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Chunk #18 — Discussion

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How to deal with the early GWAS data when imputing and combining different arrays is necessary.
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Our study illustrates that imputation, whereas combining different arrays in GWAS using data from the earliest platforms without sufficiently stringent QCs may produce false positive associations. A simple remedy to better quality is to choose a stricter threshold for inclusion at the pre- and postimputation stages. For preimputation QCs we refer to Anderson et al.6