Another limitation of this technique is that many mapping tools measure not only specific physical interactions between genes but also random contacts, the latter being much more common between genes with smaller linear genomic distance this could lead to inflated co-segregation scores. GAM has helped to resolve this issue because in GAM the detection of genomic windows is independent of any interactions with other regions. This allows for an expected interaction value to be calculated and combining this with the co-segregation results to filter out the noise of random connections this will provide a cleaner result.
