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Chunk #43 — Discussion

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A new statistic to evaluate imputation reliability.
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Based on this theory, a database can be constructed and used to filter future imputations and to avoid false positive associations. In order to advance the development of this database, we have posted IQS scores for imputation from Illumina 550 K to Illumina 1 M for CEPH on the website of the NIMH Center (http://www.nimhgenetics.org/). We envision this as a dynamic database to be updated when new datasets include subjects genotyped on multiple platforms. We will further provide IQS scores for various array combinations when the genotype data of 6,000 controls typed on both the Affymetrix 6.0 and Illumina 1 M array are available in the near future [26]. The future database will include IQS scores for the following imputations: (1) from Affymetrix 6.0 to Illumina 1 M, (2) from Illumina 1 M to Affymetrix 6.0, (3) from Illumina 300 K to Affymetrix 6.0 plus Illumina 1 M, (4) from Illumina 550 K to Affymetrix 6.0 plus Illumina 1 M, and (5) from Affymetrix 5.0 to Affymetrix 6.0 plus Illumina 1 M. Although genotyping will be ultimately required to confirm