89Abstracts / Cancer Genetics and Cytogenetics 203 (2010) 66e99

SPECIFIC CHROMOSOMAL IMBALANCES ASDETECTED BY ARRAY CGH REVEALED THATPLEOMORPHIC SARCOMA ANDLEIOMYOSARCOMAS REPRESENTGENETICALLY DISTINCT DISEASES

Sara Martoreli Silveira1, Rolando Andre Villaces1,

Isabela Werneck da Cunha2, Fernando Augusto Soares2,

Silvia Regina Rogatto1,3

1. Department of Research, Fundacao Antonio Prudente, Hospital AC

Camargo, Sao Paulo, SP, Brazil

2. Department of Anatomic Pathology, Fundacao Antonio Prudente,

Hospital AC Camargo, Sao Paulo, SP, Brazil

3. Department of Urology, FMB, UNESP-Sao Paulo State University,

Botucatu, SP, Brazil

Undifferentiated high-grade spindle/pleomorphic sarcoma (UPS)is a soft tissue sarcoma typically showing a clinically aggressivebehavior with frequent development of distant metastases andlocal recurrences after surgery. The diagnosis of UPS has becomea controversial issue, being considered rather a diagnostic waste-basket of undifferentiated and pleomorphic subtypes of otherdefined entities like liposarcoma, fibrosarcoma, or leiomyosarco-ma (LMS) rather than a distinct diagnosis. The aim of this studywas to evaluate the genomic imbalances in UPS and LMS samplesby array-based CGH (aCGH) and to correlate these data with theclinical course and histopathological findings. Array CGH wasdone using the Human 44K Agilent oligoarrays according to man-ufacturer’s instructions. Data were extracted and flagged withFeature Extraction software (version 10.1.1.1), processed usingGenomic Workbench Standard (version 5.0.14), with the statisticalalgorithm ADM-2 and a sensitivity threshold of 5.0. At least threeconsecutive probes should be present to consider a region as ex-hibiting copy number variation. DNA copy number alterationswere compared with the Database of Genomic Variants (DGV;http://projects.tcag.ca/variation/). Genomic gains were morefrequently observed in UPS, whereas losses were most commonin LMS. UPS often showed gains involving 1p, 1q, 5p, 7p, 14q,15q, 17q, 18q, 19p, and 19q. Gain at 7q21.13 is the mostfrequent genomic imbalance in UPS. Contrarily, losses werepredominantly found in LMS and involved 1p, 2p, 2q, 4q, 5q,8p, 9q, 11p, 12q, 13q, and 15q. Loss at 13q14.3 was the mostfrequent genomic imbalance in LMS. The identification ofspecific genomic imbalances suggests that UPS and LMSrepresent genetically distinct diseases and indicate putativemolecular diagnostic markers in these tumors.

EVOLUTION OF A BREAST CANCER GENOME:THE RELATIVE TIMING OF CANCER MUTATIONSAND THE DRIVER VERSUS PASSENGERPROBLEM

Scott Newman1, Karen D. Howarth1, Graham R. Bignell2,

Chris Greenman2, Paul A.W. Edwards1,

Members of the Sanger Centre Cancer Genome Project2

1. University of Cambridge Department of Pathology and Hutchison

MRC, United Kingdom

2. Wellcome Trust Sanger Institute, United Kingdom

Cancer genomes contain many mutations at both the sequence andstructural levels. Probably, only a few of these mutations providea selective advantagedthese are termed ‘driver’ mutationsdwhile most do not to contribute significantly to carcinogenesisand are termed ‘passengers’. The ongoing challenge of is howto tell driving mutations from passengers. Evidence for selectionmay come from the timing of mutations, because a mutation thathas to occur at a particular stage is probably selected. We per-formed a near complete structural analysis of the breast cancer cellline HCC1187, using data from array painting, SNP array CGH,and spectral karyotyping. The search for structural aberrationsproduced a detailed map of this genome, and we used it to askhow the karyotype had evolved. The most likely explanation forthe evolution of the HCC1187 genome was that it passed throughthree phases previously defined in primary breast tumours: (i)successive unbalanced translocations, (ii) doubling of the entireremaining genomeda process known as endoreduplication, and(iii) further unbalanced translocation. We were able to class thevast majority of known mutations as either earlier or later, accord-ing to whether they occurred before or after endoreduplication.Most loci in this genome had duplicated precisely once (at endor-eduplication), so we could infer whether a mutation probablyoccurred before or after duplication. If the mutation occurredbefore, it would usually be present on both copies of the locusafter, whereas if the mutation occurred after endoreduplication,it would usually be present on only one of two copies. We usedSanger sequencing of flow-sorted chromosome DNA to assess thisfor all known sequence-level mutations in HCC1187. Endoredu-plication formed an approximate midpoint in the evolution of thistumour cell line, as genome rearrangements and sequence-levelmutations were nearly evenly divided between earlier and latercategories. A striking finding was that the great majority of inac-tivating mutations expressed gene fusions, and all homozygousdeletions happened early. As mutations were spread evenly overtime, the only reason inactivating events and gene fusions shouldhave occurred early was that most of them were selected.