o i al ec o s wi h a long e minal e- pea (LTR). P ime s mapping LTRs p oduce sequence eads wi h LTR-ch omosome junc ions, which can be used o accu a ely de e mine he ch omosomal egion o inse ion o he i al ec o [4]. Such moni o ing is e- qui ed because i is known ha dis inc gene ans e ec o s can ha e p e e ences o a ge gene coding e- gions, CpG islands, o ansc ip ional s a si es [5–7]. He e we p esen a new web se e , VISMappe , a web ool o manage sequencing da a o he de ec ion o i al ec o inse ion si es in gene he apy expe imen s. VIS- Mappe is much as e han o he al e na i e so wa e a ailable and p o ides a comp ehensi e g aphic in e ace ha allows in e ac i e isualiza ion o he i al ISs in he genomic con ex . Implemen a ion VISMappe is w i en in Node.js (a Ja aSc ip un ime) and uses GenomeMaps [8] o he isual ep esen a ion o he esul s in he con ex o he genome. Thus he esul ing i al inse ion si es o an expe imen can be i- sualized along wi h he genomic ea u es hey ha e a ound, including eads mapped, genes and o he ype o genomic elemen s. Suppo ed assemblies o he human genome a e GRCh37 and GRCh38. Cance genes we e aken om he COSMIC [9] da a- base h ough he CellBase [10] webse ices. * Co espondence: [email p o ec ed];[email p o ec ed] † Equal con ibu o s 3 Clinical Bioin o ma ics Resea ch A ea, Fundación P og eso y Salud, Hospi al Vi gen del Rocío, 41013 Se illa, Spain 9 Bioin o ma ics and Da a Analysis Uni , Genomic Medicine Ins i u e Imegen, Valencia, Spain Full lis o au ho in o ma ion is a ailable a he end o he a icle © The Au ho (s). 2017 Open Access This a icle is dis ibu ed unde he e ms o he C ea i e Commons A ibu ion 4.0 In e na ional License (h p://c ea i ecommons.o g/licenses/by/4.0/), which pe mi s un es ic ed use, dis ibu ion, and ep oduc ion in any medium, p o ided you gi e app op ia e c edi o he o iginal au ho (s) and he sou ce, p o ide a link o he C ea i e Commons license, and indica e i changes we e made. The C ea i e Commons Public Domain Dedica ion wai e (h p://c ea i ecommons.o g/publicdomain/ze o/1.0/) applies o he da a made a ailable in his a icle, unless o he wise s a ed. Juanes e al. BMC Bioin o ma ics (2017) 18:421 DOI 10.1186/s12859-017-1837-z Resul s Da a upload and wo kspace VISMappe eads s anda d FASTQ o FASTA iles con aining eads co esponding o he inse ion si es o he i us. I FASTA iles a e p o ided, hey a e con e ed o FASTQ o ma . Since FASTA iles lack he quali y pa ame e , his is se o 20 by de aul o he FASTQ ile gene a ed. A alue o 20 minimizes he alse posi i e a e when he o iginal sequences a e s anda d quali y. In any case, he use o FASTQ con- aining quali y alues is ob iously p e e able. Files can be ZIP comp essed. Du ing he upload, use can op- ionally p o ide an email o be no i ied o he end o he da a p ocessing (gi en he speed o da a p ocess- ing i is usually unnecessa y). Read mapping Reads in he FASTQ ile a e mapped on o he e e ence human genome using BWA [11] o HPG-Align [12]. Typically mapping un imes a e in he ange o seconds, which makes o VISMappe a uly in e ac i e and ac- cu a e ool o explo ing he esul o e o i al inse ion expe imen s. IS loca ions a e de ec ed by iden i ied eads pa ially mapped. We use he CIGAR in o ma ion o his. When he CIGAR o a mapping con ains so o ha d clippings i indica es ha he co esponding ead Fig. 1 Sc eensho showing he di e en g aphical ep esen a ions in he dashboa d: he ka yo ype iewe and he genome iewe . Also, a able wi h he lis o IS ound is displayed Juanes e al. BMC Bioin o ma ics (2017) 18:421 Page 2 o 5 ha e pa o he genome sequence as well as pa o he i al sequence. The eads a e a anged by ch omosome using SAMTools [13] and a e inse ed in a MySQL da a- base o acili a ing a as e access o hem. Dashboa d The Dashboa d is a g aphical wo king en i onmen composed by h ee panels: he ka yo ype iewe , he genome iewe and he con ol panel (See Fig. 1). The ka yo ype iewe p o ides a gene al pe spec i e o all he ISs along he ch omosomes. Clicking wi h he le mouse bu on magni ies he ch omosome, wi h ISs ma ked as ed lines. Exac de ails on he IS loca ion a e p o ided by se ing he cu so o e hem. A e ical panel on i s le (See Fig. 1) allows il e ing IS by he numbe o eads suppo ing hem. I also allows sea ch- ing hose eads which a e close o oncogenes o genes ela ed o speci ic umo ypes. When he mouse ho e s he ch omosome in he ka yo ype a de ailed iew o he selec ed ch omosome wi h he IS is displayed. Se ing he mouse o e he ISs pops up in o ma ion on i s exac loca ion and he numbe o eads suppo ing i . A mo e de ailed iew o he egion in which he ISs occu ( ha can be selec ed by clicking in he ka yo ype iewe ) can be ob ained wi h he genome iewe , which implemen s GenomeMaps [8]. Se e al acks a e a ail- able a di e en de ail le el depending on he zoom le el in he genome iewe : a) he su ounding genomic e- gion, b) oncogenes loca ed in he neighbo hood ( he cu so o e hem displays in o ma ion on he genes) and c) eads mapped a ound he IS (again, in o ma ion on he ead, such as s and, mapping quali y, e c. is p o- ided by ho e ing he mouse on hem). Finally, he con ol panel allows se ing a h eshold based on he numbe o eads ha suppo ISs and al- lows inding speci ic cance genes o genes o speci ic cance ypes (see Fig. 1, le pa ). Speci ically, a box al- lows se ing a h eshold wi h he minimum numbe o eads o conside a IS (5 by de aul ). The second box al- lows selec ing a speci ic oncogene (can be sea ched by name o selec ed om a lis ). The lis o oncogenes has been ex ac ed om COSMIC. Ano he box allows dis- playing only he genes known o be associa ed wi h a gi en umo . Repo The con ol panel allows gene a ing a comp ehensi e abula epo o he esul s ound. The bu on epo di- ec s o ano he page wi h a able con aining all he ISs ound ha can be a anged by all he c i e ia shown in he heade o he columns (ch omosome, posi ion, qual- i y, e c.) Di e en il e s (numbe o eads ha suppo he IS and dis ance o a cance gene) can be applied o expand o educe he numbe o ISs o conside . This lis can be downloaded in ab delimi ed o ma and a BAM ile wi h he alignmen s ound by he mappe can also be downloaded. Fo any IS conside ed wi h he il e ing schema used, he epo con ains he ollowing i ems: –Ch omosome –Posi ion Fig. 2 Run imes obse ed o di e en p og ams QuickMap (line wi h diamonds), VISA (line wi h squa es) HISAP (line wi h iangles) and VISMappe (line wi h ci cles) wi h da ase s o inc easing sizes. In he case o QuickMap, VISA and HISAP, he lines a e in e up ed acco ding o in e nal ha d limi s o he numbe o sequences ha he p og ams can p ocess Juanes e al. BMC Bioin o ma ics (2017) 18:421 Page 3 o 5 –Numbe o eads mapped in his posi ion –A e age quali y o all he eads mapped in he posi ion –Closes oncogene –Dis ance o he oncogene (0 means ha he IS maps wi hin he oncogene) –Posi ion o he oncogene wi h espec o he IS –En ez en y o he oncogene –URL o he En ez en y o he oncogene Compa ison o o he web se e s o i al is mapping The e a e a ew web se e s o i al ec o inse ion si e analysis, such as, HISAP [14], SeqMap ( equi es use egis a ion) o QuickMap [15], o he ecen ly published VISA [16]. Howe e , all o hem use BLAST [17] o BLAT [18] o ead mapping ha in ol e compa a i ely much longe un imes. Figu e 2 shows a compa a i e o un- imes whe e he inc ease in speed gained by he use o mo e sophis ica ed mapping algo i hms in VISMappe is ob ious. The da a used in he compa ison we e aken om he VISA websi e and can also be downloaded a he VISMappe documen a ion si e (h ps://gi hub.com/ jmjuanes/ ismappe / ee/mas e /ismappe - es ). In addi ion, a mo e de ailed compa ison was made wi h he VISA p og am by gene a ing 4 da ase s wi h known numbe o IS using he IS gene a o p og am om he VISA websi e (h ps:// isa.pha macy.wsu.edu/bioin o ma - ics/ andom_si e_gene a o .h ml). Table 1 shows he e- sul s o he compa ison. Rela i e un imes a e simila o he ones shown in Fig. 2. While bo h me hods gi e a e y small numbe o alse posi i es, in gene al VISMappe is able o map a highe pe cen age o sequences and ound mo e IS si es han VISA. In addi ion, QuickMap does no p ocess mo e han 50,000 sequences and VISA limi s a e be ween 50,000 and 100,000. HISAP could manage up o 100,000 in abou 50 min, bu canno a i e o 250,000 sequences. Mo eo e , none o he o he p og ams p o ide a g aphic in e ace o analyze he esul s. Fu he mo e, QuickMap and HISAP do no suppo GRCh38. Conclusions Because o i s speed and sensi i i y, VISMappe cons i- u es an a ac i e al e na i e o he op ions a ailable o i al inse ion si e analysis. VISMappe o e s a unique, in e ac i e g aphical wo king en i onmen ha allows a de ailed and exhaus i e explo a ion o he consequences and po en ial isks o he i al ec o s inse ed in he analyzed genome. Abb e ia ions BAM: Bina y alignmen map; BWA: Bu ows–wheele algo i hm; IS: Inse ion Si e; LTR: Long e minal epea ; NGS: Nex gene a ion sequencing Acknowledgemen s No applicable Funding This wo k is suppo ed by g an s BIO2014–57291-R om he Spanish Minis y o Economy and Compe i i eness (MINECO), and Pla a o ma de Recu sos Biomolecula es y Bioin o má icos PT13/0001/0007 om he ISCIII, bo h co- unded wi h Eu opean Regional De elopmen Funds (ERDF); H2020- INFRADEV-1-2015-1 ELIXIR-EXCELERATE ( e . 676,559). None o he unding bodies played any ole in he design o conclusions o he s udy. A ailabili y o da a and ma e ials VISMappe can be ound a : h p:// ismappe .babelomics.o g. VISMappe code can be ound in he Gi Hub eposi o y h ps://gi hub.com/jmjuanes/ ismappe . Associa ed documen a ion can be ound a : h ps://gi hub.com/ jmjuanes/ ismappe /wiki. The da a used in he gene al compa ison can be ound a : h ps://gi hub.com/jmjuanes/ ismappe / ee/mas e /ismappe - es . Table 1 Compa ison o VISA and VISMappe using ou da ase s gene a ed wi h he IS gene a o p og am om he he VISMappe websi e (h ps:// isa.pha macy.wsu.edu/bioin o ma ics/ andom_si e_gene a o .h ml) Da ase Inpu size ( eads) Inse ion si es Pe o mance VISA VISMappe Inpu 1 Run ime ~72 h ~60 s 100,000 100,000 IS de ec ed 99,694 99.793 To al sequences mapped 99,694 99,881 Inpu 2 Run ime ~72 h ~60 s 50,000 50,000 IS de ec ed 49,854 49,897 To al sequences mapped 49,855 49,936 Inpu 3 Run ime ~72 h ~30 s 10,000 10,000 IS de ec ed 9992 9969 To al sequences mapped 9995 9981 Inpu 4 Run ime ~5 h ~30 s 1000 1000 IS de ec ed 906 929 To al sequences mapped 906 930 Run imes o bo h p og ams a e shown o he ou da ase s, along wi h he numbe o sequences co ec ly mapped, ha co espond o he IS de ec ed, and he o al numbe o sequences mapped, which in bo h cases is sligh ly supe io , demons a ing a low a e o alse posi i es in bo h cases Juanes e al. BMC Bioin o ma ics (2017) 18:421 Page 4 o 5 Au ho s’con ibu ions JMJ, and AG p og ammed he code, JT and IM p og ammed and op imized he mapping o sequences, FJC and PMG helped wi h he p og amming, VA coo dina ed he p og amming wo k and JD concei ed he wo k and w o e he pape . All he au ho s ead and app o ed he inal manusc ip . E hics app o al and consen o pa icipa e No applicable Consen o publica ion No applicable Compe ing in e es s The au ho s decla e ha hey ha e no compe ing in e es s. Publishe ’sNo e Sp inge Na u e emains neu al wi h ega d o ju isdic ional claims in published maps and ins i u ional a ilia ions. Au ho de ails 1 Depa amen o de In o má ica, Escuela Técnica Supe io de Ingenie ía (ETSE), Uni e sidad de Valencia, 46100 Valencia, Bu jasso , Spain. 2 Compu a ional Genomics Depa men , P ince Felipe Resea ch Cen e , 46012 Valencia, Spain. 3 Clinical Bioin o ma ics Resea ch A ea, Fundación P og eso y Salud, Hospi al Vi gen del Rocío, 41013 Se illa, Spain. 4 Bioin o ma ics in Ra e Diseases (BiER), Cen o de In es igación Biomédica en Red de En e medades Ra as (CIBERER), Hospi al Vi gen del Rocío, 41013 Se illa, Spain. 5 HPC Se ice, Uni e si y In o ma ion Se ices, Uni e si y o Camb idge, Camb idge, UK. 6 Geno yping and Gene ic Diagnosis Uni , Heal h Resea ch Ins i u e, INCLIVA, Valencia, Spain. 7 CIBERDem, Heal h Ins i u e Ca los III, Mad id, Spain. 8 Ins i u e o In eg a i e Sys ems Biology (I2SysBio), Uni e sidad de Valencia-CSIC, 46980 Valencia, Pa e na, Spain. 9 Bioin o ma ics and Da a Analysis Uni , Genomic Medicine Ins i u e Imegen, Valencia, Spain. 10 Func ional Genomics Node, INB-ELIXIR-es, Hospi al Vi gen del Rocío, 42013 Se illa, Spain. 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Genome Res. 2002;12(4):656–64. • We accep p e-submission inqui ies • Ou selec o ool helps you o ind he mos ele an jou nal • We p o ide ound he clock cus ome suppo • Con enien online submission • Tho ough pee e iew • Inclusion in PubMed and all majo indexing se ices • Maximum isibili y o you esea ch Submi you manusc ip a www.biomedcen al.com/submi Submi you nex manusc ip o BioMed Cen al and we will help you a e e y s ep: Juanes e al. BMC Bioin o ma ics (2017) 18:421 Page 5 o 5