Positional effects of polymorphisms in probe-target sequences on genoplot images of oligonucleotide microarrays

Single nucleotide polymorphisms (SNPs) present in probe-target sequences (SPTS) have been shown to be associated with abnormal genoplot images. We explored the effects of SPTS positions on genoplot images using a data set from a genome-wide association study typed on an Illumina Human Hap300 platform. We screened the physical genomic positions of 308,330 autosomal probes to identify SPTS candidates deposited in dbSNP. The genoplot images across 293 individuals were inspected further in SNPs bearing an SPTS candidate. We identified 35,185 SNPs bearing a single SPTS candidate, including 264 SNPs showing abnormal genoplot images. The frequencies of SPTS at distances within 10 bases from the target SNP were significantly higher in the 264 SNPs showing abnormal genoplot images, than in the remaining 34,921 SNPs (49.62 vs 12.87%; Fisher exact test; P = 2.2 x 10(-16)). Of these 264 SNPs, we randomly selected 20 SNPs and resequenced them in 97 individuals. An SPTS within 10 bases of the target SNP was confirmed in all 20 SNPs, except for one SNP with a small deletion (7 bases) in the probe-target sequence. Taken together, these results suggest an association of a proximal SPTS with an abnormal genoplot image, which could result in spurious genotype detections, highlighting the importance of minimizing systematic errors in microarray experiments.

Correlation between Parameters of Optical Diffusion Imaging and Prognostic Factors of Breast Cancer

Background: Total hemoglobin (HBT) and oxygen saturation (SO2) of optical diffusion imaging might be useful to predict extensive intraductal component (EIC) and lymphovascular invasion (LVI) in patients with breast cancer.To determine if the parameters of optical diffusion imaging correlate with the prognostic factors of breast cancer.Method and materials: A total of 95 patients who underwent surgery due to breast cancer were included in our study from March to October 2008. We obtained HBT, SO2 and synthesis diagnosis index (SDI) from optical diffusion imaging. Prognostic factors including estrogen receptor, progesterone receptor, HER-2/neu, HER-1, CK5/6, p53 status, LVI, EIC, lymph node metastasis and histologic grade were reviewed from pathologic report. We correlated HBT, SO2 and SDI on optical diffusion imaging with prognostic factors using Pearson correlation coefficient test.Result: Negative EIC showed correlation with low level of HBT and positive EIC showed correlation with high level of HBT (p=0.022). Negative LVI showed correlation with high level of SO2 and positive LVI showed correlation with low level of SO2 (p=0.038). Other prognostic factor shows no significant correlation with HBT and SO2. SDI shows no significant correlation with any prognostic factors.Conclusion: HBT and SO2 on optical diffusion imaging correlated with EIC and LVI, which enable prediction of EIC and LVI in patients with breast cancer.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 5018.

Surface geometry of C(60) on Ag(111)

The geometry of adsorbed C(60) influences its collective properties. We report the first dynamical low-energy electron diffraction study to determine the geometry of a C(60) monolayer, Ag(111)-(2 square root of 3 x 2 square root of 3) 30 degrees -C(60), and related density functional theory calculations. The stable monolayer has C(60) molecules in vacancies that result from the displacement of surface atoms. C(60) bonds with hexagons down, with their mirror planes parallel to that of the substrate. The results indicate that vacancy structures are the rule rather than the exception for C(60) monolayers on close-packed metal surfaces.

Use of tumor volume as measured on F18FDG-PET/CT scan as a predictive biomarker for head and neck cancer

e17019

Background: Functional imaging, PET and its fusion with anatomical modalities, PET/CT promise to improve detection and characteristic disease. The objective of this study was to evaluate metabolic tumor volume as measured on F-18 FDG-PET/CT and its association with treatment response and prognosis in patients with head and neck cancer. Methods: The study population consisted of patients received neoadjuvant chemotherapy for a maximum of three cycles followed by radiation therapy. Before treatment patients were taken FDG-PET/CT scan, SUVmax, tumor volume, metastasis were recorded. Results: We enrolled 59 patients with stage III ann IV head and neck cancer. The median age was 66 years (range 47–81). There were 32 patients with stage III and 27 with stage IV. The mean SUVmax was 8.8 (range, 1.478). The mean tumor volume was 21.3 cm3 (range, 0.2–170). There was no correlation between tumor volume and SUVmax (correlation coefficient 0.295). Higher SUVmax was not associated with an increased risk of lymph node and distant metastasis at diagnosis (p = 0.968). But higher tumor volume was associated with an increased risk of lymph node and distant metastasis at diagnosis (p = 0.063). The metabolic tumor volume as measured on PET/CT scans was predictor of treatment response and disease -free survival. The response rate were 84% (21/25) for an SUVmax <5.5, 55% (19/34) for an SUVmax > 5.5 (p = 0.038). The disease free survival were 31.1month for an SUVmax <5.5, 4.6months for an SUVmax > 5.5 (p = 0.025). Conclusions: The metabolic tumor volume as measured on F-18FDG-PET/CT is a predictive biomarker of treatment response and disease free survival for patients with head and neck cancer.

No significant financial relationships to disclose.

Correlation between kinetic features on breast MRI computer-aided detection (CAD) and prognostic factors of breast cancer

Abstract #4015

The purpose of this study was to correlate the kinetic features of breast MR computer-aided detection (CAD) with the prognostic factors of breast cancer.&#x2028; A total of 65 patients were included in our study from December 2007 to March 2008. We reviewed kinetic features of MR CAD such as proportion of initial rapid rise enhancement, percentage of washout, and enhancement patterns. We also recorded prognostic factors such as tumor size, estrogen receptor, progesterone receptor, HER-2/neu status, lymphovascular invasion, and histologic grade on pathology. We correlated the kinetic features on MR CAD with prognostic factors. Pearson and Spearman correlation test were used to evaluate correlation between kinetic features and tumor size. Fisher exact test also used for the statistical analysis between kinetic features and other prognostic factors.&#x2028; In 65 cases, 59 cases showed rapid washout enhancement patterns, 5 cases showed rapid plateau pattern and only one case showed medium plateau. Tumor size showed correlation with the initial rapid rise enhancement (p=0.03) on Pearson correlation test and the delayed washout percentage (p=0.05) on Spearman correlation test.&#x2028; Positive progesterone receptor status was significantly associated with rapid early enhancement (p=0.023) and delayed washout (p=0.05), respectively. HER-2/neu status showed trend with the early enhancement (p=0.063). Other prognostic factors such as estrogen receptor, lymphovascular invasion and histologic grade showed no significant correlation with the kinetic features on MR CAD.&#x2028; Several kinetic features on MR CAD were correlated with the specific prognostic factors of breast cancer. Recognition of several kinetic features correlated with prognostic factors might help to predict of patients' prognosis and to decide the treatment plan.

Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 4015.

Improved intra-operative reduction control using a three-dimensional mobile image intensifier - a proximal tibia cadaver study

This study aimed to analyse whether the precision of a three-dimensional mobile image intensifier (ISO-C 3D) differs from conventional two-dimensional fluoroscopy and high resolution CT scan in a fracture model of the proximal tibia. A depression fracture of the medial plateau (AO/OTA 41-B2.3) was created in 12 formalin-fixed, human cadaver knees. The cartilage of the depression could be positioned above (+1mm, +2mm), below (-1mm, -2mm), or in line with the joint surface. Fluoroscopy, computed tomography (CT) scans, and ISO-C 3D scans (four different protocols: 100 images, 66 images, 50 images, and 33 images) were done for each fracture level. Three independent observers assessed each imaging set. The difference between the estimated reduction and the real reduction was used for statistical analysis. Our hypothesis was that no differences in the precision exist between the imaging techniques (p<0.05). The conventional image intensifier group (0.7 mm+/-0.67) showed significantly higher deviations than the CT group (0.3 mm+/-0.43; p<0.001) and significantly higher deviations than all ISO-C 3D groups (0.4-0.5 mm; p<0.001). Of the ISO-C 3D groups, only the scan protocol with the lowest number of images (0.5 mm+/-0.51) showed significantly lower precision than the CT group (p<0.001). It was concluded that the three-dimensional mobile image intensifier showed higher precision in reduction assessment in a fracture model of the tibial plateau compared to fluoroscopy. High resolution CT scans should remain the standard for post-operative assessment of reduction outside the operating theatre.