Inherited what I believe to be a good implementation of PureCN for use in analyzing WXS in a cohort. We see that while there are only a few gene or regional CN/LOH datapoints, some values occur frequently (CN of 7.00 is observed in 90% of the ~150 alterations observed throughout the cohort). This occurs in multiple cohorts with the same sequencing and downstream analyses, which might lead us to believe it is something due to our data source, or perhaps a mis-step in our analysis.
Has this been observed before? We have some samples/regions which are less peculiar (CN is still above and below 7 in some cases). I am naively trying to identify if this issue could be an artifact/bias or misstep in my implementation.