Genotyper analysis data comparison

FIGURE 1.11 Comparison of data from Genotyper analysis. Comparing PCR products with fragments of allelic ladders, intra- and interlaboratory data exchange is possible. Upper panel allelic ladder of markers D3S1358, THOl, andD18S51 used for human identification shown at the lower panel DNA profiles from four different DNA samples. 

Statistical analysis should be appropriate to the types of outcome data collected and the number of genotypes nsed in the analysis. The handling of missing data should be clearly stated. Corrections for multiple comparisons (e.g., controlling for false discovery rates 36) should be performed if multiple statistical tests are carried out. 

Le Hellard S, Ballereau SJ, Visscher PM, Torrance HS, Pinson J, Morris SW, Thomson ML, Semple CA, Muir WJ, Blackwood DH, Porteous DJ, Evans KL. SNP genotyping on pooled DNAs comparison of genotyping technologies and a semi automated method for data storage and analysis. Nucleic Acids Res... 

The raw data analysis and genotype calling is the first step and handled by the instrumentation software to yield genotype calls for each SNP and subject. The PG SNP Screen software links the sample identifiers back to the clinical database and performs extensive quality control analysis. Quality control includes comparison of genotypes from replicates of the same sample and from control samples to known genotypes. Verification of Hardy Weinberg equilibrium and analysis of quality scores supplied by the instrumentation software assists in establishing quality thresholds on SNPs and DNA samples. 

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