Based on these simulated marker genotype data sets, we apply our algorithm on the marker panel to obtain the most diverse reference panels of 200 haplotypes.
The panel obtained additional information by court order.
Therefore, a low-density marker panel is desired to obtain a favorable cost-benefit ratio for GS.
The panels obtained after this simple operation corroborated two ideas.
We then randomly selected one-third of the SNPs to obtain a random marker panel (21 k random panel) that had 10-fold greater marker density than the AIMs panels.
In addition, we believe that using this classification system provides a reflection of the complex molecular portrait of BC more than that could be obtained using the three marker panel (ER, PgR and HER2) assessed in routine practice.
The putative 530 SNP marker panel was then used to score RAD sequences obtained from each of the DH individuals.
In contrast to the two previously reported AM studies, our results were obtained using a different and independent marker panel, a different and independent patient sample set, and two different analytic approaches.
They obtained an imputation accuracy of 0.87 on chromosome 1 with a 384 marker panel, and an imputation accuracy of 0.97 with a 3 k panel if the sire and the grand sires were genotyped at high-density (scenario s5_25% in their paper).
This will mimic a high-density marker panel, and according to the results reported here, the overall imputation accuracy would be higher than that obtained by direct imputation from the lower density SNP chip.
