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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