A single run of sequencing won't cover the entire genome, in most cases. That's why they do multiple rounds in order to increase horizontal (covering more regions of genome) and vertical (a.k.a depth; more reads per locus so that you can be more confident) coverage.
Edit by dd3:
In the cases where "a new gene is discovered", i.e. genome reannotation, it is possible to go back and look at previously stored sequence data to find out what alleles a person has (everyone has every gene, unless they have a deletion that spans the full length of the gene). This is a bioinformatics project, and if you are interested in learning more, I would recommend searching for recent publications on genome reannotation and remapping of sequence reads.
Whole genome sequencing is generally not recommended for prognosis of a specific disease like breast cancer. The common approach is to do a PCR of the biomarker loci and if necessary do a Sanger sequencing. However, if you have the money you can get your whole genome sequencing done :P
The number of runs required to increase the depth varies for different genomic regions. This article says that CpG islands require more runs. According to this article, the depth should be >3 per genotype marker.