!Name=Breast Cancer aCGH !ExptSetNo=1635 !Description=Genomic DNA copy number alterations are key genetic events in the development and progression of human cancers. Here we report a genome-wide microarray comparative genomic hybridization (array CGH) analysis of DNA copy number variation in a series of primary human breast tumors. We have profiled DNA copy number alteration across 6,691 mapped human genes, in 44 predominantly advanced, primary breast tumors and 10 breast cancer cell lines. While the overall patterns of DNA amplification and deletion corroborate previous cytogenetic studies, the high-resolution (gene-by-gene) mapping of amplicon boundaries and the quantitative analysis of amplicon shape provide significant improvement in the localization of candidate oncogenes. Parallel microarray measurements of mRNA levels reveal the remarkable degree to which variation in gene copy number contributes to variation in gene expression in tumor cells. Specifically, we find that 62% of highly amplified genes show moderately or highly elevated expression, that DNA copy number influences gene expression across a wide range of DNA copy number alterations (deletion, low-, mid- and high-level amplification), that on average, a 2-fold change in DNA copy number is associated with a corresponding 1.5-fold change in mRNA levels, and that overall, at least 12% of all the variation in gene expression among the breast tumors is directly attributable to underlying variation in gene copy number. These findings provide evidence that widespread DNA copy number alteration can lead directly to global deregulation of gene expression, which may contribute to the development or progression of cancer. !Name=1X vs 2X (svi112) !Exptid=3554 !Name=2X vs 2X (svi111) !Exptid=3551 !Name=3X vs 2X (svi110) !Exptid=3550 !Name=4X vs 2X (svi109) !Exptid=3548 !Name=5X vs 2X (svi108) !Exptid=3544 !Name=BT474 vs NF !Exptid=3395 !Name=MCF7 vs NF (svi121) !Exptid=3423 !Name=MDA157 vs NF (svi029) !Exptid=3549 !Name=MDA361 vs NF (svi030) !Exptid=3406 !Name=SKBR3 vs NF (svi024) !Exptid=3400 !Name=T47D vs NF (svi122) !Exptid=3556 !Name=UACC-812 vs NF (svi027) !Exptid=3541 !Name=UACC-893 vs NF (svi028) !Exptid=3547 !Name=ZR75-1 vs NF (svi025) !Exptid=3401 !Name=ZR75-30 vs NF (svi026) !Exptid=3403 !Name=107B vs NF (svi032) !Exptid=3649 !Name=110B vs NF (svi033) !Exptid=3650 !Name=111A vs NF (svi034) !Exptid=3652 !Name=112B vs NF (svi036) !Exptid=3655 !Name=114A vs NF (svi037) !Exptid=3656 !Name=115B vs NF (svi038) !Exptid=3657 !Name=116A vs NF (svi039) !Exptid=3658 !Name=117A vs NF (svi040) !Exptid=4465 !Name=118B vs NF (svi041) !Exptid=4468 !Name=111B vs NF (svi035) !Exptid=3654 !Name=122A vs NF (svi042) !Exptid=4473 !Name=123B vs NF (svi043) !Exptid=4476 !Name=124A vs NF (svi044) !Exptid=4480 !Name=206A vs NF (svi045) !Exptid=4482 !Name=208A vs NF (svi046) !Exptid=4483 !Name=213B vs NF (svi047) !Exptid=4484 !Name=214B vs NF (svi048) !Exptid=4485 !Name=305A vs NF (svi049) !Exptid=4486 !Name=308B vs NF (svi050) !Exptid=4495 !Name=309A vs NF (svi051) !Exptid=4497 !Name=402B vs NF (svi052) !Exptid=4500 !Name=406A vs NF (svi053) !Exptid=4501 !Name=708B vs NF (svi054) !Exptid=4502 !Name=709B vs NF (svi055) !Exptid=3670 !Name=710A vs NF (svi056) !Exptid=3672 !Name=711B vs NF (svi057) !Exptid=4516 !Name=805A vs NF (svi058) !Exptid=4517 !Name=807A vs NF (svi059) !Exptid=4519 !Name=808A vs NF (svi060) !Exptid=3567 !Name=BC-2 vs NF (svi061) !Exptid=3568 !Name=BC-4 vs NF (svi062) !Exptid=3571 !Name=BC-14 vs NF (svi063) !Exptid=3573 !Name=BC-16 vs NF (svi114) !Exptid=3408 !Name=BC-17 vs NF (svi064) !Exptid=3574 !Name=BC-21 vs NF (svi065) !Exptid=4521 !Name=BC-23 vs NF (svi066) !Exptid=4525 !Name=BC-24 vs NF (svi067) !Exptid=4529 !Name=BC-31 vs NF (svi115) !Exptid=3409 !Name=BC-34 vs NF (svi116) !Exptid=3410 !Name=BC-35 vs NF (svi117) !Exptid=3411 !Name=BC-38 vs NF (svi118) !Exptid=3413 !Name=BC-39 vs NF (svi119) !Exptid=3414 !Name=BC-40 vs NF (svi120) !Exptid=3422 !Name=BC-A vs NF (svi113) !Exptid=3407 !Name=BT-474/ATCC !Exptid=2213 !Name=MCF7-NCI !Exptid=2163 !Name=SK-BR-3 !Exptid=2210 !Name=T47D !Exptid=2275 !Name=BC107B-BE !Exptid=2157 !Name=BC110B-BE !Exptid=2287 !Name=BC111A-BE !Exptid=2183 !Name=BC112B-BE !Exptid=2299 !Name=BC114A-BE !Exptid=2222 !Name=BC115B-BE !Exptid=2279 !Name=BC116A-BE !Exptid=2248 !Name=BC117A-BE !Exptid=2317 !Name=BC118B-BE !Exptid=2191 !Name=BC111B-BE !Exptid=2251 !Name=BC123B-BE !Exptid=2168 !Name=BC124A-BE !Exptid=2219 !Name=BC206A-BE !Exptid=2216 !Name=BC208A-BE !Exptid=2269 !Name=BC213B-BE !Exptid=2291 !Name=BC214B-BE !Exptid=2302 !Name=BC305A-BE !Exptid=5750 !Name=BC308B-BE !Exptid=2318 !Name=BC309A-BE !Exptid=2201 !Name=BC402B-BE !Exptid=2151 !Name=BC406A-BE !Exptid=2177 !Name=BC708B-BE !Exptid=2271 !Name=BC709B-BE !Exptid=2154 !Name=BC710A-BE !Exptid=2277 !Name=BC711B-BE !Exptid=2316 !Name=BC805A-BE !Exptid=2281 !Name=BC807A-BE !Exptid=2312 !Name=BC808A-BE !Exptid=2314 !Name=BC2 !Exptid=2198 !Name=BC14 !Exptid=2174 !Name=BC16 !Exptid=2180 !Name=BC17 !Exptid=2232 !Name=BC23 !Exptid=2319 !Name=BC24 !Exptid=2239 !Name=BC35-0 !Exptid=2238 !Name=BC38 !Exptid=2282 !Name=BC-A !Exptid=2278