From: A classification model for distinguishing copy number variants from cancer-related alterations
Variable-Definition |
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Length - length of a segment in bases |
Segmental duplication - 1 if the candidate is overlapping known region of segmental duplication, 0 otherwise. All regions listed in [32] that could be successfully translated into hg18 by hgLiftOver utility http://genome.ucsc.edu/cgi-bin/hgLiftOver were used, see Additional file 1, Table S2 |
Closeness to centromere - 1 if the candidate endpoints are within 2 Mb of the centromere, 0 otherwise |
Closeness to telomere - 1 if the candidate endpoints are within 2 Mb of the telomere, 0 otherwise |
Sign - 1 if the candidate is a gain, -1 if it is a loss |
Height - absolute value of the candidate segment mean |
Relative height - absolute value of the candidate segment mean divided by the median absolute deviation of the array residuals |
Break - absolute di_erence between means of two segments surrounding the candidate divided by the median absolute deviation of the array residuals |
Surrounded by Normals - 1 if both surrounding intervals are normals, 0 if one of them is a gain or a loss |
Overlap with other patients - factor with levels: GG if there is one or more other patients in the cohort that have overlapping candidates, all of them are gains; LL if there is one or more other patients in the cohort that have overlapping candidates, all of them are losses; GL if there are at least two patients with overlapping candidates, some of them are gains and some are losses; None if there are no other patients with overlapping candidates |
Overlap with other patients - percent - proportion of other patients in the cohort that have overlapping candidate |
Matching breakpoint in other patients - percent - proportion of other patients in the cohort that have a candidate with at least one exactly matching breakpoint |
Close to other candidates - 1 if there is another candidate CNV within 500 kb on the same chromosome in this patient |
Percent of Normal - percent of markers on a chromosome where candidate is located that are not lost or gained |
Database score of other candidates - average Database score of other candidates on the same chromosome |
Overlap with CNAs - number of other patients that have overlapping non-candidate segment of the same sign as the candidate (gain or loss) |