Automated Genotyping of Biobank Samples by Multiplex Amplification of InsertionDeletion Polymorphisms.docVIP

AutomatedGenotypingofBiobankSamplesbyMultiplex AmplificationofInsertion/DeletionPolymorphisms LucyMathot1,ElinFalk-So¨rqvist1,LotteMoens1,MarieAllen1,TobiasSjo¨blom1,MatsNilsson1,2* 1DepartmentofImmunology,GeneticsandPathology,ScienceforLifeLaboratory,UppsalaUniversity,Uppsala,Sweden,2DepartmentofBiochemistryandBiophysics, ScienceforLifeLaboratory,StockholmUniversity,Solna,Sweden Abstract Thegenomicrevolutioninoncologywillentailmutationalanalysesofvastnumbersofpatient-matchedtumorandnormal tissue samples. This has meant an increased risk of patient sample mix up due to manual handling. Therefore, scalable genotyping and sample identification procedures are essential to pathology biobanks. We have developed an efficient alternative to traditional genotyping methods suited for automated analysis. By targeting 53 prevalent deletions and insertionsfoundinhumanpopulationswithfluorescentmultiplexligationdependentgenomeamplification,followedby separation in a capillary sequencer, a peak spectrum is obtained that can be automatically analyzed. 24 tumor-normal patient samples were successfully matched using this method. The potential use of the developed assay for forensic applicationsisdiscussed. Citation:MathotL,Falk-So¨rqvistE,MoensL,AllenM,Sjo¨blomT,etal.(2012)AutomatedGenotypingofBiobankSamplesbyMultiplexAmplificationofInsertion/ DeletionPolymorphisms.PLoSONE7(12):e52750.doi:10.1371/journal.pone.0052750 Editor:ClaireWade,UniversityofSydney,UnitedStatesofAmerica ReceivedOctober22,2012;AcceptedNovember21,2012;PublishedDecember27,2012 Copyright: ? 2012 Mathot et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricteduse,distribution,andreproductioninanymedium,providedtheoriginalauthorandsourcearecredited. Funding:ThisworkhasbeensupportedbygrantsfromtheSwedishresearchcouncil,VINNOVAandtheInnovativeMedicinesInitiativeJointUndertakingunder grantagreementnu115234(OncoTrack),resourcesofwhicharecomp