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.
- Tummala P, Mali RS, Guzman E, Zhang X, Mitton KP
Temporal ChIP-on-Chip of RNA-Polymerase-II to detect novel gene activation events during photoreceptor maturation.
Mol Vis. 2010 Feb 17; 16:252-71 - Kozulin P, Provis JM
Differential gene expression in the developing human macula: microarray analysis using rare tissue samples.
J Ocul Biol Dis Infor. 2009 Nov 22; 2(4):176-189 - Arora A, Guduric-Fuchs J, Harwood L, Dellett M, Cogliati T, Simpson DA
Prediction of microRNAs affecting mRNA expression during retinal development.
BMC Dev Biol. 2010 Jan 6; 10:1 - Bassnett S, Wilmarth PA, David LL
The membrane proteome of the mouse lens fiber cell.
Mol Vis. 2009 Nov 24; 15:2448-63 - 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
- Finnegan S, Robson J, Hocking PM, Ali M, Inglehearn CF, Stitt A, Curry WJ
Proteomic profiling of the retinal dysplasia and degeneration chick retina.
Mol Vis. 2010 Jan 11; 16:7-17 - Schmiedt ML, Bessa C, Heine C, Ribeiro MG, Jalanko A, Kyttälä A
The neuronal ceroid lipofuscinosis protein CLN5: new insights into cellular maturation, transport, and consequences of mutations.
Hum Mutat. 2010 Mar; 31(3):356-65 - Gao BB, Phipps JA, Bursell D, Clermont AC, Feener EP
Angiotensin AT1 receptor antagonism ameliorates murine retinal proteome changes induced by diabetes.
J Proteome Res. 2009 Dec; 8(12):5541-9 - 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]
- 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 - 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]
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.
