Purpose: Targeting subclinical disease in the bone marrow is particularly relevant in metastatic Ewing family tumors (EFT) where cure is difficult. Genome-wide expression arrays can uncover novel genes differentially expressed in tumors over normal marrow/blood, which may have potentials as markers of subclinical disease. Experimental Design: Gene expression array data were obtained on 28 EFT tumors using the Affymetrix U133 gene chip and compared with 10 normal blood samples. Ten genes with high tumor to blood ratios were identified. Quantitative reverse transcription-PCR was done to study (a) the dynamic range of detection of rare tumor cells, (b) the gene expression in normal blood/ marrow samples, (c) the gene expression among EFT tumors, and (d) the detection and prognostic impact of marker positivity in histology-negative diagnostic marrows of EFT patients. Before the era of effective chemotherapy, 5-year overall survival for Ewing family tumors (EFT) was V20%, largely because of uncontrolled subclinical metastatic disease (1). Despite the advent of modern chemoradiotherapy, the 5-year progression-free survival was only 30% among patients with overt metastases at the time of diagnosis, although many of them had achieved near complete clinical remission following induction therapy. In fact, even for patients presenting with localized disease at diagnosis, their overall survival decreased from 70% at 5 years to f50% at 10 years (1). The failure to cure is likely due to occult cancer cells that metastasize by hematogenous spread (2). Accurate and sensitive markers of EFT in the marrow or blood may help in the early detection of distant metastasis. More importantly, testing marrow or blood can facilitate the application of novel treatment approaches directed at minimal residual disease in the adjuvant setting, when there is no radiographic or histologic evidence of disease.All EFT tumors are characterized by similar chromosomal translocations that result in the fusion of the EWS gene on chromosome 22q12 with different ETS-related genes. More than 85% of analyzed cases of EFT are characterized by a t(11;22)(q24;q12) translocation. The most common fusion is made up of exon 7 of the EWS gene and exon 6 of the FLI1 gene (type 1 fusion), which was associated with favorable prognosis (3). Less common translocations (<10%) in EFT involve other members of the ETS family of transcription factors. These include ERG (located on chromosome 21), ETV1 (located on chromosome 7), E1AF (located on chromosome 17), and FEV (located on chromosome 2), resulting in t(21;22), t(7;22), t(17;22), and t(2;22) translocations, respectively (1). Among the chimeric transcripts resulting from such fusion, EWS-FLI1 (type 1 or 2) and EWS-ERG fusion transcripts are most widely used as molecular markers. Nested reverse transcription-PCR (RT-PCR) of fusion sequences (4) has enabled tumor detection at frequency of 10 -6 and has provided highly specific and sensitive tools for detecting circulating EFT in the bone marrow and blood. In fac...