Welcome to the Vanderbilt Vision Research Center Microarray Core webpage, spotlighting the latest information regarding genomic technologies as they relate to VVRC interests. Members of the VVRC 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
Complement factor H polymorphism in age-related macular degeneration.
Science. 2005 Apr 15; 308(5720):385-9 [Epub 2005 Mar 10]
This manuscript used whole-genome mapping technology to uncover the role of a single nucleotide polymorphism (SNP) in age-related macular degeneration (AMD), a major cause of blindness in the elderly. The Affymetrix GeneChip Mapping 100K Set of microarrays was used to perform a genome-wide screen of 96 cases and 50 controls for polymorphisms associated with AMD. This mapping assay consisted of two chips (XbaI and HindIII) with approximately 50,000 SNPs each that were run using DNA from every individual in the study. Over 116K SNPs were genotyped and tested for allelic association with disease status. On initial analysis, two SNPs (rs380390 and rs10272438) were found to be strongly associated with disease status. SNP rs380390 was successfully genotyped in all individuals. No genotype was determined for SNP rs10272438 in 21 individuals, and upon further analysis, it appeared to be excessively out of Hardy-Weinberg equilibrium, indicating possible genotyping errors. Missing genotypes of rs10272438 were determined by resequencing and after inclusion of this data, the association with AMD was no longer significant. However, SNP rs380390, an intronic and common variant in the complement factor H gene (CFH), was found to be strongly associated with AMD. Since this manuscript was published, other groups have continued to profile the role of CFH in AMD in different populations.
- Berthaut A, Mirshahi P, Benabbou N, Azzazene D, Bordu C, Therwath A, Legeais JM, Mirshahi M
Vascular endothelial growth factor receptor-1 (VEGFR-1) expression in human corneal fibroblast decreased with age.
Mol Vis. 2009 Sep 29; 15:1997-2007 - Kurji K, Cui J, Lin T, Harriman D, Prasad S, Kojic L, Matsubara J
Microarray Analysis Identifies Changes in Inflammatory Gene Expression in Response to Amyloid-Beta Stimulation of Cultured Human Retinal Pigment Epithelial Cells.
Invest Ophthalmol Vis Sci. 2009 Sep 24; [Epub ahead of print] - Zeitz C, Labs S, Lorenz B, Forster U, Ueksti J, Kroes HY, De Baere E, Leroy BP, Cremers FP, Wittmer M, van Genderen MM, Sahel JA, Audo I, Poloschek CM, Mohand-Saïd S, Fleischhauer JC, Hueffmeier U, Moskova-Doumanova V, Levin AV, Hamel CP, Leifert D, Munier FL, Schorderet D, Zrenner E, Friedburg C, Wissinger B, Kohl S, Berger W
Genotyping microarray for CSNB-associated genes.
Invest Ophthalmol Vis Sci. 2009 Jul 2; [Epub ahead of print] - Matzkin LM, Markow TA
Transcriptional regulation of metabolism associated with the increased desiccation resistance of the cactophilic Drosophila mojavensis.
Genetics. 2009 Aug; 182(4):1279-88 [Epub 2009 Jun 1] - Wang K, Takahashi Y, Gao ZL, Wang GX, Chen XW, Goto J, Lou JN, Tsuji S
Mitochondrial ND3 as the novel causative gene for Leber hereditary optic neuropathy and dystonia.
Neurogenetics. 2009 Oct; 10(4):337-45 [Epub 2009 May 21]
- Harder N, Mora-Bermúdez F, Godinez WJ, Wünsche A, Eils R, Ellenberg J, Rohr K
Automatic analysis of dividing cells in live cell movies to detect mitotic delays and correlate phenotypes in time.
Genome Res. 2009 Nov; 19(11):2113-24 [Epub 2009 Oct 1] - Luttropp K, Lindholm B, Carrero JJ, Glorieux G, Schepers E, Vanholder R, Schalling M, Stenvinkel P, Nordfors L
Genetics/Genomics in chronic kidney disease--towards personalized medicine?
Semin Dial. 2009 Jul-Aug; 22(4):417-22 - Collins FA
Genetics terminology for respiratory physicians.
Paediatr Respir Rev. 2009 Sep; 10(3):124-33 [Epub 2009 Jun 2] - Herrick J, Bensimon A
Introduction to molecular combing: genomics, DNA replication, and cancer.
Methods Mol Biol. 2009; 521:71-101
- Liu X, Li G, Zhang B, Wang L, Li XH, Li XP
[Influence of suppression of Epstein-Barr Virus-encoded latent membrane protein 1 by rAAV vector mediated RNA interference on metastatic ability of nasopharyngeal cancer cells in vivo]
Zhonghua Zhong Liu Za Zhi. 2009 May; 31(5):324-9 - Harder N, Mora-Bermúdez F, Godinez WJ, Wünsche A, Eils R, Ellenberg J, Rohr K
Automatic analysis of dividing cells in live cell movies to detect mitotic delays and correlate phenotypes in time.
Genome Res. 2009 Nov; 19(11):2113-24 [Epub 2009 Oct 1] - Zhu J, Wang YS, Zhang J, Zhao W, Yang XM, Li X, Jiang TS, Yao LB
Focal adhesion kinase signaling pathway participates in the formation of choroidal neovascularization and regulates the proliferation and migration of choroidal microvascular endothelial cells by acting through HIF-1 and VEGF expression in RPE cells.
Exp Eye Res. 2009 May; 88(5):910-8 [Epub 2008 Dec 14]
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
Altered retinal microRNA expression profile in a mouse model of retinitis pigmentosa.
Genome Biol. 2007; 8(11):R248
Loscher et al utilized two different microRNA microarrays (Exiqon and Ambion) to construct a miRNA profile of retinitis pigmentosa in mice.
Molecular and phenotypic analysis of a family with autosomal recessive cone-rod dystrophy and Stargardt disease.
Mol Vis. 2007 Aug 31; 13:1568-72
Using a custom Affymetrix resequencing microarray, Yzer et al identified a shared ABCA4 mutation in a family with high incidence of two related retinal dystrophies. In addition, they identified a novel mutation shared by the patients with with arCRD, and a separate novel mutation in the patient with STGD1.
