Table 1 Characteristics of individual data sets used in the present study stratified by microarray platform
From: Landscape of somatic allelic imbalances and copy number alterations in HER2-amplified breast cancer
Data Set | # HER2-amplified | Platform | BAFA | GISTIC/GAP B | # Cell lines | Matching GEX | ER: -/+ | LN C: -/+ | Grade: 1/2/3 | PR D: -/+ |
|---|---|---|---|---|---|---|---|---|---|---|
GSE10099 [11] | 27 | Affymetrix 100K | Yes | Yes/Yes | 0 | 27 | 11/16 | 25/0 | 0/1/10 | 11/12 |
GSE16619 [9] | 11 | Affymetrix 250K Nsp | Yes | Yes/Yes | 0 | NA | 2/3 | 3/8 | 1/3/7 | 4/1 |
14 | Affymetrix 5.0 | No | Yes/No | 0 | NA | 5/5 | 3/9 | 0/3/11 | 5/4 | |
Nikolsky [16] | 9 | Affymetrix 250K Sty | Yes | Yes/Yes | 0 | NA | NA | NA | NA | NA |
GSE19399 [17]* | 32 | Affymetrix 250K Sty | Yes | Yes/Yes | 6 | NA | NA | NA | NA | NA |
GSE7545 [8] | 5 | Affymetrix 250K Nsp | Yes | Yes/Yes | 0 | NA | 1/0 | 0/5 | NA | 1/0 |
GSE13696 [22] | 6 | Affymetrix 100K | Yes | No/No | 6 | NA | NA | NA | NA | NA |
GSK [23] | 4 | Affymetrix 250K Nsp | Yes | No/No | 4 | NA | NA | NA | NA | NA |
Van Loo [10] | 20 | Illumina 109K | Yes | Yes/Yes | 0 | 20 | 14/6 | 5/14 | 0/7/13 | NA |
GSE11977 [21] | 1 | Illumina 550K | Yes | Yes/Yes | 0 | NA | 0/1 | 1/0 | NA | 0/1 |
GSE20393 [19] | 42 | Agilent 244K | No | Yes/No | 0 | NA | 2/1 | NA | NA | 2/0 |
GSE20394 [18] | 15 | Agilent 244K | No | Yes/No | 0 | 7 | 9/6 | 5/10 | 0/6/9 | 4/11 |
GSE17907 [20] | 48 | Agilent 244K | No | Yes/No | 0 | 45 | 20/21 | 12/27 | 3/10/28 | 23/18 |
Lund-HER2-SNP set | 5 | Illumina 1M | Yes | No/No | 0 | NA | 4/1 | 1/4 | NA | 4/1 |
21 | Illumina 2.5M | Yes | No/No | 0 | NA | 15/6 | 13/8 | NA | 16/5 |