Genomics Resources

Genomics and Microarray Resource CN 4116C The MCG Cancer Center 1120 15th Street Augusta, GA 30912 Director: Lesleyann Hawthorn, PhD Office: (706) 721-4384 Fax: (706) 721-1670 E-mail: lhawthorn@mcg.edu Facility Personnel: Nikki Harvel Research Associate Phone: (706) 721-5471 Fax: (866) 326-4086 E-mail: nharvel@mcg.edu Operating Hours: M-F, 9 am-5 pm

The Genomics and Microarray Resource, operational since October 2008, provides Microarray technology to researchers at The MCG Cancer Center through Affymetrix and Agilent Scanner Platforms. The combination of the two platforms allows for nearly an unlimited use of different array formats from a multitude of different suppliers.

Bioinformatics and support

The Resource aims to provide Cancer Center researchers access to microarray technology and bioinformatics at an affordable cost.* It offers consultation, training and educational seminars on:

• analysis of microarray data;
• programs designed to analyze large data sets;
• gene expression;
• the roles of DNA sequence variation in the genome.

Software, training and support is also available for researchers to enable them to analyze large data sets and obtain meaningful results from these experiments. A large number of state-of-the-art programs are available to afford analyses of different data types and the expertise is available to implement and advise on their usage.

Arrays: exon-specific, oligonnucleotide and genome-wide

The gene expression arrays that provide estimates of mRNA levels in tumors have given rise to exon-specific arrays that can identify both gene expression levels, alternative splicing events and mRNA processing alterations. Oligonucleotide arrays are also being used to interrogate single nucleotide polymorphisms (SNPs) throughout the genome for linkage and association studies, and these have been adapted to quantify copy number abnormalities and loss of heterozygosity events.

Genome-wide tiling arrays have been developed to identify as yet unknown transcripts. Global DNA methylation changes can be detected using array platforms. Addtionally, it has now become possible to identify DNA-protein interactions using chromatin immunoprecipitation (ChIP) on Chip protocols. With all of these capabilities becoming routine in genomics laboratories, the idea of a systematic characterization of the sum genetic events that give rise to a cancer cell is rapidly becoming a reality.

Equipment / Infrastructure

• Affymetrix GeneChip Scanner 3000 7G Plus
• Affymetrix Hybridization Oven 640
• Affymetrix Fluidics Station 450 (x2)
• Agilent Microarray Scanner
• Agilent Hybridization Oven for Array Slides
• Agilent 2100 Bioanalyzer
• Applied Biosystems GeneAmp 9700 Thermocycler
• NanoDrop 1000

Data Analysis*

• Affymetrix Genotyping Console
• Affymetrix Expression Console
• Affymetrix GCOS, GTYPE and CNAT
• Agilent GeneSpringGX
• Agilent Feature Extraction
• Clustall
• CNAG
• GO
• Ingenuity Pathway Analysis
• OGT CytoSure Visualization Software
• Partek Genomics Suite
• TreeView

*Initial data analysis included in array fee*

 

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