Emory GRA Genome Center
Overview
The Emory GRA Genome Center (EGC) was set up to provide convenient, cost-effective access to “next generation” sequencing technologies. In the first 18 months after opening in Summer 2009 the EGC performed more than 120 projects for customers at Emory, across the US and internationally. The EGC has experience in a wide array of different nextgen applications and has already been chosen as a beta test site of a number of new sequencing instruments.
We look forward to talking with you about your project!
Instrumentation
The EGC currently runs two state-of-the art sequencing platforms. In December 2010 the EGC received delivery of its new Illumina HiSeq2000 instrument. This instrument will be phased into production in early 2011 to replace the EGC’s exsiting Illumina GAIIx machine. The HiSeq2000 is expected to produce 300-400M high quality reads of 50-100 nt (rising to 150 nt by the end of 2011) in a single flow cell of 8 lanes (one lane is reserved for controls). Reads can be multiplexed using 12 separate tags. Paired-end read runs from both sides of a DNA fragment are commonly run on the Illumina platform. Mate pair libraries representing fragments up to 6kb are also possible. Typical applications for the GAII include whole genome resequencing (human, plants, bacteria), RNA-seq, MicroRNA and Chip-Seq.
The Roche/454 GS-FLX Titanium instrument is capable of sequencing 300-600 Mb, with reads lengths of 300-450 nt. Reads can be multiplexed using 12 or more individual ‘MID’ tags. Mate pair libraries spanning insert sizes of up to 20 kb can be constructed. A GS-FLX picotiter plate is divided into 2,4,8, or 16 regions. Applications range from de novo bacteria and viral genome sequencing, deep-sequencing of PCR amplicons, metagenomics, ancient DNA sequencing and expression tag sequencing.
Other major equipment ancillary instruments include a Covaris E210 Acoustic Focusing Instrument, using for DNA nebulization and Roche LightCycler 480 II used for nextgen library quantitation. Libraries for nextgen sequencing are commonly made using a Beckman SPRI-TE robot.
Using the EGC
Projects at the EGC commonly move through 5 phases:
1. Consultation: the investigator contacts an EGC staff member and we discuss which sequencing technology is most appropriate as well as planning for downstream analysis.
2. Service Agreement: the EGC draws up a standard service agreement that includes all costs.
3. Sample Quality Evaluation: The EGC will usually evaluate DNA samples in the laboratory before commencing with library construction. Any problems at this stage will be discussed with the customers.
4. Library construction/ Sequencing: the EGC provides a full service inclusive of labor and reagents.
5. Post run analysis: the EGC will provide quality assessment of the data and a basic remapping if requested. We will to transfer the customer’s data by the most convenient format. We can offer advice on analysis software tools and research groups or companies that can help with data crunching.
Collaboration with Emory’s Cancer Genomics Shared Resource (CGSR)
The CSGR provides state-of-the-art sample preparation and genotyping services in a CLIA (#11D1086150) certified environment. The EGC has a close relationship with the CSGR and can work together to offer complete solutions for projects. Compatible services offered by the CSGR include:
Sample Preparation
• Robotic RNA and DNA sample prep and QC
• Fluidigm Access Array system for PCR-based target enrichment Genotyping
• Ion Torrent PGM sequencer
• Affymetrix GeneChip System
• Illumina HiScan
• TaqMan
Governance
The Director of the EGC is Dr. Timothy Read. The EGC has an internal advisory board consisting of Prof. David Stephens, M.D., Prof. Stephen Warren, Ph.D., Prof. Michael Zwick, Ph.D., Prof. Carolyn Meltzer, M.D. and Ms. Patricia Haugaard.
EGC accounting follows OMB CIRCULAR A-21 “Cost Principles for Education Institutions” . This means that the EGC is operated on an annual cost-recovery basis and service fees are not used to fund major capital equipment purchases. Customers therefore get the lowest service fees possible. Funding sources for equipment purchases include the Georgia Research Alliance (GRA), the Atlanta Clinical & Translational Science Institute (ACTSI) and the Emory University Department of Human Genetics.
Guidelines for use of the EGC
• EGC expects all relevant human/animal use protocols to have been completed by user before sample submission
• Researchers are to provide at least 5 g purified DNA per library, unless a different amount has been previously approved.
• Please submit samples in TE ph 8.0 not dH20.
• ECG will verify quantity and quality of input DNA prior to runs. We will advise customers if DNA quantity/ quality is likely to result in below standard performance.
• Library quantitation determined by real-time PCR or spectroscopy.
• On-machine titration of libraries is charged as a separate instrument run
• Basic Illumina and 454 analysis and remapping will be provided by EGC
• ECG cannot store customer data long term. ECG will offer opportunity for customers to transfer the data to their own external hard drives.
• Costs for Courier shipment of hard drives/DVDs, samples, etc will be paid by customer.
• All DNA samples, libraries and data are the property of the customers.
• Any concerns or disputes should be referred to the EGC Advisory Board
• If the data is eventually used in a publication, we kindly ask that you mention the Emory Genomics Center and sources of funding for equipment, the Georgia Research Alliance and Atlanta Clinical & Translational Sciences Institute, in the acknowledgements section.
Last updated January 2011
Acknowledgement & Authorship
The Core Facilities at Emory are here to support your research. In order to ensure that the appropriate recognition is attributed to the facilities, please acknowledge the facilities on all publications.