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Monte Carlo simulations were used to populate the pelvic structure pools with random F2 individuals, and the number of markers that passed our scoring thresholds was assayed.
Biallelic GBS markers that passed the latter test were then incorporated into a high density, framework map and ordered according to their positions in the reference genome.
Simulations showed that this approach had superior performance when compared to the conventional way of including only the markers that passed the Bonferroni threshold.
No minor allele frequency limit was set for the used markers and all markers that passed quality control were tested for association.
The eight markers that passed analysis in the Filtering set, as well as two previously validated EOC markers (MUC16 and MSLN [17], [26]), were further tested in the Mini-Triage serum set (n = 71).
To compute G, only the HD markers that passed quality control (described later) were used.
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Thus, finding SNP markers that pass certain quality filters for all sequenced individuals is not trivial.
We chose the conservative value of 0.032 for the error rate that we used in Probability of Incorrect Assignment (PIA) computations (see Methods); however, we expect that the true error rate is much lower (<0.001) when considering only the markers that pass the strict quality thresholds described below.
N, the total number of tests; tN, the estimated number of tests representing true null hypotheses; fN the estimated number of tests representing falsified null hypotheses (i.e., true marker-QTL linkage); PFP, the 0.20 PFP CWER P-value thresholds; oN, the observed number of marker tests that passed the significance threshold; Power, the estimated power of the test; ND, not done.
Using markers of the HD chip that passed quality control (see below), four 15 K chips were simulated based on selection of one marker from each window of 29 subsequent markers, according to the UMD v3.1 assembly.
These markers were then applied to mineral oil that passed standard quality control testing but had been recalled by the manufacturer due to potential toxicity to human embryos.
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