bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract 1146: Three-color array CGH differentiates constitutional from acquired CNVs in cancer genomes
Authors: Jewell Ursula R. , Moon So Young , Benjes Suzanne M. , Morris Christine M. 
Published: February 2011

Abstract
In recent years microarray-based comparative genomic hybridisation (CGH) has become the assay of choice for high-resolution screening of genetic aberrations in research and clinical diagnostics, and has revealed a plethora of small, constitutional copy number variations (CNVs) in healthy individuals. The appearance of these benign CNVs on the array profile affects the ability to identify CNVs that are acquired and pathogenic, in particular if these are also small in size. It is possible to eliminate constitutional CNVs by using a matched self-reference for each sample, but this compromises ability to compare array profiles between different individuals. In addition, the ability to link specific constitutional CNVs or combinations of these to disease susceptibility is lost.
We have developed a new 3-color microarray CGH assay which allows identification of constitutional CNVs while retaining the ability to compare between different samples by simultaneous application of two distinctly labelled reference samples. The new 3-color microarray CGH assay uses three spectrally distinct fluorescent dyes to label the test sample, matched self-reference, and generic reference, for simultaneous hybridization to the same array platform. We have applied this new protocol to the analysis of samples from healthy individuals, leukemia patients, and the leukemia-derived cell line K562, and performed pair-wise comparison of 26 array-CGH profiles from the new 3-color array with corresponding profiles from conventional 2-color arrays.
Our results demonstrate that introducing the third dye has no adverse effect on array assay noise, as measured by paired ttest of the standard deviation of the log2 ratio of all clones on the 2-color and 3-color array profile. Copy number calls from the new 3-color array assays show a consistency of up to 97% with the corresponding conventional 2-color array assays, equivalent to the level of consistency that was achieved when repeating array-CGH on the same sample using the same protocol. The prevalence-adjusted Cohen Kappa test indicates almost perfect agreement between the new 3-color assay and conventional 2-color assay. Application of the new 3-color microarray assay has enabled us to identify 44 constitutional CNVs in 57% of our leukemia samples. At least one third of these CNVs have been reported as sites of normal copy number variation and are listed in The Human Genome Variation Database.
Introducing a third sample into the microarray assay is a new and more economical approach for high resolution genome-wide comparison of DNA, and therefore potentially amenable to uptake in both research and diagnostics.
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 1146.
Abstract 1152: A novel, practical method for improving the sensitivity and reproducibility of immunodetection
Authors: Hofseth Lorne J. , Bailey Anne 
Published: February 2011

Abstract
The sedentary nature of standard immune-detection techniques on a slide (e.g. immunohistochemistry, immunocytochemistry, and/or immunofluorescence) leads to the potential for tissue drying, and antibody pooling, ultimately resulting in uneven and inconsistent staining which can yield false negative or under readings. We therefore hypothesized that if we could provide motion in the antibody fluid while submerging the tissue laden slide, we could prevent such disadvantages. Here, we present data indicating that rocking such slides in an antibody bath leads to extremely even staining, highly reproducible results and greatly enhanced sensitivity. We found that for both nuclear and anti-nuclear antibodies, reaction sensitivity was increased 1000X to 1,000,000X over best practice with standard immune detection techniques. The immunodetection scores for p-P53/Serine 15, Ki-67 and Hsp 70 as well as experiment photographs comparing the sedentary to dynamic methods results are presented. References are also given.
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 1152.
Abstract 1156: Applying targeted Next-Gen Sequencing and miRNA expression profiling for cancer biomarker discovery
Authors: Leonard Jack T. 
Published: February 2011

Abstract
The Biomarker Discovery Center in Heidelberg, Germany develops new approaches to cancer biomarker identification and validation using high throughput targeted next-generation sequencing and miRNA assays to characterize patient samples from the German Cancer Research Center (DKFZ) and other leading research institutions. Using HybSelect™, febit's product for sequence capture, we demonstrated high throughput processing of patient samples upstream of targeted Next-Gen Sequencing. Overlapping probes were designed to capture the genomic regions of interest (i.e., targets), and then the Geniom Biochips were synthesized for the HybSelect procedure. DNA libraries were prepared from clinical specimens using bar-coded sequencing adaptors from Life Technologies, and the targets were enriched using the HybSelect Sequence Capture Protocol. Bar-coded targets from hundreds of patient samples were sequenced using a SOLiD System with a febit Geniom RT Analyzer. The variants were compared to the reference sequences from healthy individuals. In a related study, changes in miRNA expression profiles were examined in certain cancers. The relative stability of miRNA and the relatively accessible nature of bodily fluids such as blood make miRNA a promising molecule for cancer biomarker discovery. For evaluation of the miRNA expression profiles of cancer patients, we utilized a Microfluidic Primer Extension Assay (MPEA), which starts with the hybridization of unlabeled total RNA samples to Geniom miRNA Biochips. After hybridization, selective enzymatic elongation of the correctly hybridized miRNAs was carried out with biotinylated nucleotides, and then detected with SAPE (streptavidin-conjugated phycoerythrin). The content included on Geniom miRNA Biochips was based on the latest Sanger miRBase update, thus guaranteeing that all human miRNAs, including the most recently validated miRNAs were addressed. With only 130 ng of total RNA required, this method dramatically reduced the amount of sample needed to reliably measure miRNAs and to develop predictive miRNA signatures. Analyses of complex miRNA expression patterns in blood of cancer patients compared to those of healthy donors allowed for distinct classification of the samples.
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 1156.
Abstract 1158: Single step multiplex amplification and barcoding of FFPE samples for Next-Gen sequencing
Authors: Isaksson Magnus , Johansson Henrik , Roos Fredrik , Falk Elin , Moens Lotte , Ericsson Olle , Nilsson Mats 
Published: February 2011

Abstract
We present data outlining application of the Selector Technology to successfully amplify and sequence sets of exons in both fresh frozen and formalin fixed paraffin embedded tumor samples. We also show preliminary data where the Selector Technology has been adapted to incorporate sequencing primers and barcodes during amplification thereby replacing the laborious sample preparation with a single PCR step which open up for streamlined large scale parallel sample preparation of patient cohorts. The technology has been scaled to amplify as many as 17,000 amplicons in one single reaction tube. The Selector Technology is suitable for convenient and scalable single tube amplification of large sets of genes. The technology provides unbiased amplification of exons for resequencing providing unparalleled on target alignment of &gt;95% of reads mapping to amplified regions and &gt;90% of exon base bp at 20-30% of average amplicon sequencing depth providing cost effective high coverage resequencing. Concordance with HapMap genotypes is 99% and the reproducibility (R2) between replicates is 0.98 at the single nucleotide level. High reproducibility provides the possibility to score copy number variations in tumor samples as well as calling copy number neutral loss of heterozygosity. These features are demonstrated using matched tumor-normal breast cancer samples. Conclusively, the Selector Technology is a convenient, high performance technology for large scale sample preparation of cancer samples.
Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend.
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 1158.
Abstract 1164: Parallel preparation of targeted resequencing libraries from 480 genomic regions using multiplex PCR on the Access Array system
Authors: Kaper Fiona , Wang Jun , Anderson Megan J. , Chen Peilin , Lin Min , Pieprzyk Martin , Jones Robert C. , May Andrew P. 
Published: February 2011

Abstract
Next generation sequencing platforms have dramatically reduced sequencing costs. However, it currently remains too expensive to routinely resequence entire human genomes in order to discover genetic variants or somatic mutations underlying tumorigenesis. Therefore, a need exists for multiplexed, targeted amplification methods that allow for the analysis of multiple genomic regions in large cohorts. Available targeted enrichment technologies are either aimed at the capture of regions of interest from a single sample, exhibit uneven representation or require significant amounts of input material. The novel microfluidic platform, the Access Array system, combines 48 samples with 48 primer sets resulting in 2,304 simultaneously occurring PCR amplifications requiring as little as 50ng DNA per sample. PCR products generated on the Access Array system can be used for sequencing on all next-generation sequencing platforms, including 454 GS FLX and Illumina GAII. To increase coverage and throughput, PCR reactions can be multiplexed within Access Array chips generating up to 480 amplicons per sample.
As proof-of-principal experiments, we have carried out multiplexed amplifications of a set of commonly mutated cancer gene exons across 48 genomic DNA samples. In initial experiments, 580 primer pairs were validated in individual PCR reactions in 96-well plates. Each primer pair was designed to include 5’ sequences that allow for the incorporation of 454 and Illumina adapters necessary for subsequent emPCR and cluster generation, respectively. 480 primer pairs that produced a single band of the correct size, as determined on a Caliper LabChip system, were selected for multiplex PCR experiments. Primer pairs yielding amplicons with a similar size were combined in groups of 10 sets, resulting in 48 primer pools of 10 primer pairs each. Multiplex PCR was carried out on Access Array chips, followed by harvesting of the 48 amplicon pools. Each pool was diluted and then subjected to a second round of PCR in standard 96-well plates with barcoded universal primers corresponding to the 454 and Illumina sequences. The resulting products are 48 uniquely barcoded amplicon pools, each comprising 480 amplicons derived from one sample, that are ready for sequencing. We will present sequencing data generated on both 454 and Illumina systems.
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 1164.
Abstract 1165: Image-guided Raman endoscopy for in vivo clinical detection of cancer in the stomach
Authors: Zheng Wei , Teh Seng Khoon , Ho Khek Yu , Teh Ming , Yeoh Khay Guan , So Jimmy Bok Yan , Zhu Feng , Huang Zhiwei 
Published: February 2011

Abstract
Objective: Raman spectroscopy is a unique optical vibrational spectroscopic technique that is capable of noninvasively probing biomolecular changes associated with cancerous transformation. The aim of this study was to investigate the feasibility of a novel imaged-guided Raman endoscopy system developed for distinguishing cancer lesions from the non-cancerous tissues in the human stomach in vivo.
Materials and Methods: A fiber-optic Raman endoscopy system was utilized for tissue Raman spectroscopic measurements at 785 nm laser excitation. A total of 20 in vivo gastric Raman measurement sites were used in this study, in which 15 sites were from 10 patients who underwent gastroscopic inspection, and 5 were from the suspicious lesion sites of 5 patients who underwent endoscopic ultrasound procedure. The histopathogical examinations on the biopsied tissues from the Raman measurement sites showed that 15 were non-cancerous and 5 were cancers. Multivariate statistical algorithms including principal component analysis (PCA) and linear discriminant analysis (LDA) were employed to determine the diagnostic sensitivity and specificity.
Results: High-quality in vivo gastric Raman spectra in the range of 800-1800 cm−1 can be collected in less than 1 second, together with the simultaneous utilization of white-light reflectance imaging modality for guiding the Raman endoscopic probe to the suspicious tissue sites. Raman spectral shapes were significantly different between non-cancerous and cancers, particularly in the spectral ranges of 850-900 cm−1, 1000-1090 cm−1, 1200-1305 cm−1 and 1600-1800 cm−1 which contain signals related to hydroxyproline for collagen, phenylalanine, amide III, amide I and C=C stretching of lipids. The Raman technique together with PCA-LDA-based analytic algorithm yielded diagnostic sensitivity of 96.1% and specificity of 100% for detection of cancer from the non-cancerous gastric tissues in vivo.
Conclusion: This study illustrates for the first time that the image-guided Raman endoscopy technique has promising clinical potential for rapid in vivo diagnosis of cancer tissues in the stomach.
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 1165.
Abstract 1174: Mechanisms of Fn14 overexpression in invasive breast tumors
Authors: Niska Joshua R. , Willis Amanda L. , Ramos Pilar , Mancini Catherine M. , Getz Julie E. , Cunliffe Heather E. 
Published: February 2011

Abstract
The fibroblast growth factor-inducible 14 (Fn14) signaling axis plays an important role in the regulation of breast cancer cell invasion. Breast tumors express Fn14 whereas normal mammary epithelium does not, and Fn14 expression correlates with poor prognostic indicators. The molecular mechanisms driving aberrant Fn14 expression in breast cancer have not yet been determined. This investigation aims to elucidate the mechanisms underlying Fn14 over-expression. Soluble tumor necrosis factor-like weak inducer of apoptosis (TWEAK), the cognate ligand for Fn14, was found to induce Fn14 expression in some breast cancer cell lines via a proposed autoregulatory mechanism. We also provide evidence to support the likelihood that membrane-bound TWEAK can stimulate Fn14 expression through adjacent tumor-cell interaction. EGF and a variety of other receptor tyrosine kinase ligands known to play a role in breast tumor progression stimulated de novo Fn14 expression in a panel of breast cancer cell lines. We therefore hypothesized that Fn14 expression may be induced by aberrant activation of the MAPK signaling pathway. Using an MCF7 model of TPA-mediated MAPK pathway activation and in vitro invasion using Matrigel-coated Transwell Boyden chambers, we observed TPA-mediated expression of Fn14 concomitant with a dramatic increase in cell invasion. Fn14 expression and invasion in this model were abrogated in the presence of U0126, a specific inhibitor of Mek1/2, implicating a role for MAPK signaling in regulation of Fn14 expression. From previously published microarray-based surveys of genomic aberrations in breast cancer, we also hypothesized that constitutive Fn14 expression may be due to Fn14 gene amplification. We performed fluorescence in situ hybridization analysis of 53 breast tumors and identified 15/53 (28%) tumors with additional copies of Fn14 relative to centromere 16. Fn14 was not amplified in normal breast epithelium or in Fn14-negative cell lines. We conclude that deregulation of Fn14 expression can occur through diverse molecular mechanisms associated with breast tumor progression. A more complete definition of the spectrum of molecular aberrations leading to induction of Fn14 expression in breast cancer requires further studies.
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 1174.
Abstract 118: Analysis of biological pathways associated with epirubicin and/or cyclophosphamide response by pathway enrichment analysis in human breast cancers
Authors: Shen Kui , Rice Shara , Wang Dakun , Gingrich Dave , Brower Stacey , Ervin Paul , Gabrin Michael , Song Nan 
Published: February 2011

Abstract
Recently, a number of different approaches for improving cancer treatment have been developed. One scientific approach is to understand the biochemical pathways and coding genes involved in cancer causation, while other approaches look to distinguish the biochemical pathways involved in drug response. Many chemotherapeutic drugs have been developed targeting different cellular properties, and even more targeted therapies impacting specific oncogenic pathways are on the horizon. Pathways implicated in drug response have been studied to determine why some tumors might respond to a given chemotherapy while others do not. Understanding these pathways may provide potential for improving therapeutic efficacy. Pathway analysis methods have been proposed to discover pathways of interests using gene expression profiling.
In this study, the biological pathways associated with response to Epirubicin (E), Cyclophosphamide (C) or the combination of the two drugs (combo EC) were evaluated in both breast cancer cell lines and patients. Thirty immortalized breast cancer cell lines were evaluated for response to these drugs using ChemoFx®. Area under the dose-response curve (AUC) was calculated to measure the chemosensitivity. We applied pathway enrichment to detect specific biochemical pathways associated with these drugs based on biological pathway databases (Kyoto Encyclopedia of Genes and Biocarta), breast cancer cell lines’ drug responses and public microarray data. Comparison of pathways associated with single drug E, C, and combo EC revealed that there are pathways associated with drug combination but not significantly associated with single drugs. These drug response-associated pathways offer great potential for new biomarker identification and drug targeting discovery.
In addition, EC associated pathways in breast cancer patients were identified using public microarray data and the associated patient clinical outcomes. Of importance, four biological pathways related to adherens junction, leukocyte transendothelial migration, regulation of actin cytoskeleton and ribosomal protein were identified as EC response-associated pathways in both breast cancer cell lines and patients. These common EC response-associated pathways indicate the potential possibility to use cell line in vitro drug responses to predict patient chemotherapy outcomes.
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 118.
Abstract 1186: PTEN expression predicts biochemical recurrence in prostate cancer
Authors: Stone Steven , Sangale Zaina , Veneroni Silvia , Reid Julia , Colecchia Maurizio , Carlson Amy , Valdagni Riccardo , Gutin Alexander , Daidone Maria G. , Zaffaroni Nadia 
Published: February 2011

Abstract
Prostate cancer is the most commonly diagnosed malignancy in men, but many patients have indolent disease that is unlikely to cause significant morbidity or mortality. Biomarkers that accurately predict disease severity would enable physicians to more appropriately manage patient care. Data from previous studies indicated that the molecular status of PTEN (phosphatase and tensin homolog) might be prognostic in prostate cancer patients after radical prostatectomy (RP). PTEN expression was evaluated on surgical specimens by IHC using anti-PTEN antibody 138G6 (Cell Signaling Technology) in 132 men treated with RP. Approximately half the patients also had neoadjuvant hormonal blockade therapy (BAT). PTEN IHC scores were derived from the weighted average of percent positive cells x intensity (0, 1 or 2). PTEN status (positive or negative) was determined using a predefined IHC score of ≤ 20 for negatives. Using this scoring system, 24% of the tumors were PTEN negative. Association with biochemical recurrence was evaluated using Cox PH models and likelihood ratio tests. Since we were testing a prior hypothesis about the prognostic utility of PTEN, the corresponding p-values are one-sided. In a univariate analysis on the overall series, PTEN status was associated with biochemical recurrence (p-value = 0.0046, HR = 2.3; 95% CI: 1.27, 4.33). Most of the clinical parameters typically associated with recurrence were affected by neoadjuvant therapy and rendered uninterpretable. Nevertheless, pathological tumor stage (p-value = 4.3 × 10−6, HR = 6.0; 95% CI: 2.35, 15.22) was still associated with outcome. In multivariate analyses, PTEN status was a significant predictor of outcome after adjusting for pathological stage (p-value = 0.009), neoadjuvant therapy (p-value = 0.014), or both (p-value = 0.04). These data support the hypothesis that PTEN status predicts outcome after RP, and suggest further, that PTEN may be a clinically important molecular marker for defining aggressive prostate 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 1186.