Welcome to the Vanderbilt-Ingram Cancer Center Microarray Core webpage, spotlighting the latest information regarding genomic technologies as they relate to VICC interests. Members of the VICC are urged to contact the VMSR to find out how microarray, genotyping, and RNAi technologies may enhance their research. Three VMSR bioinformaticists are available to help members design and plan experiments, obtain high-quality data, and prepare the data for publication. New platforms, products, and analysis techniques allow exploration of genomics in ways never before possible.
Featured research
Genome-wide association study identifies a new breast cancer susceptibility locus at 6q25.1.
Nat Genet. 2009 Mar; 41(3):324-8 [Epub 2009 Feb 15]
Wei Zheng and colleagues performed a large, multi-stage genomewide association study on breast cancer in Chinese women. They present a novel risk variant on 6q25.1, near the ESR1 gene, and verified it in a cohort of European ancestry. In the first stage of the study, 1,374 cases and 1,402 controls were genotyped at the VMSR using the Affymetrix Genomewide SNP 6.0 array. In addition to the 900,000 SNPs available on that array, Zheng et al imputed a further 1.14 million genotypes using HapMap data. From this initial stage, they identified 29 SNPs as 'promising', and genotyped them in an independent set of 1,554 cases and 1,576 controls using the Sequenom platform. Four SNPs were identified in the second stage as highly associated with breast cancer, and these four SNPs were genotyped in a third stage of 3,472 cases and 900 controls. In each stage individually, and in a pooled analysis of all three stages, rs2046210 showed very consistent and strong association. A final verification was performed on a cohort of 1,590 cases and 1,466 controls of European ancestry, which yielded results consistent with the three Chinese cohorts.
- Nagashio R, Sato Y, Matsumoto T, Kageyama T, Satoh Y, Shinichiro R, Masuda N, Goshima N, Jiang SX, Okayasu I
Expression of RACK1 is a novel biomarker in pulmonary adenocarcinomas.
Lung Cancer. 2009 Nov 3; [Epub ahead of print] - Hu P, Greenwood CM, Beyene J
Using the ratio of means as the effect size measure in combining results of microarray experiments.
BMC Syst Biol. 2009 Nov 5; 3(1):106 [Epub ahead of print] - Hiroki E, Akahira JI, Suzuki F, Nagase S, Ito K, Suzuki T, Sasano H, Yaegashi N
Changes in microRNA expression levels correlate with clinicopathological features and prognoses in endometrial serous adenocarcinomas.
Cancer Sci. 2009 Oct 8; [Epub ahead of print] - Gao C, Zhang Z, Liu W, Xiao S, Gu W, Lu H
Reduced microRNA-218 expression is associated with high nuclear factor kappa B activation in gastric cancer.
Cancer. 2009 Nov 4; [Epub ahead of print] - Mollweide A, Staege MS, Hoeschen C, Hideo Y, Burdach S, Richter GH
Only therapeutic ICOS:ICOSL blockade alleviates acute graft versus host disease.
Klin Padiatr. 2009 Nov-Dec; 221(6):344-50 [Epub 2009 Nov 4]
- Kubo T, Kuroda Y, Kokubu A, Hosoda F, Arai Y, Hiraoka N, Hirohashi S, Shibata T
Resequencing analysis of the human tyrosine kinase gene family in pancreatic cancer.
Pancreas. 2009 Oct; 38(7):e200-6 - Thomas DM
Wnts, bone and cancer.
J Pathol. 2009 Nov 3; [Epub ahead of print] - Koukourakis MI, Giatromanolaki A, Sheldon H, Buffa FM, Kouklakis G, Ragoussis I, Sivridis E, Harris AL, for the Tumour and Angiogenesis Research Group
Phase I/II Trial of Bevacizumab and Radiotherapy for Locally Advanced Inoperable Colorectal Cancer: Vasculature-Independent Radiosensitizing Effect of Bevacizumab.
Clin Cancer Res. 2009 Nov 3; [Epub ahead of print] - Ji NY, Park MY, Kang YH, Lee CI, Kim DG, Yeom YI, Jang YJ, Myung PK, Kim JW, Lee HG, Kim JW, Lee K, Song EY
Evaluation of annexin II as a potential serum marker for hepatocellular carcinoma using a developed sandwich ELISA method.
Int J Mol Med. 2009 Dec; 24(6):765-71
- Wu ZL, Zheng SS, Li ZM, Qiao YY, Aau MY, Yu Q
Polycomb protein EZH2 regulates E2F1-dependent apoptosis through epigenetically modulating Bim expression.
Cell Death Differ. 2009 Nov 6; [Epub ahead of print] - Lovejoy CA, Xu X, Bansbach CE, Glick GG, Zhao R, Ye F, Sirbu BM, Titus LC, Shyr Y, Cortez D
Functional genomic screens identify CINP as a genome maintenance protein.
Proc Natl Acad Sci U S A. 2009 Nov 4; [Epub ahead of print] - Rosse C, Formstecher E, Boeckeler K, Zhao Y, Kremerskothen J, White MD, Camonis JH, Parker PJ
An aPKC-exocyst complex controls paxillin phosphorylation and migration through localised JNK1 activation.
PLoS Biol. 2009 Nov; 7(11):e1000235 [Epub 2009 Nov 3]
News and Notes
- Previously analyzed data could benefit from a second look using new analysis techniques and software, which can uncover expression patterns, provide pathway analysis, or drug discovery information.
- Agilent arrays are now offered for CGH and gene expression analysis.
- Interested in miRNA detection? Exiqon miRCURY™ LNA microRNA Arrays offer high-quality miRNA data from total RNA - no fractionation required!
- Tiling arrays are a discovery tool for studying gene regulation, including mapping sites of protein/DNA interaction in ChIP experiments, discovering new RNA transcripts, and understanding DNA methylation or acetylation.
- VMSR functional genomics capabilities include RNAi and full-length cDNA libraries, with clones available to Vanderbilt researchers at a fraction of the cost of commercial websites. Synthetic RNAi libraries with specific focuses are also available, including Human Druggable Genome, Protein Kinase, Phosphatases, and GPCR screening libraries.
- The newest DNA Mapping arrays probe almost 1 million SNPs and an additional 1 million copy number analysis probes. High-throughput handling in the VMSR has yielded decreased costs, making genotyping affordable to any budget. Copy number analysis can be done on as little as one tumor or diseased sample, when compared to publicly available normal controls.
Selected papers of interest
Analysis of host- and tumor-derived proteinases using a custom dual species microarray reveals a protective role for stromal matrix metalloproteinase-12 in non-small cell lung cancer.
Cancer Res. 2006 Aug 15; 66(16):7968-75
Acuff et al designed a custom Affymetrix protease array to distinguish human and mouse genes. By then using a xenograft approach in which human lung tumor cells are injected into a mouse, they could identify the genes transcribed by the tumor (human) and the host (mouse), allowing a better understanding of the cross-talk between proteases in the tumor and the surrounding microenvironment. These results were compared to a data set of human lung adenocarcinoma specimens from the Carbone lab run on Affymetrix U133 Plus 2.0 arrays by the VMSR. MMP-12, MMP-13, and cathepsin K showed an increase in expression in human tumors compared with normal lung similar to that seen in the orthotopic model
Characterizing the cancer genome in lung adenocarcinoma.
Nature. 2007 Dec 6; 450(7171):893-8 [Epub 2007 Nov 4]
Weir et al present the results of a systematic copy number analysis of 371 lung adenocarcinoma tumors. Using the Affymetrix 250K SNP Mapping (Sty) array, they identify 57 significantly recurrent amplifications and deletions and present several candidate oncogenes.
RNAi screening of the tyrosine kinome identifies therapeutic targets in acute myeloid leukemia.
Blood. 2008 Feb 15; 111(4):2238-45 [Epub 2007 Nov 19]
Tyner et al report on the development of an RNAi screen to identify tyrosine kinase targets in specific cancer samples
