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.
- McCurley AT, Callard GV
Time Course Analysis of Gene Expression Patterns in Zebrafish Eye During Optic Nerve Regeneration.
J Exp Neurosci. 2010 Jul 13; 2010(4):17-33 - Chen M, Muckersie E, Forrester JV, Xu H
Immune activation in Retinal Aging: A Gene Expression Study.
Invest Ophthalmol Vis Sci. 2010 Jun 10; [Epub ahead of print] - Schaeferhoff K, Michalakis S, Tanimoto N, Fischer MD, Becirovic E, Beck SC, Huber G, Rieger N, Riess O, Wissinger B, Biel M, Seeliger MW, Bonin M
Induction of STAT3-related genes in fast degenerating cone photoreceptors of cpfl1 mice.
Cell Mol Life Sci. 2010 Sep; 67(18):3173-86 [Epub 2010 May 14] - Medina RJ, O'Neill CL, Sweeney M, Guduric-Fuchs J, Gardiner TA, Simpson DA, Stitt AW
Molecular analysis of endothelial progenitor cell (EPC) subtypes reveals two distinct cell populations with different identities.
BMC Med Genomics. 2010 May 13; 3:18 - Mitra M, Kandalam M, Verma RS, UmaMaheswari K, Krishnakumar S
Genome-wide changes accompanying the knockdown of Ep-CAM in retinoblastoma.
Mol Vis. 2010 May 11; 16:828-42
- Zwart H
The Nobel Prize as a Reward Mechanism in the Genomics Era: Anonymous Researchers, Visible Managers and the Ethics of Excellence.
J Bioeth Inq. 2010 Sep; 7(3):299-312 [Epub 2010 Jul 9] - Wörz S, Sander P, Pfannmöller M, Rieker RJ, Joos S, Mechtersheimer G, Boukamp P, Lichter P, Rohr K
3D geometry-based quantification of colocalizations in multichannel 3D microscopy images of human soft tissue tumors.
IEEE Trans Med Imaging. 2010 Aug; 29(8):1474-84 [Epub 2010 Jun 17] - Dahdul WM, Lundberg JG, Midford PE, Balhoff JP, Lapp H, Vision TJ, Haendel MA, Westerfield M, Mabee PM
The teleost anatomy ontology: anatomical representation for the genomics age.
Syst Biol. 2010 Jul; 59(4):369-83 [Epub 2010 Mar 29] - Bhartiya D, Maini J, Sharma M, Joshi P, Laddha SV, Jalali S, Patowary A, Purkanti R, Lalwani M, Singh AR, Chauhan R, Singh N, Bhardwaj A, Scaria V, Sivasubbu S
FishMap Zv8 update--a genomic regulatory map of zebrafish.
Zebrafish. 2010 Jun; 7(2):179-80
- Shamir L, Eckley DM, Delaney J, Orlov N, Goldberg IG
An Image Informatics Method for Automated Quantitative Analysis of Phenotype Visual Similarities.
IEEE NIH Life Sci Syst Appl Workshop. 2009 Apr 9; 2009:96-99 - Li M, Xu J, Chen X, Sun X
RNA interference as a gene silencing therapy for mutant MYOC protein in primary open angle glaucoma.
Diagn Pathol. 2009 Dec 16; 4:46 - 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
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.
