LocusScorer

Score entities for single or combined imbalances:

The region entry field accepts one or multiple regions to be matched, which represent the minimum region(s) to be matched completely in single cases. The format can be cytobands or Golden Path intervals, appended by the type of imbalance required (1=gain, -1=loss, 9=both; use "0" to exclude a region):

 8q24:1
 13q14:-1

... will find all cases with gain / amplification on 8q24 and concomitant deletion involving (but not limited to) 13q14.

 8:120000000-127000000:1
 13q14:0

... will find all cases with gain / amplification on 8q24 (represented by the map positions), but exclude all cases with any change on 13q14.

Min. Case Number and Min. Percents will set thresholds on the subsets displayed in the result. "Case Number" allows to exclude small subsets from the listing (e.g. ICD codes with fewer than "Min. Case Number" cases), wile "Min. Percents" set a requirement on the proportion of matching cases in the returned subsets. However, single cases etc. will still be included in the caselist returned, and will show up in the downstream analysis.

Presentation of results

The analysis will return the plots of the corresponding chromosomes from all entities matching the threshold criteria for cases with hits. Results are sorted for the highest scoring subsets, considering the overall instability of the subset's cases (i.e. matches from subsets with lower overall complexity are considered less specific).

Please be aware that the chromosome plots will show the distribution of changes in the whole subset, not only the matching cases!

Downstream analysis

All matching cases are linked for download & further downstream analysis.