Complete(Genome(analysis:( Structural(varia5on(detec5on( ( - - PowerPoint PPT Presentation

Complete(Genome(analysis:( Structural(varia5on(detec5on( ( SVDetect(tutorial(

Alban&LERMINE&–&Ins/tut&Curie,&INSERM&U900,&Mines&ParisTech&

Workshop(outlines(

1) SVDetect(tool(presenta5on( ( (Methodology(&(func5onali5es( 2)(SVDetect(tutorial(on(Galaxy( ( (Hands(on(workshop(

SVDetect(

SVdetect(is(a(tool(dedicated(to(detec5on(and(predic5on(of(inter/intra(chromosomal( rearrangements(from(pairedFend/mateFpair(sequencing(data( ( This(tool(detect(structural(varia5on((SV's)(by(using(sliding(windows(and(clustering( strategies,(and(also(allows(you(to(visualize(them(at(genome(scale(

Different(classes(of(SV’s(

Lot(of(Tumors(have(chromosomal(muta5ons(in(their(genome.(This(can(affect( the(number(of(chromosomes,(and(also(its(structure,(implica5ng(large(events( such(as(dele5ons,(inser5ons,(duplica5ons,(inverisons,transloca5ons,(etc.(

Alkan&et&al&2012&

SV's(discovery(from(sequencing(data(

4(different(methods:( ( F(Based(on(coverage(depth(differences((ControlF(FREEC)( F(SpliVed(reads(method,(local(reads(realignment(around(breaking(point( (Pindel)( F(De(novo(assembly,(new(sequences(F(inser5ons(F( F(PairedFend/mateFpair(sequences(constraints((Breakdancer,(PEMer,( SVDetect)( ( Reviews(on(thema:(

Computa/onal&methods&for&discovering&structural&varia/on&with&nextKgenera/on& sequencing( Paul(Medvedev(et(al,(Nature(Methods(6,(S13(F(S20((2009)( (( Genome&structural&varia/on&discovery&and&genotyping.&& Alkan(C(et(al,(Nat(Rev(Genet.((2012)((

SVDetect(>(strategy(

PairedFend/mateFpair(based(methods,(such(as(SVDetect,(evaluate(reads(distance,(

• rder,(and(orienta5on(a^er(alignment(on(a(reference(genome.(Abnormal(or(

discordants(pairs(are(clustered(to(define(their(type(of(SV(

Ex:(SOAPdenovo(

Reference Sample Mapping Normally mapped pairs NO5SV Distance5<5cutoff LARGE5INSERTION5? Distance5>5cutoff LARGE5DELETION5? Abnormally mapped paired in5the5same chromosome INTRA&CHROMOSOMAL-REARRANGEMENTS- Reference PairedFends reads ALIGNMENT5OF5PAIRED5ENDS

1 2

Ordering Orientation Distance CONSTRAINTS CHR5A CHR5B Abnormally5mapped5paired5in5two5different5chromosomes Reference Mapping INTER&CHROMOSOMAL-REARRANGEMENTS- TRANSLOCATION5? Reference Sample Mapping

Zeitouni&et&al&2010&

SVDetect(>(implementa?on(

Genome(frac?onned((5kb(fragments)( Reference'genome' Abnormal'pairs' 'BAM'file'' Values(for(median(reads(distance,(order(and(

• rienta?on(

Circos(ou(Bed(output( Cluster(filtering:(chromosomes,(number(of(pairs,( distance/order/orienta?on(coherence( SV(poten?al(type(defini?on( BAL/UNBAL(transloca?on( SV's(comparison(for(2(samples:(common,(specific(

DETECTION( FILTERING( COMPARE( CIRCOS( SVDETECT' (perl)' BED(

4'different'funcBons&

BAM' preprocessing'

LINKING( FILTERING( LINKS2CIRCOS( LINKS2BED( COMPARE(

SVDETECT'

ConfiguraBon'file' ' C'DetecBon'parameters' mandatory'or'opBonal' C'Filtering'parameters' C'VisualizaBon'opBons' C'Parallelized'computaBon& Chromosomal(links(crea?on(between(each(fragments(pairs( supported(by(paired(reads(>(clusters(

Tes?ng(data(

(Biological(data(coming(from(neuroblastoma(tumor( (Two(samples:(Tumoral(vs(Control((Cons5tu5onal(DNA)( (( (Illumina(GAII(mateFpair(sequencing,(50x50(bp,(insert(size(of(3kb( (( (Alignments(files(in(binary(format:(BAM( (( (SVDetect(need(2(types(of(files(as(input:( (( ( (F(Bam(file(containing(all(apparied(and(aligned(reads( ( (>(«(sample_mates.bam(»(&(«(reference_mates.bam(»( ( (( (F(LEN(file(giving(reference(chromosome(size( ( (>(«(hs18_chr5_chr11.len(»(

((

(1 !chr5 ! !180857966! !2 !chr11 ! !134452384!

Let’s(start(hands(on(SVDetect(tutorial!(