Figure 2

Analysis of the 8p21.3 amplicon. (a) and (b) BAC and fosmid array CGH of the 8p21.3 amplicons in BT-20 and MDA-MB-134 respectively. (a) BT-20 showed amplification between BAC clones RP11-419L22 (21.13 Mb; positions are given as midpoints on NCBI Build 36) and RP11-582J16 (22.50 Mb). (b) MDA-MB-134 showed amplification between BAC clones RP11-458H21 (21.28 Mb) and RP13-600L4 (22.04 Mb). The distal edges of both amplicons fell in a region containing no known genes but extended proximally into a gene-dense region. Genes within the overlap are marked. Log₂ ratio of the fluorescence intensity is plotted against position on 8p. Grey squares, fosmids; Black diamonds, BACs. (c) FISH of the three chromosomes containing material from the 8p21.3 amplicon in BT-20. Blue, chromosome 8 paint; Green, RP11-459H21 (21.29 Mb); Red, RP11-235B11 (22.38 Mb). (d) FISH of the three chromosomes containing material from the 8p21.3 and 8p12 amplicons in MDA-MB-134. Blue, chromosome 8 paint; Green, BAC RP11-135I5 (21.49 Mb); Red, RP11-104D16 (40.25 Mb). (e) FISH of the 8p21.3 amplicon on a primary breast tumour paraffin section. Red, BAC pool positioned in the amplicon (centred at 21.9 Mb); Green (also indicated by arrows), BAC pool distal to the amplicon (centred at 19.5 Mb); Grey, inverted DAPI. (f) Expression levels of the five genes included in both the BT-20 and MDA-MB-134 amplicons, shown on the y-axis as a log₁₀ scale of -fold expression compared to normal breast cell line HB4a and normalised to GAPDH as an internal control. Expression levels of (g) FGF17 and (h) NPM2 in primary tumours and normal controls. Crosses, purified luminal samples; Open circles, possible outliers (value more than 1.5× inter-quartile range above the third quartile); Filled circles, outliers (value more than 3× inter-quartile range above the third quartile).