We constructed a tiling resolution array consisting of 32,433 overlapping BAC clones covering the entire human genome. This increases our ability to identify genetic alterations and their boundaries throughout the genome in a single comparative genomic hybridization (CGH) experiment. At this tiling resolution, we identified minute DNA alterations not previously reported. These alterations include microamplifications and deletions containing oncogenes, tumor-suppressor genes and new genes that may be associated with multiple tumor types. Our findings show the need to move beyond conventional marker-based genome comparison approaches, that rely on inference of continuity between interval markers. Our submegabase resolution tiling set for array CGH (SMRT array) allows comprehensive assessment of genomic integrity and thereby the identification of new genes associated with disease.Identification of chromosomal imbalances and variation in DNA copy-number is essential to our understanding of disease mechanisms and pathogenesis. Array CGH 1 or matrix CGH 2 offers the highest resolution for practical genome-wide detection of chromosomal alterations. This technique is derived from the concept of conventional CGH 3 , which has contributed greatly to the molecular characterization of both somatic and constitutional genomic DNA mutations over the last decade 4-6 . The primary limitation of conventional CGH is its resolution (∼20 Mb), as this method detects segmental copy-number changes on metaphase chromosomes 3 . In array CGH, the metaphase chromosome spread is replaced by BACs, PACs or YACs containing human DNA as targets, increasing the resolution to the distance between the selected marker DNA clones 1,2 . Genome screening using array CGH has great potential in the characterization of numerous chromosomal disorders.Efforts to construct DNA arrays spanning the human genome consisted of spotting 2,460 (ref. 7) or 3,500 (ref. 8) marker BAC clones representing the sequenced genome at an average interval of ∼1 Mb.These studies showed that sufficient target-DNA printing solution could be generated from individual BACs using PCR-based protocols. Because the target product is PCR-derived, it is easily replenishable, obviating the need for multiple rounds of laborious large-scale BAC DNA preparations. These arrays are sensitive enough to detect singlecopy changes, but the technique is limited by the small number of BAC markers representing the genome on the slide, rather than the methodology. Even at this resolution, array CGH is useful for detecting chromosomal aberrations associated with congenital abnormalities and somatic malignancies [9][10][11][12] .Recent studies focused on higher-density regional arrays for fine mapping and identifying new genes in specific chromosomal regions [13][14][15][16][17][18] . For example, a candidate oncogene for association with

Osteosarcoma (OS) is characterized by chromosomal instability and high-copy-number gene amplification. The breakage-fusion-bridge (BFB) cycle is a well-established mechanism of genomic instability in tumors and in vitro models used to study the origins of complex chromosomal rearrangements and cancer genome amplification. However, until now, there have been no high-resolution cytogenetic or genomic array studies of BFB events in OS. In the present study, multicolor banding (mBAND) FISH and submegabase resolution tiling set (SMRT) array comparative genomic hybridization (CGH) were used to identify and map genomic signatures of BFB events in four OS cell lines and one patient tumor. The expected intermediates associated with BFB-dicentric chromosomes, inverted duplications, and intra- and interchromosomal amplifications-were identified. mBAND analysis provided detailed mapping of rearrangements in 1p, 6p, and 8q and showed that translocation junctions were often in close proximity to fragile sites. More detailed mBAND studies of OS cell line MG-63 revealed ladderlike FISH signals of equally spaced interchromosomal coamplifications of 6p21, 8q24, and 9p21-p22 in a homogeneously staining region (hsr). Focal amplifications that concordantly mapped to the hsr were localized to discrete genomic intervals by SMRT array CGH. The complex amplicon structure in this hsr suggests focal amplifications immediately adjacent to microdeletions. Moreover, the genomic regions in which there was deletion/amplification had a preponderance of fragile sites. In summary, this study has provided further support for the role of the BFB mechanism and fragile sites in facilitating gene amplification and chromosomal rearrangement in OS.

Current cytogenetic methods (e.g., G-banding and multicolor chromosomal painting) allow detection of translocation events but lack the resolution to (a) locate the breakpoints precisely at the chromosome band level or (b) discriminate balanced translocations from translocations with copy number alterations not previously reported, or imperfectly balanced translocations. In this study, we demonstrate that cytogenetically balanced translocations are in fact frequently associated with segmental gain or loss of DNA. The recent development of a whole genome tiling path BAC array has enabled tiling resolution analysis of genomic segmental copy number status. Combining tiling resolution BAC array comparative genomic hybridization (array CGH) with G-Banding analysis and multicolor chromosomal painting approaches such as spectral karyotyping (SKY) facilitates high-resolution mapping of genomic alterations associated with imperfectly balanced translocations. Using a refined version of our CGH array we have deduced the copy number status throughout the genomes of three cytogenetically well-characterized prostate cancer cell lines (PC3, DU145, LNCaP) to determine whether translocations are associated with focal gains and losses of DNA. At 78 kb tiling resolution we identified the boundaries of 170, 80, and 34 known and novel copy number alterations (CNA) in these cell line genomes, respectively. Thirty-three of the 36 known translocations (92%, P < 0.001) in DU145 were associated with segmental CNA. Likewise, 80% (P < 0.001) of the known translocations showed association in LNCaP. Although many translocation breakpoints exhibit segmental alteration in PC3, the pattern of chromosomal rearrangements is too complex for use in comprehensive association with CNA boundaries. Our results reveal that imperfectly balanced translocations in tumor genomes are a phenomenon that occurs at frequencies much higher than previously demonstrated.

Placentae with mesenchymal dysplasia (PMD) are typically larger than average and show cystic areas on ultrasonography. Fetal outcomes are variable and are often associated with growth restriction. However, enigmatically, some associated fetuses show signs of Beckwith-Wiedemann syndrome (BWS). PMD has recently been shown to result from androgenetic (complete paternal uniparental disomy) chimerism in the placenta in pregnancies that were associated with some fetal growth restriction. Cases of PMD associated with overgrowth have not previously been investigated molecularly. We present a case of focal PMD associated with a male fetus showing overgrowth with an enlarged heart, marked fetal ascites and intrauterine fetal death at 34 weeks, but no other BWS manifestations. Mosaicism for an unbalanced translocation leading to deletion of the maternal copy of the BWS region on 11p15.5 and partial duplication of 17q was observed in placenta, but not fetal samples. While the placental findings of PMD can be caused by an unbalanced dosage of genes in 11p15.5 alone, fetal growth parameters appear to depend on the underlying mechanism and likely also the level and distribution of abnormal cells.