Citations

Abstract Microarray technologies are powerful assays, which can identify copy-number abnormalities (CNA) underlying the pathogenesis of cancer. Several commercial arrays are available but it is unclear which is the best platform. We did a side-by-side comparison between two leading arrays; the Affymetrix SNP6 and Agilent 1M, to compare data compression, noise, gene and exon coverage, and CNA detection. Five samples were run on both platforms and analyzed as recommended by the manufacturer. We first performed an in silico comparison to define the number of probes per serial 5k interval, number of probes per gene and exon, and the coefficient of variation of different smoothing windows. Comparing the CV of the two arrays showed a similar level of variation between a 3 and 5 probe averaging on the 1M and SNP6, respectively. Using these smoothing levels the 1M interrogates 81.2% of the genes in the genome compared to 69.3% on the SNP6. At the exon level the 1M has at least one probe in 64.8% compared to 41.2% on the SNP6. We observed a similar level of data compression (∼10%) on the two arrays but the SNP6 had nearly twice the noise (SD 0.38 versus 0.21). Finally, there was a marked increment in the number of CNA identified by 1M (mean of 78.5) than SNP6.0 (59.5). In this comparison the Agilent 1M out performed the Affymetrix SNP6. Even with half the number of probes, the 1M was superior in CNA detection, gene/exon coverage and showed less signal variation. A comparison with previous platforms showed that these two arrays did not identify new gene amplifications but did detect new deletions, however, neither platform detected several known deletions detected by other methods. Therefore, we designed a custom, exon-centered, 2×400K array (Agilent) with the goal of identifying additional deletions. The design outline was: a) all the probes from the Agilent CGH 44K array; b) 3 probes per exon across the human exome; c) high resolution tiling of 1450 cancer implicated genes; and d) tiling the 4kb flanking all MIRs. To improve performance, we only included probes with performance scores higher than 0.8 and 0.85 in queries b) and c), respectively. Lastly, 15000 probes from the 1M array that map to exons missed by our design parameters were also included. Our custom array has half the probes (415K) of the 1M (960K) and 4.5x less than the SNP6 (1.85M) but shows the best gene and exon coverage. When the minimum number of probes needed for calculating a CNA is considered, 86% of genes are interrogated compared to 81.2% (1M) and 69.3% (SNP6). The difference is even more marked at the exon level with 84% covered by at least one probe and at least 63.2% interrogated by two probes compared to 5.3% (1M) and 18.0% (SNP6). The promising in silico comparison of this exon-centered array, its more stringent design parameters in combination with significantly reducing the cost per run should make this a very promising array design for CNA analysis of tumor samples in the future Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 4957.

Abstract Introduction: Alterations in components of the stromal tissue that underlie the epithelium can initiate, promote or inhibit epithelial tumorigenesis. Decorin (DCN) and lumican (LUM) are stromal genes with reduced expression in serous ovarian cancer. We hypothesized that single nucleotide polymorphisms (SNPs) in these genes may influence susceptibility to serous ovarian cancer. Methods: To test this hypothesis, we compared genotype frequencies of 11 tagSNPs in DCN and LUM between 397 Caucasian cases with primary serous ovarian cancer and 920 Caucasian controls in two studies conducted at Mayo Clinic and Duke University (discovery set). Associations were evaluated further in a third Caucasian population of 436 cases and 1,098 controls in Australia (replication set). TagSNPs were selected from unrelated Caucasian samples within HapMap based on the following criteria: (i) minor allele frequency ≥ 0.05, (ii) pairwise linkage disequilibrium (LD) of r2 ≥ 0.8, and (iii) location within, and 5kb upstream and downstream of, each gene region. Genotyping was performed using the Illumina GoldenGate™ assay and associations between SNPs and serous cancer were evaluated using unconditional logistic regression to estimate per allele odds ratios (OR) and 95% confidence intervals (95%CI). Untyped genotypes for DCN rs13312816 in the discovery set, and for DCN rs3138165 and LUM rs17018765 in the replication set, were imputed using the MACH software. Results: In the discovery set, we observed inverse associations between DCN rs3138165 (OR=0.7; 95%CI=0.5-1.0), DCN rs13312816 (OR=0.7; 95%CI=0.5-1.0), DCN rs516115 (OR=0.8; 95%CI=0.7-1.0) and LUM rs17018765 (OR=0.7; 95%CI=0.5-1.0) and risk of serous ovarian cancers (all Ptrend=0.06). Associations were confirmed in the replication set for DCN rs3138165 (OR=0.6; 95%CI=0.4-0.9; Ptrend=0.009), DCN rs13312816 (OR=0.7; 95%CI=0.5-0.9; Ptrend=0.01) and LUM rs17018765 (OR=0.6; 95%CI=0.4-0.9; Ptrend=0.008), but not for DCN rs516115 (Ptrend=0.20). To increase statistical power, data from the discovery and replication sets were combined (833 cases and 2,013 controls) following confirmation of no statistical heterogeneity in the ORs between study sites. In the combined sample, associations were strengthened for DCN rs3138165 (OR=0.7; 95%CI=0.5-0.9; Ptrend=0.002), DCN rs13312816 (OR=0.7; 95%CI=0.5-0.9; Ptrend=0.002), DCN rs516115 (OR=0.9; 95%CI=0.8-1.0; Ptrend=0.03) and LUM rs17018765 (OR=0.6; 95%CI=0.5-0.8; Ptrend=0.001). All four SNPs were in the same LD block on chromosome 12, suggesting that serous ovarian cancer susceptibility may be driven by a single, correlated variant in the region. Conclusion: The findings of this study suggest that genetic variation in DCN and LUM may influence susceptibility to serous ovarian cancer and contribute to the mounting evidence that supports the role of the stroma in epithelial ovarian cancer. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2854.

Abstract There is increasing evidence that neighboring stromal cells are not uninvolved bystanders in the pathway to cancer. We hypothesized that SNPs in genes expressed as a consequence of interactions between ovarian cancer cells and the host micro-environment could contribute to ovarian cancer susceptibility. We therefore used a two-stage approach to comprehensively evaluate common single nucleotide polymorphisms (SNPs) in the Ovarian Cancer Association Consortium (OCAC) for 173 genes involved in stromal-epithelial interactions. Cases with epithelial ovarian cancer (n=675) and controls (n=1,162) were genotyped at 1536 SNPs using an Illumina GoldenGate™ BeadArray array. Logistic regression was used to estimate odds ratios (ORs) and adjust for potential confounders. Based on Positive Predictive Value estimates, three SNPs - PODXL rs1013368, ITGA6 rs13027811 and MMP3 rs522616 - were selected for replication using TaqMan genotyping in 3,734 serous invasive cases and 10,067 controls from 16 OCAC case-control studies. An additional 18 SNPs with Pper-allele <0.05 in the test set, and which fitted into an iPLEX design, were selected for replication by a subset of five OCAC studies (n=1771 serous invasive cases; n=4022 controls). The associations observed in the test set for the PODXL, ITGA6 and MMP3 SNPs were completely attenuated in the replication set (adj. Pper-allele ≥0.5). However, TERT rs7726159 showed evidence of a log additive association with ovarian cancer risk in the replication study (Pper-allele =0.03). Combined analysis of the test and replication sets for this SNP showed a significant association with risk of serous ovarian cancer among non-Hispanic whites [adj. ORper-allele 1.14 (1.04 - 1.24) p = 0.003]. A stronger association was observed for serous invasive cases when data for all ethnicities were included [adj. ORper-allele 1.18 (1.09 - 1.28) p = 2.46 × 10−5]. Stratification by histological subtype and malignant potential showed that TERT rs7726159 was also associated with risk of serous borderline tumors, but not with any other subtypes. Although TERT variants have not been previously reported to be associated with ovarian cancer, multiple genome-wide association studies have reported associations with this locus and risk of glioma, basal cell carcinoma, and several cancer types that are known to originate in the epithelium, including lung, bladder, prostate and cervical cancer. Further analysis of this locus is necessary to definitively identify the causal SNP(s). Our study adds to the growing evidence that, as well as 8q24, the TERT locus at 5p15.33, is a general cancer susceptibility locus. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 4727.

Object Synovial cysts of the cervical spine are rare. Further, synovial cysts of the C1–2 articulation, or retroodontoid cysts, are very rare, with fewer than 20 cases reported overall. The authors report on a single-institution series of 10 patients with C1–2 retroodontoid synovial cysts. Methods The charts of 10 patients with pathologically confirmed synovial cysts following resection between January 1998 and June 2009 were reviewed. The clinical presentation, radiographic findings, surgical management, and pre- and postoperative functional levels (reported as a modified Rankin outcome) are reported. Results All 10 patients underwent attempts at complete resection of the synovial cyst; none of the lesions were simply aspirated. All 4 patients with an initial recommendation of observation alone ultimately underwent surgery because of their swift neurological deterioration. The mean age at surgery was 75.4 ± 4.6 years (range 54–81 years). The mean presenting cyst volume was 4.6 ± 1.7 cm3. Nine of 10 patients underwent transoral resection of the cyst with posterior fusion. Six of the 10 patients underwent additional posterior laminectomy for decompression. The hospital length of stay varied from 2 to 45 days, with a mean of 19 ± 7 days. All patients undergoing transoral decompression had varying degrees of difficulty with postoperative dysphagia, diagnosed using videofluoroscopy. All patients improved in their modified Rankin Scale score after surgical intervention with a mean follow-up of 42 months (95% CI 12–72 months). Conclusions Synovial cysts of the atlantoaxial joint are rare. They occur in older patients in whom clinical deterioration is likely to occur. In most cases, these cysts can be diagnosed preoperatively. Transoral decompression with posterior fusion is an effective treatment for C1–2 degenerative cysts and can be accomplished with few complications. However, the ideal treatment for these lesions remains unknown.

Abstract The molecular target(s) cooperating with proteasome inhibition in multiple myeloma (MM) remain unknown. We therefore measured proliferation in MM cells transfected with 13 984 small interfering RNAs in the absence or presence of increasing concentrations of bortezomib. We identified 37 genes, which when silenced, are not directly cytotoxic but do synergistically potentiate the growth inhibitory effects of bortezomib. To focus on bortezomib sensitizers, genes that also sensitized MM to melphalan were excluded. When suppressed, the strongest bortezomib sensitizers were the proteasome subunits PSMA5, PSMB2, PSMB3, and PSMB7 providing internal validation, but others included BAZ1B, CDK5, CDC42SE2, MDM4, NME7, RAB8B, TFE3, TNFAIP3, TNK1, TOP1, VAMP2, and YY1. The strongest hit CDK5 also featured prominently in pathway analysis of primary screen data. Cyclin-dependent kinase 5 (CDK5) is expressed at high levels in MM and neural tissues with relatively low expression in other organs. Viral shRNA knockdown of CDK5 consistently sensitized 5 genetically variable MM cell lines to proteasome inhibitors (bortezomib and carfilzomib). Small-molecule CDK5 inhibitors were demonstrated to synergize with bortezomib to induce cytotoxicity of primary myeloma cells and myeloma cell lines. CDK5 regulation of proteasome subunit PSMB5 was identified as a probable route to sensitization.

Background: Posterior tibial tendon dysfunction (PTTD) is a common malady leading to acquired flatfoot, which frequently causes foot and ankle pain and swelling. We hypothesized that patients with PTTD and pitting edema along the course of the posterior tibial tendon (PTT) would have evidence of fluid within the tendon sheath on MRI. We introduce and validate a novel, yet simple physical examination finding, the posterior tibial edema (PTE) sign, to help distinguish PTTD from other causes of foot and ankle pain and swelling. Patients and Methods: To determine an association between the PTE sign and changes to the PTT evident on MRI, we reviewed the medical records of patients with PTTD who underwent magnetic resonance imaging (MRI). Results: Of 186 patients identified with PTTD, 49 underwent MRI, and 42 (86%) demonstrated imaging characteristics consistent with tendonitis, tendinosis, or tenosynovitis. Presence or absence of increased posterior malleolar pitting edema agreed with presence or absence of these MRI findings in 43 patients (88%), making the clinical examination finding significantly predictive of MRI results ( p = 0.01). The sensitivity of the test for PTE was 86%, with specificity of 100%. Conclusion: The PTE sign refers to pitting edema along the course of the PTT, not associated with acute trauma and not accompanied by other areas of edema. Physical examination signs that are highly sensitive and specific to the condition may help lower the cost of diagnosis by eliminating the need for expensive tests that are not always necessary.

Object Little information is available on follow-up MR imaging after treatment of spinal dural arteriovenous fistulas (DAVFs). The authors studied MR imaging findings in treated spinal DAVFs in relation to clinical outcomes. Methods A retrospective review of patients with spinal DAVFs who had undergone both pre- and postoperative spinal MR imaging was conducted. Postoperative MR images were obtained as routine follow-up studies or because of subjective or objective clinical deterioration. Several pre- and posttreatment MR imaging characteristics were evaluated by 2 neuroradiologists blinded to the clinical outcome. Clinical outcomes of motor, sensory, and urinary function (in relation to the patient's preoperative status) at the time of the postoperative MR imaging were obtained from the clinical record. The chi-square, Fisher exact, and rank-sum tests were performed to correlate imaging findings and changes with clinical outcomes. Results Thirty-four patients met inclusion criteria. Treatment was surgical in 33 patients and endovascular in 1 patient. Follow-up MR imaging was performed at a mean 168 ± 107 days after treatment. Twenty-seven patients (79.4%) were either clinically stable or improved, and 7 (20.6%) experienced worsening in one or more clinical outcomes. Most patients were found to have improvement of MR imaging changes. However, some degree of persistent spinal cord signal abnormality, enhancement, and swelling was observed in 31 (91.2%), 29 (85.3%), and 18 (52.3%) patients, respectively. Changes in these MR imaging characteristics compared with preoperative MR imaging did not correlate with clinical outcomes (p > 0.05), with the one exception of a significant correlation between change in urinary function and extent of spinal cord contrast enhancement (p = 0.026), a correlation of uncertain importance. Ten of the 34 patients underwent posttreatment digital subtraction angiography, and 3 of these patients had recurrent/residual DAVFs. Worsening of motor function significantly correlated with recurrent/residual DAVF (p = 0.053). Conclusions Spinal cord abnormalities persist on postoperative MR imaging studies in patients with treated spinal DAVFs, and although they tend to mildly improve with time, these changes may not correlate with clinical outcomes. However, regardless of imaging findings, worsening motor function may correlate with a recurrent or residual DAVF.

Although more prevalent in males in the 6th and 7th decade of life, spinal dural arteriovenous fistulas (SDAVFs) are an uncommon cause of progressive myelopathy. Magnetic resonance imaging and more recently Gd bolus MR angiography have been used to diagnose, radiographically define, and preprocedurally localize the contributing lumbar artery. Three-dimensional myelographic MR imaging sequences have recently been developed for anatomical evaluation of the spinal canal. The authors describe 3 recent cases in which volumetric myelographic MR imaging with a 3D phase-cycled fast imaging employing steady state acquisition (PC-FIESTA) and a 3D constructive interference steady state (CISS) technique were particularly useful not only for documenting an SDAVF, but also for providing localization when CT angiography, MR imaging, MR angiography, and spinal angiography failed to localize the fistula. In a patient harboring an SDAVF at T-4, surgical exploration was performed based on the constellation of findings on the PC-FIESTA images as well as the fact that the spinal segments leading to T-4 were the only ones that the authors were unable to catheterize. In a second patient, who harbored an SDAVF at T-6, after 2 separate angiograms failed to demonstrate the fistula, careful assessment of the CISS images led the authors to focus a third angiogram on the left T-6 intercostal artery and to perform superselective microcatheterization. In a third patient with an SDAVF originating from the lateral sacral branch, the PC-FIESTA sequence demonstrated the arterialized vein extending into the S-1 foramen, leading to a second angiogram and superselective internal iliac injections. The authors concluded that myelographic MR imaging sequences can be useful not only as an aid to diagnosis but also for localization of an SDAVF in complex cases.

AbstractGenome‐wide association studies (GWAS) are being conducted at an unprecedented rate in population‐based cohorts and have increased our understanding of the pathophysiology of complex disease. Regardless of context, the practical utility of this information will ultimately depend upon the quality of the original data. Quality control (QC) procedures for GWAS are computationally intensive, operationally challenging, and constantly evolving. Here we enumerate some of the challenges in QC of GWAS data and describe the approaches that the electronic MEdical Records and Genomics (eMERGE) network is using for quality assurance in GWAS data, thereby minimizing potential bias and error in GWAS results. We discuss common issues associated with QC of GWAS data, including data file formats, software packages for data manipulation and analysis, sex chromosome anomalies, sample identity, sample relatedness, population substructure, batch effects, and marker quality. We propose best practices and discuss areas of ongoing and future research. Curr. Protoc. Hum. Genet. 68:1.19.1‐1.19.18 © 2011 by John Wiley & Sons, Inc.

Abstract Abstract #75 Background: The primary aims of this study were to determine 1) if a concurrent regimen of therapy containing cyclophosphamide compared to a sequential regimen containing cyclophosphamide would prolong disease-free survival (DFS) and overall survival (OS) and 2) if a regimen without cyclophosphamide was at least as efficacious as the two regimens containing cyclophosphamide. The secondary aims were to compare toxicities among the three regimens and to compare differences in amenorrhea in premenopausal women in each arm and its relationship to outcome.
 Materials and Methods: 5351 pts with cT1-3, N0-1, M0 were enrolled from 3/1/99 to 3/31/2004. 1783 pts were randomized to Group 1 [doxorubicin (A) 60 mg/m2 and C 600 mg/m2 q 3 weeks (wks) x 4 followed by docetaxel (T) 100 mg/m2 q 3 wks x 4], 1784 pts to Group 2 [A 50 mg/m2 and T 75 mg/m2 q 3 wks x 4], and 1784 to Group 3 [A 50 mg/m2 T 75 mg/m2 and cyclophosphamide (C) 500 mg/m2 q 3 wks x 4]. All patients with ER-positive tumors received hormonal therapy after completing chemotherapy. The protocol specifies that 800 deaths are required for the definitive analysis. This is expected to occur by Fall 2008.
 Results: Mean time on study is currently 79 months. At entry, 46% of pts were < 49 yrs; 54% were > 50 yrs. 82% were white, 10% black, 4% Hispanic. 66% had 1-3 positive nodes, 26% had 4-9, and 8% had 10+. 75% of pts were ER pos. 49% had lumpectomy, 51% mastectomy, and 24% local/regional radiotherapy. Mean tumor size was 2.5 cm. The presentation will include the first results of DFS, OS, and relevant toxicities from the trial. Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 75.