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.
- Ray MJ, Singh SS, Davis W, McCann WE, Mohler JL, Marshall JR
Variability in visual segmentation of digitized prostate tissue microarray cores.
Anal Quant Cytol Histol. 2010 Dec; 32(6):301-10 - Godley LA, Cunningham J, Dolan ME, Huang RS, Gurbuxani S, McNerney ME, Larson RA, Leong H, Lussier Y, Onel K, Odenike O, Stock W, White KP, Le Beau MM
An integrated genomic approach to the assessment and treatment of acute myeloid leukemia.
Semin Oncol. 2011 Apr; 38(2):215-24 - Schwartz DA
Environmental genomics and human health.
G Ital Med Lav Ergon. 2011 Jan-Mar; 33(1):31-4 - Audo I, Lancelot ME, Mohand-Saïd S, Antonio A, Germain A, Sahel JA, Bhattacharya SS, Zeitz C
Novel C2orf71 mutations account for ∼1% of cases in a large French arRP cohort.
Hum Mutat. 2011 Apr; 32(4):E2091-103 [Epub 2011 Feb 8] - Nagineni CN, Kommineni VK, William A, Detrick B, Hooks JJ
Regulation of VEGF expression in human retinal cells by cytokines: implications for the role of inflammation in age-related macular degeneration.
J Cell Physiol. 2011 Mar 3; [Epub ahead of print]
- Barnhart KT
Epidemiology of male and female reproductive disorders and impact on fertility regulation and population growth.
Fertil Steril. 2011 Apr 8; [Epub ahead of print] - Guggenheim JA, Chen YP, Yip E, Hayet H, Druel V, Wang L, Erichsen JT, Tumlinson AR, Povazay B, Drexler W, Hocking PM
Pre-treatment choroidal thickness is not predictive of susceptibility to form-deprivation myopia in chickens.
Ophthalmic Physiol Opt. 2011 Mar 29; [Epub ahead of print] - Brunicardi FC, Gibbs RA, Wheeler DA, Nemunaitis J, Fisher W, Goss J, Chen C
Overview of the Development of Personalized Genomic Medicine and Surgery.
World J Surg. 2011 Mar 22; [Epub ahead of print] - Schwartz DA
Environmental genomics and human health.
G Ital Med Lav Ergon. 2011 Jan-Mar; 33(1):31-4
- Neely GG, Hess A, Costigan M, Keene AC, Goulas S, Langeslag M, Griffin RS, Belfer I, Dai F, Smith SB, Diatchenko L, Gupta V, Xia CP, Amann S, Kreitz S, Heindl-Erdmann C, Wolz S, Ly CV, Arora S, Sarangi R, Dan D, Novatchkova M, Rosenzweig M, Gibson DG, Truong D, Schramek D, Zoranovic T, Cronin SJ, Angjeli B, Brune K, Dietzl G, Maixner W, Meixner A, Thomas W, Pospisilik JA, Alenius M, Kress M, Subramaniam S, Garrity PA, Bellen HJ, Woolf CJ, Penninger JM
A genome-wide Drosophila screen for heat nociception identifies α2δ3 as an evolutionarily conserved pain gene.
Cell. 2010 Nov 12; 143(4):628-38 - Djaballah H
An interview with Hakim Djaballah, Ph.D. Interview by Vicki Glaser.
Assay Drug Dev Technol. 2010 Oct; 8(5):519-25 - 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
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.