Third, at each SNP j we delete marker genotypes at random from the nmis individuals, where c is chosen such that the overall proportion of missing data is fixed value.
This process was iterated until deleting markers did not affect the marker orders, and thus the framework genetic map was constructed.
The marker data was further edited by deleting markers with a minor allele frequency less than 0.01.
Filtering was performed by first removing markers that had more than 80% of lines with missing values and then deleting markers with MAF ≤0.05.
We deleted markers that had a minor allele frequency less than 1% among the phenotyped individuals and this reduced the number of markers to 5896.
LOH was investigated in 13 commonly informative and deleted markers on chromosome 16 (six markers), chromosome 17 (two markers), and chromosomes 1, 8, 9, 11, and 13 (one marker each).
After deleting markers that were located in the same position or were unlinked, only 429 (POP-1) and 344 (POP-2) markers were used for linkage map construction (Table 2).
We thus performed multiplex differential genomic DNA PCR to detect OPCML deletion for a region spanning the frequently deleted marker D11S4085 in epithelial ovarian cancer.
Gene-deleted marker vaccines offer the advantage of deletion of specific viral genes that are non-essential for viral replication [ 6, 7] while inducing a substantial protein-specific immune response.
The deleted marker data were inspected visually again and corrected if there were errors.
