Table 1. Mutational analysis of FBXW7 in ductal invasive breast tumors. Exons 5-9 and 11 were sequenced in 62 ductal invasive breast tumors analyzed previously by array CGH (Fridlyand et al., 2006). No mutations were found in FBXW7, although single base changes were found in the introns before exon 5 in S0041, exon 7 in S1551, and exon 11 in S0065.

Case / ER1 / CGH
Subtype2 / FBXW7
Sequence3 / Number of whole chr. changes4 / Number of
copy number transitions5 / Number of Amplifications6 / FGA7 / FBXW7
copy number level8 / CCNG2
copy number level8 / NEK1
copy number level8
S0001 / pos / amplifier / exons 5-9, 11 / 3 / 42 / 16 / 0.8391933 / -1 / -1 / -1
S0013 / neg / complex / exons 5-9, 11 / 1 / 61 / 2 / 0.6286744 / -2 / -2 / -2
S0021 / pos / amplifier / exons 5-9, 11 / 0 / 33 / 8 / 0.4652998 / 0 / 0 / 0
S0024 / pos / amplifier / exons 5-9, 11 / 2 / 16 / 0 / 0.6476364 / 0 / 0 / 0
S0033 / neg / amplifier / exons 5-9, 11 / 1 / 9 / 0 / 0.1440605 / 0 / 0 / 0
S0041 / pos / amplifier / exons 5-9, 11 / 0 / 32 / 0 / 0.4004351 / 0 / 0 / 0
S0043 / neg / complex / ND / 2 / 34 / 10 / 0.4909483 / 1 / 3 / 1
S0050 / pos / amplifier / exons 5-9, 11 / 2 / 32 / 25 / 0.2333892 / 0 / 0 / 0
S0051 / pos / amplifier / exons 5-9, 11 / 0 / 14 / 10 / 0.144009 / 0 / 0 / 0
S0052 / pos / amplifier / ND / 1 / 31 / 3 / 0.7128236 / -1 / 0 / -1
S0055 / neg / amplifier / exons 5-9, 11 / 0 / 52 / 19 / 0.9176404 / -1 / 0 / -3
S0059 / pos / amplifier / exons 5-9, 11 / 0 / 25 / 6 / 0.2726178 / 0 / -1 / -1
S0065 / pos / amplifier / exons 5-9, 11 / 4 / 17 / 2 / 0.6783056 / 0 / 0 / 0
S0066 / pos / amplifier / ND / 4 / 19 / 0 / 0.7624885 / 2 / 2 / 2
S0071 / neg / complex / exons 6-9 / 0 / 30 / 0 / 0.4188164 / 0 / -1 / -1
S0073 / neg / amplifier / ND / 1 / 19 / 0 / 0.3931232 / 0 / 0 / 0
S0077 / pos / 1q16q / exons 5-9, 11 / 2 / 4 / 0 / 0.1720423 / 0 / 0 / 0
S0081 / pos / amplifier / exons 5-9, 11 / 4 / 7 / 4 / 0.6045404 / 0 / 0 / 0
S0104 / pos / amplifier / exons 5-9, 11 / 3 / 39 / 2 / 0.6882213 / 1 / 2 / 1
S0117 / pos / 1q16q / exons 5-9, 11 / 0 / 16 / 0 / 0.1004448 / 0 / -1 / 0
S0122 / neg / amplifier / ND / 1 / 37 / 3 / 0.466187 / 0 / 0 / 0
S0126 / neg / amplifier / exons 5-9, 11 / 0 / 40 / 9 / 0.2495644 / 0 / NA / 0
S0127 / pos / amplifier / exons 5-9, 11 / 0 / 20 / 5 / 0.0863179 / 0 / 0 / 0
S0132 / pos / amplifier / exons 5-9, 11 / 0 / 20 / 19 / 0.5079806 / 0 / 0 / 0
S0136 / neg / complex / exons 6-9 / 2 / 39 / 0 / 0.6430595 / 0 / 1 / 0
S0184 / neg / complex / exons 6-9 / 0 / 38 / 28 / 0.6095217 / -1 / -1 / -1
S0195 / neg / complex / exons 6-9 / 1 / 44 / 12 / 0.6987591 / -1 / 0 / -1
S0203 / neg / complex / exons 6-9 / 2 / 47 / 0 / 0.6910537 / -2 / 2 / -2
S0221 / neg / complex / exons 6-9 / 3 / 44 / 0 / 0.6810696 / -2 / -2 / -2
S0222 / neg / complex / exons 6-9 / 0 / 47 / 2 / 0.3584542 / -1 / -1 / -1
S0252 / neg / amplifier / exons 6-9 / 4 / 19 / 5 / 0.4725911 / 1 / 1 / 0
S0256 / neg / amplifier / ND / 0 / 15 / 0 / 0.1532544 / 0 / 0 / 0
S0257 / neg / amplifier / ND / 0 / 38 / 22 / 0.6272821 / 0 / 0 / 0
S0269 / neg / complex / exons 6-9 / 0 / 47 / 31 / 0.3888889 / 0 / -1 / 0
S0303 / pos / amplifier / exons 5-9, 11 / 2 / 21 / 4 / 0.2766204 / 0 / 0 / 0
S0304 / neg / complex / exons 6-9 / 0 / 53 / 0 / 0.887717 / -1 / -1 / -1
S0385 / neg / complex / ND / 3 / 24 / 26 / 0.486559 / 0 / 0 / 0
S0394 / neg / amplifier / ND / 2 / 19 / 17 / 0.5934204 / -1 / -1 / -1
S1503 / neg / amplifier / exons 5-9, 11 / 0 / 61 / 5 / 0.8693552 / -2 / -1 / -2
S1504 / pos / 1q16q / exons 5-9, 11 / 3 / 7 / 0 / 0.1869047 / 0 / 0 / 0
S1506 / pos / amplifier / ND / 1 / 9 / 3 / 0.0628036 / 0 / 0 / 0
S1508 / pos / amplifier / exons 5-9, 11 / 0 / 30 / 12 / 0.4968196 / 0 / 0 / 0
S1511 / pos / complex / exons 6-9, 11 / 3 / 23 / 5 / 0.562182 / -2 / -2 / -2
S1515 / pos / amplifier / exons 5-9, 11 / 4 / 15 / 0 / 0.9657689 / -1 / -1 / -1
S1519 / pos / amplifier / exons 5-9, 11 / 1 / 15 / 0 / 0.5867945 / 0 / 0 / 0
S1522 / pos / amplifier / exons 5-9, 11 / 2 / 38 / 22 / 0.6632908 / -1 / 0 / -1
S1523 / pos / 1q16q / exons 5-9, 11 / 0 / 8 / 0 / 0.0550943 / 0 / 0 / 0
S1524 / neg / complex / ND / 0 / 47 / 38 / 0.7345038 / -1 / 2 / -1
S1526 / neg / complex / exons 5-9, 11 / 0 / 20 / 19 / 0.2174748 / 0 / 0 / 0
S1534 / pos / amplifier / exons 5-9, 11 / 2 / 18 / 22 / 0.1629718 / 0 / 0 / 0
S1536 / pos / amplifier / exons 5-9, 11 / 0 / 40 / 0 / 0.5735783 / 1 / 0 / 1
S1539 / pos / amplifier / exons 5-9, 11 / 3 / 38 / 19 / 0.7676945 / 0 / 0 / 0
S1541 / pos / 1q16q / exons 5-9, 11 / 4 / 12 / 0 / 0.3571901 / 0 / 0 / 0
S1542 / pos / amplifier / exons 5-9, 11 / 2 / 36 / 0 / 0.7104714 / -2 / 1 / -2
S1545 / pos / amplifier / exons 5-9, 11 / 0 / 18 / 1 / 0.1155948 / 0 / 0 / 0
S1551 / pos / 1q16q / exons 5-9, 11 / 2 / 17 / 0 / 0.2626225 / 0 / 0 / 0
S1572 / neg / amplifier / exons 5-9, 11 / 2 / 17 / 0 / 0.1900305 / 0 / 0 / 0
S1575 / pos / amplifier / exons 5-9, 11 / 4 / 21 / 0 / 0.4850172 / 0 / 0 / 0
S1579 / pos / amplifier / exons 5-9, 11 / 0 / 64 / 5 / 0.668274 / -1 / 0 / 0
S1598 / pos / amplifier / exons 5-9, 11 / 3 / 29 / 82 / 0.36994 / 1 / 1 / 1
S1608 / pos / 1q16q / exons 5-9, 11 / 0 / 13 / 0 / 0.1362249 / 0 / 0 / 0
S1616 / neg / complex / exons 5-9, 11 / 0 / 75 / 0 / 0.7671819 / -1 / -1 / -1

1Estrogen receptor status of tumors, positive (pos) or negative (neg)

2Subtype defined by hierarchical clustering based on copy number alterations

3Cycle sequencing was performed on exons 5-9 and 11 of FBXW7, which had been amplified from genomic DNA using the following primers: Exon 5 (F: 5' GAA TCA GAG TGC AGA ATT A 3' and R:5' GAT TTT ATC ATA AGT AGC TGA 3'); Exon 6 (F: 5'CCA GAA GTG GAA TTG CTA GA 3' and R: 5' TTC AGT TAC CTT AGG AGA TTT GAG 3'); Exon 7 (F ; 5' CTG GAT TCG TCA GCC AGG A 3' and R: 5' TAA ACT TAC TTT GCC TGT GAC TGC 3'); Exon 8 (F: 5' TAA ACT TAC TTT GCC TGT GAC TGC 3' and R: 5' CAC TGT CAC TAT TTC AGT AA 3'); Exon 9 (F: 5' CTG GAG AGT TGT TAG CGG TTC TCG 3' and R: 5' CCT TAT GAT TCA TCA GGA GA 3'); and Exon 11 (F: 5' CTA CAA ATT ATA ATG TAA CTA 3' and R: 5' GTC TAG GTC CCA ACA AGC ATC AGA 3').

4Number of whole chromosome gains or losses(Fridlyand et al., 2006)

5Number of copy number transitions(Fridlyand et al., 2006)

6Number of amplifications(Fridlyand et al., 2006)

7FGA(Fridlyand et al., 2006)

8Copy number level as determined by circular binary segmentation(Fridlyand et al., 2006)