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To facilitate collaborative research efforts between multi-investigator teams using DNA microarrays, we identified sources of error and data variability between laboratories and across microarray platforms, and methods to accommodate this variability. RNA expression data were generated in seven laboratories, which compared two standard RNA samples using 12(More)
BACKGROUND Preclinical studies have shown synergistic antitumour activity by inhibition of insulin-like growth factor-1 receptor (IGF-1R) and mTOR. The expression of IGF-1R seems to be crucial for this effect. We investigated the safety and efficacy of the combination of the IGF-1R antibody cixutumumab and the mTOR inhibitor temsirolimus in patients with(More)
Identification of differentially expressed genes and clustering of genes are two important and complementary objectives addressed with gene expression data. For the differential expression question, many "per-gene" analytic methods have been proposed. These methods can generally be characterized as using a regression function to independently model the(More)
OBJECTIVE To determine the prognostic significance of histologic type/subtype in a large series of patients with primary resected retroperitoneal sarcoma. BACKGROUND The histologic diversity and rarity of retroperitoneal sarcoma has hampered the ability to predict patient outcome. METHODS From a single-institution, prospective database, 675 patients(More)
BACKGROUND Leiomyosarcoma is a soft tissue sarcoma whose outcome has historically been confounded by the inclusion of gastrointestinal stromal tumors. Thus, we sought to determine the factors that predict survival and recurrence in patients with primary leiomyosarcoma alone. METHODS During 1982-2006, a total of 353 patients with primary resectable(More)
Angiosarcomas (AS) represent a heterogeneous group of malignant vascular tumors occurring not only in different anatomic locations but also in distinct clinical settings, such as radiation or associated chronic lymphedema. Although representing only 1% to 2% of soft tissue sarcomas, vascular sarcomas provide unique insight into the general process of tumor(More)
Malignant peripheral nerve sheath tumors (MPNSTs) represent a group of highly aggressive soft-tissue sarcomas that may occur sporadically, in association with neurofibromatosis type I (NF1 associated) or after radiotherapy. Using comprehensive genomic approaches, we identified loss-of-function somatic alterations of the Polycomb repressive complex 2 (PRC2)(More)
Ssd1 is an RNA-binding protein that affects literally hundreds of different processes and is polymorphic in both wild and lab yeast strains. We have used transcript microarrays to compare mRNA levels in an isogenic pair of mutant (ssd1-d) and wild-type (SSD1-V) cells across the cell cycle. We find that 15% of transcripts are differentially expressed, but(More)
There are many options in handling microarray data that can affect study conclusions, sometimes drastically. Working with a two-color platform, this study uses ten spike-in microarray experiments to evaluate the relative effectiveness of some of these options for the experimental goal of detecting differential expression. We consider two data(More)
PURPOSE To develop a nomogram based on clinicopathologic factors to quantify the risk of local recurrence (LR) after limb-sparing surgery without adjuvant radiation (RT). METHODS Review of our prospective sarcoma database identified 684 patients with primary, nonmetastatic, extremity STS treated with limb-sparing surgery alone between June 1982 and(More)