Table 2.
Summary of the 12 common CNAs obtained from 500 K and SNP 6.0 platform.
| Cytogenetic Loci | GISTIC Wide Peak Region (Mb a) | Size (Mb) | Total Frequency (%, n = 72) | Cases with CNAs by 500-K Platform (n = 26) | Cases with CNAs by SNP 6.0 Platform (n = 46) | Candidate Genes |
|---|---|---|---|---|---|---|
| Gains | ||||||
| 7p11.2 b | 54.62–55.86 | 1.24 | 51 | 14 | 23 | SEC61G, EGFR |
| 11q13.3 b | 68.96–70.32 | 1.36 | 51 | 14 | 23 | MYEOV1, CCND1, ORAOV1, FADD, CTTN |
| Losses | ||||||
| 2q23.3–q24.2 b | 124.78–243.20 | 118.24 | 10 | 3 | 4 | ING5, LRP1B, DAPL1 |
| 3p14.2–p12.1 | 25.64–93.78 | 68.14 | 42 | 12 | 18 | FHIT, MLH1, BAP1, SETD2, PBRM1 |
| 4q35.2 b | 187.48–188.24 | 0.76 | 33 | 8 | 16 | FAT1 |
| 7q33–q34 b | 97.61–159.14 | 63.91 | 18 | 6 | 7 | MIR335, ING3 |
| 9p21.3 b | 21.56–22.00 | 0.44 | 26 | 4 | 15 | CDKN2A |
| 11q22.3–q24.3 b | 72.39–135.01 | 62.62 | 38 | 10 | 17 | ATM, MRE11A, CHEK1, H2AFX |
| 16q23.1 | 75.46–79.63 | 4.17 | 11 | 2 | 6 | WWOX |
| 18q11.2–q22.3 b | 18.69–78.08 | 59.39 | 40 | 9 | 20 | DCC |
| 21q21.1 | 10.19–29.10 | 18.91 | 33 | 7 | 17 | CHODL |
| 21q22.3 b | 44.30–48.13 | 3.83 | 33 | 6 | 18 | NDUFV3 |
a Mb: mega base; b CNAs also identified when validating the dataset extracted from the Gene Expression Omnibus data repository (accession number GSE25103).