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What methods or tools doyou use for the analysisand visualization of data?Excel and SPSS analysis.—Hsueh-Wei ChangWe are using home-grown visualization software to,for example, display coverage of a gene of interest ina candidate gene study. In some cases, we plugit into graphical user interfaces like that offered bythe HapMap.Secondly, we are using commercial software forlinkage analysis. We do a lot of linkage analysis withAffymetrix's 10K. We are using commercial softwareas well as relying on ourstatistical collaborators toanalyze the linkage data.We're relying on manymore statistical collaboratorsand evolving software forwhole-genome scans. Whilewe have ideas about how toanalyze that data today, thisis really an evolving area ofresearch, and I rely on mystatistical collaborators fordirection in analysis.Some of us researchers play a key role inproviding statisticians with direction, and some of usare taking a stab at the analysis itself, but that's alittle dangerous. We're not statisticians and we couldbe creating more havoc than help. Just as we sawwith the microarray world 10 years ago, we're seeingsoftware companies bring, in some cases, userfriendlysoftware to market that a lot of statisticiansare having a hard time swallowing. Because ease-ofusedoesn't mean statistical robustness. Just becauseyou can select an algorithm or a test, it doesn't mean“Some of us researchers play akey role in providing statisticianswith direction, and some of us aretaking a stab at the analysis itself,but that's a little dangerous.”it's the right test. It doesn't substitute for having astatistician on your team.— David DugganFor analyzing the genotyping data, we actually usethe Sequenom Typer software for the Sequenomplatform, and we use the Applied BiosystemsGeneMapper software for the Applied Biosystemsplatform. We supply back to our clients thegenotypes only. Clients may request the mass spectraor electropherograms; however, these are notroutinely supplied as themajority of our clients do— David Duggannot have the software toanalyze these.We also analyze ascatter plot of the peakareas of the two alleles toensure that our genotypesare clustered very clearly.They fall into three separategroups: homozygous wildtype, heterozygous, andhomozygous mutant. Thisplot gives us a lot of information about the quality ofthe DNA that's going through and the accuracy ofthe genotypes. We always expect to see threeseparate groups, but on occasion, we have observeda split in the heterozygous groups, which indicatesthat there is a copy number variant and this is alsoadvised back to our clients.We find the Sequenom platform is a very usefultool for looking at copy number variants because itcan perform quantitative genotyping to a high levelof accuracy. Sequenom's platform can perform16 SNP Genotyping Tech Guide Genome Technology
quantitative genotyping to look at allelic frequenciesin pooled DNA samples. We can use the samemethodology to analyze individual DNA samples forcopy number variants with little additional cost.— Darryl IrwinThe genotypes we collect are all derived fromintensity measurements on spotted arrays. We usethe ArrayVision software (GE Healthcare) to semiautomaticallyextract the intensity data, and with thisdata in hand use custom scripts written in the freelyavailable statistical programming language R tocluster the individuals and call genotypes. Thesescripts are described in Macdonald et al. (2005). Theadvantage of R over licensed commercial software isthat scripts can be easily customized. Since there is awide community of academics developing R scriptsand depositing them in accessible databases, oftenthere are useful scripts and functions readily availablefor downstream analysis of the genotype data.— Stuart MacdonaldIn general we use the methods provided with a givenplatform. For Amplifluor and TaqMan, we have usedApplied Biosystem's SDS2.0 software, and forSNPlex, the Genemapper software. For the GOODassay, software called SNPmaster has beendeveloped for internal use at the French NationalGenotyping Center. Following analysis, genotypingdata is submitted to a database located at the INRA'sUnité de Recherche Génomique-Info.— Heather McKhannWe have created our own database for storing thedata. Statistical analyses are mainly performed inJMP IN, which also provides graphs, etc.— Louise NordforsThe traditional statistical ones: Excel sometimes, andmainly SPSS, STATA, Episheet, and EPI-Info.— Jose Luis RoyoIllumina Gencall, Sequenom MassArray typer, andPerkinElmer SNPscorer. All work reasonably well.— Huanming YangGenome Technology SNP Genotyping Tech Guide 17
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