Table 1. Regions of copy change and LOH.
Shown are significant regions of copy number loss or LOH. Regions within cloned fragile sites (top set), associated with fragile sites (2nd from top), near fragile sites (within 10 Mb, 3rd from top), or at non-fragile sites (bottom set) are shown. Cytogenetic band locations and the chromosome positions (start and end) are noted; the latter indicates the largest extent of the chromosomal region identified by STAC as being statistically altered. The frequency of each alteration is shown. Frequency and footprint p-values were generated in STAC.
| Alteration(s) | Cytoband(s) | Start (Mb) | End (Mb) | Fragile Site | Type | Distance to Fragile Site | Frequency | Frequency p value | Footprint p value |
|---|---|---|---|---|---|---|---|---|---|
|
CLONED FRAGILE SITES
| |||||||||
| copy loss | 3p14.2 | 59 | 62 | FRA3B | common | 80.00% | 0.001 | 0.004 | |
| copy loss | 18q22.1 | 63 | 66 | FRA18C | rare | 35.00% | 0.001 | 0.004 | |
| copy loss | 16q23.3-24.1 | 76 | 78 | FRA16D | common | 35.00% | 0.001 | 0.004 | |
| copy loss | 7q31.2 | 117 | 118 | FRA7G | common | 20.00% | 0.001 | 0.002 | |
| LOH | 3p14.2 | 59 | 61 | FRA3B | common | 60.00% | 0.001 | 0.002 | |
| LOH | 16q23.3-24.1 | 77 | 79 | FRA16D | common | 35.00% | 0.001 | 0.002 | |
|
| |||||||||
|
ASSOCIATED WITH FRAGILE SITES
| |||||||||
| copy loss | 9p21 | 21 | 23 | FRA9A/9C | rare | 75.00% | 0.001 | 0.008 | |
| copy loss | 5p14 | 23 | 30 | FRA5E | common | 55.00% | 0.001 | 0.004 | |
| copy loss | 4p15 | 33 | 36 | FRA4D | common | 45.00% | 0.001 | 0.004 | |
| copy loss | 5p13 | 29 | 30 | FRA5A | common | 45.00% | 0.0010 | 0.0040 | |
| copy loss | Xq22.1 | 98 | 99 | FRAXC | common | 35.00% | 0.013 | 0.01 | |
| copy loss | 1q31 | 185 | 187 | FRA1K | common | 30.00% | 0.001 | 0.006 | |
| copy loss | 12q21.3 | 81 | 85 | FRA12B | common | 30.00% | 0.013 | 0.002 | |
| copy loss | 10q21 | 67 | 69 | FRA10C | common | 15.00% | 0.071 | 0.006 | |
| copy gain | 8q24.3 | 144 | 146 | FRA8D | common | 25.00% | 0.385 | 0.006 | |
| copy gain | 19p13 | 0 | 5 | FRA19B | rare | 35.00% | 0.011 | 0.01 | |
| LOH | 9p21 | 21 | 23 | FRA9A/9C | rare | 55.00% | 0.001 | 0.012 | |
|
| |||||||||
|
NEAR FRAGILE SITES
| |||||||||
| copy loss | 5q14.3 | 83 | 90 | (FRA5B/5D) | common | 1.9 Mb | 50.00% | 0.001 | 0.004 |
| copy loss | 3q25-26.1 | 163 | 170 | (FRA3D) | common | 1.8 Mb | 45.00% | 0.001 | 0.004 |
| copy loss | 13q31.1 | 81 | 86 | (FRA13B) | common | 9.9 Mb | 40.00% | 0.001 | 0.004 |
| copy loss | 11p13 | 38 | 39 | (FRA11E) | common | 1.6 Mb | 35.00% | 0.033 | 0.004 |
| copy loss | 7q21.11 | 84 | 86 | (FRA7E) | common | 4.9 Mb | 35.00% | 0.001 | 0.002 |
| copy loss | 6q21 | 101 | 104 | (FRA6F) | common | 0.8 Mb | 30.00% | 0.045 | 0.006 |
| copy loss | 7p22 | 9 | 11 | (FRA7B) | common | 1.8 Mb | 20.00% | 0.017 | 0.012 |
| copy loss | 11q22.1 | 97 | 98 | (FRA11F) | common | 8.1 Mb | 20.00% | 0.005 | 0.004 |
| copy loss | 11q14.2 | 89 | 90 | (FRA11F) | common | 1.1 Mb | 20.00% | 0.005 | 0.004 |
| copy gain | 10q26.3 | 134 | 135 | (FRA10F) | common | 6 Mb | 15.00% | 0.023 | 0.03 |
|
| |||||||||
|
NON-FRAGILE SITES
| |||||||||
| copy loss | Xp21.1 | 31 | 33 | 45.00% | 0.001 | 0.006 | |||
| copy loss | 3p12.1 | 83 | 87 | 40.00% | 0.001 | 0.004 | |||
| copy loss | Xq25 | 125 | 126 | 40.00% | 0.003 | 0.01 | |||
| copy loss | 6q22.31 | 124 | 125 | 35.00% | 0.003 | 0.004 | |||
| copy loss | 21q21.1 | 20 | 22 | 25.00% | 0.01 | 0.04 | |||
| copy gain | 9q34.2 | 135 | 138 | 20.00% | 0.001 | 0.004 | |||
| copy gain | 20q13.33 | 60 | 61 | 20.00% | 0.011 | 0.002 | |||