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The flag_hw module flags markers that fail Hardy Weinberg equilibrium.
Eliminating markers that fail HWE tests also may be eliminating SNPs associated with the disease.
Previous work has identified that it is worth retesting any markers that fail to amplify at the first PCR attempt [ 21].
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However, there were 61 N-type markers that failed to match the current reference genome sequence.
Finally, markers that failed to be assigned with confidence to only one LG were not considered in further analysis.
Markers that failed Hardy Weinberg equilibrium in controls or were missing >10% of genotypes were excluded from analyses.
Diamandis provided accounts of initially promising tumor markers that failed to make it into clinical practice because of errors made during validation of the markers' clinical performance [ 4].
All markers that failed to amplify were therefore rechecked by performing a repeat PCR and the majority amplified at the second PCR attempt.
Several candidate markers that failed validation in univariate and multivariate analyses such as Chrom19 deletion, Chrom8q amplification, and BAP1 and TP53 mutations had low prevalence ≤10%.
In addition, we also conducted single-marker regression analysis on markers that were excluded due to segregation distortion, and markers that failed to be grouped with the current linkage groups at an LOD threshold of 4.0 (unlinked).
Markers with MAF <1%, SNPs with >5% missing genotypes and markers that failed an exact test of HWE (P < 5 × 10−6) were excluded from further analyses leaving 310,505 SNPs that passed quality control.
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