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A chromosome from any of the pairs may be duplicated (trisomy) or absent (monosomy); an entire set of 23 chromosome pairs can be duplicated three (triploidy) or more (polyploidy) times; or one arm or part of one arm of a single chromosome may be missing (deletion).
Although the run-time of this algorithm was acceptable for GWAS data, we found it was missing deletion calls in genomic regions of complex deletion signature.
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Still, it remains possible that there might be some discordance between p53 immunoreactivity and the genetic abnormality: for example, the presence of missing deletions may result in the abolishment of protein production, and some point mutations may lead to the production of unstable proteins without an increase of the half-life (Wynford-Thomas, 1992).
Our method, however, does have limitations as it would miss deletions at the site of PCR primers, whole gene deletions, or deletions within the promoter region all of which have been infrequently detected in PJS (Volikos et al, 2006).
A pileup for a representative example is included in the Additional file 1. Increasing the read depth does reduce the number FNs that result from variation in filtering, but not the missed deletions.
The aligner might prefer an alignment without the deletion near the end, which can lead to a false-positive SNP call in addition to missing the deletion.
The health worry subscale had lower reliability and was not robust under different missing value deletion methods.
Due to listwise deletion of missing values and the deletion of 10 outliers (Mahalanobis distance < 0.001), model n = 998.
Both in the earlier study [ 17] and in the present study, using zero to replace N/A, with listwise deletion and treating N/A as missing with pairwise deletion yielded similar results.
Results obtained from a second set of analyses, when N/A responses were coded as missing with listwise deletion of missings, are also reported where relevant.
In case of missing data, listwise deletion of missing cases was applied.
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