全基因组的比较基因组杂交技术介绍（WholeGenome and Custom FineTiling Array CGH）

Whole-GenomeandCustomFine-TilingArrayCGH

ComparativeGenomicHybridization(CGH)measuresDNAcopynumberdifferencesbetweenareferencegenomeandyoursamplegenome.NimbleGenofferstwohigh-definitionarrayCGHproducts:whole-genomearrayCGHandfine-tilingarrayCGH.Whole-genomeCGHmeasurescopynumberdifferencesinDNAacrossentiregenomes,whilefine-tilingCGHdeterminesbreakpointsatultrahighresolutioninDNAtargetslocatedinanysubsetofDNA(eitheracontiguousregionormanydifferentregionsofinterest). KeyfeaturesofNimbleGen’smicroarrays-ultra-highdensityandlongoligoprobes-yieldapowerful,high-definitionCGHplatformforwholegenomeanalysis.WiththeflexibilityofNimbleGenarraysynthesis,chromosomalaberrationsidentifiedinwhole-genomesurveyscanbereADIlyexaminedatevenhigherresolutionwithcustomfine-tilingarrayCGH.Suchstudiescanmapgenomicchangesdowntothegeneandevenexonlevelandenablebreakpointmappingtolessthan500bpintervals.NimbleGen’sarrayCGHdetectsbothsingleandmultiplecopychanges.

AdvantagesofNimbleGenArrayCGH

HighestResolutionArrayCGH

NimbleGen"shighcapacitymicroarrayscontain385,000probesonasingleglassslide.ThisfeaturedensityenablesdesignofahumanwholegenomeCGHarraywithprobestiledthroughgenicandintergenicregionsatamedianprobespacingof6,000bp.Thistilingpatharraydesignapproachensuresyougetthecompletepictureongenome-widecopynumberchanges.Ultra-highresolutiondetectionofsmalldeletionsandamplifications,aswellasbreakpointmappingtolessthan500bpintervals,canbeachievedusingNimbleGen"sfine-tilingarrayswithprobesasdenseas10bpspacing.

Isothermal(Tm-Balanced),Long-OligonucleotideProbes

NimbleGen"sexclusiveisothermalarraydesignapproachenablesuniformprobeperformance,eliminatinghybridizationartifactsand/orbiasandprovidinghigherqualitydata.Probelengthsareadjusted(45mer-85mer)toequalizethemeltingtemperature(Tm=76°C)acrosstheentireset.Thus,probesareoptimizedtoperformequivalentlyatagivenstringencyinthegenomicregionsyourexperimentsrequire,includingAT-andGC-richregions.

CustomArrayCGH

NimbleGen"shighlyflexIBLeMasklessArraySynthesistechnologyenablesrapidprototypingofnewarraydesigns.Thisflexibilityenablescost-effectivearrayCGHdesignforyourorganismofinterestatthewhole-genomelevelorfocusedonspecificchromosomalregions.

MostUp-to-dateGenomeBuild

NimbleGenCGHarraysarealwayscurrentwiththelatestgenomebuilds,sothere’snoneedtoputyourexperimentsonholdforanewarrayCGHdesign.Inaddition,youcancontinuetoaccessarraydesignsbasedonpastgenomedatabuilds,whichcanbeparticularlyusefulforcomparisonstopriorstudies.

ProductsandServices

HumanWhole-GenomeArrayCGH

Withacapacityof385,000isothermalprobes,NimbleGen"shigh-density,longoligoarraysspantheentirenon-repetitiveregionsofthehumangenomeinasinglearray,tilingthefullgenomeatamedianprobespacingof6,000bp.NimbleGen"sHumanWhole-GenomeArrayCGH,availableasacatalogdesign(nodesignfees),isacost-effectiveplatformforgenome-wideanalysisofcopynumberchanges.Unlikeothercommercialwhole-genomearrayCGHplatforms,NimbleGen"sHumanWhole-GenomeArrayCGHtilesthroughbothgenicandintergenicregionsofthegenome,providingthemostthorough,unbiasedcoverageavailable.

HumanWhole-GenomeArrayCGHAnalysisofHumanTumorCellLineThelargearraycapacity(385,000features),longoligoprobes,andtilingpathmicroarraydesignenablesgenome-widedetectionofcopynumberchangesingenicandintergenicregions.

FigureA:Whole-genomearrayCGHresultsdisplayedinan“allchromosomes”viewinNimbleGen"sSignalMapbrowser,whichincludesgeneannotationwithdirectlinkstoNCBI.DataareprovidedasGeneralFeatureFormat(GFF)filesforusewithSignalMapandothergenomebrowsers.[ClickforSignalMapview)

FigureB:Whole-genomeplotofdataprocessedwitha50Kbaveragingwindowforaglobalviewofcopynumberchanges.FigureC:Zoomed-inviewofaregioninchromosome3showingasinglecopylossand50Kbmicrodeletion.Toptrackisgeneannotation,middletrackisaverageddatawithsegmentationanalysis(redhorizontallinesdemarcatecopynumberchanges),andbottomtrackisindividualprobedata(unaveraged).

CustomFine-TilingArrayCGH

NimbleGen"sCustomFine-TilingArrayCGHcanbeusedtodetectdeletionsandamplificationsandtomaptheassociatedbreakpointswithunprecedentedresolution.Youcanchooseyourregion(s)ofinterestforafine-tilingarraydesignwithprobesspacedasdenseas10bp.Thisdensityofprobeplacementenablesultra-highresolutionmappingofbreakpointstoanintervalthatcanbevalidatedbyPCRamplificationandsequencing.Theselectedregionsneednotbecontiguousorevenwithinthesamechromosome.Forexample,thecopynumberchangesidentifiedinawhole-genomearrayCGHexperimentcanbecombinedandtiledathigherresolutiononaCustomFine-TilingCGHArray.

Fine-TilingArrayCGHAnalysisofHumanTumorCellLineRegionsfromfourseparatechromosomesweretiledathighresolution,enablingprecisedeterminationofbreakpoints.

FigureD:Fullfine-tilingdatasetinSignalMapbrowserFigureE:Detectionofan~80KbdeletionFigureF:Detectionofasingle-copychangebreakpoint

Applications

NimbleGenarrayCGHisasignificantadvanceovercurrentarrayCGHmethodsforthedetectionofDNAcopynumberchangesandmappingoftheassociatedbreakpoints.Whilethesechangesarecommonlyrecognizedastheunderlyingbasisformanycongenitaldisordersandcomplexdiseases(suchascancer),variationincopynumberisalsocommonlyfoundbetweenhealthyindividuals.Characterizingnormalversusaberrantchromosomaldifferenceswillbekeytounderstandingthemolecularmechanismsforagivendisease.

NimbleGenarrayCGHprovidesthehighestlevelresolutionfordetectingawiderangeofcopynumberchangesoneitheragenome-wideorfine-tilinglevel,including:

• Homozygousandhemizygousdeletions
• Singleandmultiplecopyamplifications
• Unbalancedtranslocations

NimbleGenServiceOverviewNimbleGen"sCGHmicroarrayserviceconsistsofthefollowingsteps:

1. CustomerandNimbleGencreatecustomarraydesign,andNimbleGenmanufacturesthearray.
2. Customersupplies1-3µgpurified,undegradedsampleandreferencegenomicDNA(referenceoptional).
3. NimbleGenlabelsthesample,performstheCGHhybridization,scansthearray,extractsthedata,andperformsthesegmentationanalysis.

DataDeliveryThedatadeliveredwithNimbleGen"sCGHserviceincludes:

• Rawdata
• SegmentationanalysisbasedontheDNACopypackage
• SegmentationGFFfile
• GenomeannotationGFFfile
• SignalMap™GFFvisualizationsoftware

DatasetsareprovidedinGFFfileformatforeasydatasetanalysiswiththeSignalMap™databrowsersoftware.SignalMapdisplaysthesegmentationanalysisinrelationtotheknownstateofsequenceannotation,includinggenes,exons,andrepetitiveelements.

NimbleGenArrayCGHGeneralSpecifications

AvailableArrayDesigns