I manually sequenced and covered a wide genomic region for one specific patient and all it's SNPs within this region are homozygous. While in the other hand all the other samples have shown heterozygosity for the same SNP's and same genomic region. I was wondering whether this patient could have a LOH. In order to asses this hypothesis I'd like to perform a fragment analysis experiment. For this purpose, I am trying to select a STS marker (microsatellite marker) with the highest heterozygosity and as close as possible. The only one I found is 200 KB far. Is this too far?
it will not be too far if it inside a region of homozygosity. Too far is a marker outside your region ie outside of a heterozygous marker. If the patient is deleted on one chromosome ,for instance , the deletion could be millions of bases