Gregory Wray, PhD
Holly Dressman, PhD
Genome Sequencing & Analysis Core Resource
IGSP, Duke University
119 Biological Sciences Bldg.
130 Science Drive
Durham, NC 27708
Microarray Core Facility
Duke University Medical Center
Duke Institute for Genome Sciences and Policy
101 Science Drive
Rm 2208B CIEMAS
Durham, NC 27708
The Integrative Cancer Genomics Shared Resource was created by the recent merger of two existing units, the Microarray Core Facility and the Genome Sequencing and Analysis Core Facility. Each of these predecessor cores has a track record more than a decade long of providing constantly updated, state-of-the-art genomic services to DCI members. The new Integrative Cancer Genomics Shared Resource brings all of the robust genomic technologies on campus under a single organization, making it much simpler for researchers to find the right service for their needs. Administratively, the merger provides comprehensive consultation, seamless management of complex projects that span multiple services, and enhanced operational flexibility.
The Integrative Cancer Genomics Shared Resource provides a unified core for one-stop access to all of the major research protocols and instrumentation platforms used in contemporary cancer genomics research. Consultation and sample drop-off for microarray services are located in the CIEMAS building, a short walk from the laboratories of the majority of DCI researchers. For services based on DNA sequencing, consultation and sample drop-off are located in the nearby Biological Sciences building.
This Shared Resource supports a wide range of projects from DCI investigators, including SNP discovery, mapping chromatin modifications, measuring mRNA levels at several scales (single genes, cancer panels, entire transcriptome), sequencing exomes, whole genome sequencing, identifying DNA methylation, and mapping transcription factor binding sites (see Technologies, below). The Shared Resource assists investigators with data quality control, versioning, statistical analysis, and dissemination for all of these services, as listed here.
The Integrative Cancer Genomics Shared Resource offers a wide and constantly updated range of genomic technologies in support of DCI researchers. All of the technologies listed here are available to DCI members through use of the Shared Resource.
Sample Preparation and Quality Control
Measurement of Gene Expression
Other Functional Genomic Assays
Detection and Measurement of Genetic Variation
By operating an extensive suite of state-of-the-art instrumentation, the Integrative Cancer Genomics Shared Resource provides DCI members access to the full range of instrumentation platforms used in contemporary genomics research, as well as the capacity to handle large projects. This approach allows the Shared Resource to provide investigators the ability to choose the optimal solution for their project. Primary instrumentation for high-throughput DNA sequencing thus includes all four of the major next-generation and third-generation platforms currently on the market: Illumina, IonTorrent, Pacific Biosciences, and 454. Primary instrumentation for microarray services includes the two major commercial platforms: Affymetrix and Agilent.
The services offered by Shared Resource fall into two general categories, with distinct policies for each. DCI members always receive scheduling priority.
(1) Access to instrumentation. The smaller category of services provides DCI investigators with self-service access to a wide range of equipment. This includes instruments for RT-PCR, microarray scanning, shearing nucleic acids, and nucleic acid quantitation. Shared Resource staff provide training, ensure that the instruments are calibrated and operating correctly, and carry out routine maintenance and software updates. Investigators schedule time on these instruments though an on-line sign-up form.
(2) Drop-off services. The majority of services provide sample processing and data analysis. The workflow for these services begins with an initial consultation with Dr. Dressman that covers the most appropriate genomic technology for the project, experimental design, sample preparation requirements, data analysis, and data storage. Depending on that conversation, she may recommend additional consultations with Dr. Fédrigo or Dr. Qin. Once a plan for the project has been formulated, investigators can obtain quotes for their project through the LIM systems (http://www.genome.duke.edu/cores/microarray/forms/submission/ for microarray services and http://www.dugsim.net for DNA sequencing services). When samples are ready for processing, investigators fill out an on-line submission form and drop off their samples. Samples are processed in order of receipt, with DCI investigators given priority over other users. Samples are tracked throughout processing by Shared Resource staff using the LIM systems. Investigators can log in at any time through a web portal to follow their samples throughout the steps of processing. Once the data have been generated, they are checked against quality control benchmarks and some preprocessing may be done with the data (depending on the particular service and specifications from the investigator). After the bioinformatician has reviewed and approved the data, the LIM systems send an email to the investigator informing them that their data set is ready to be downloaded from the secure server. Once the data have been retrieved, Dr. Dressman follows up with the investigator to ensure that they are satisfied with the service and to provide any needed assistance with data analysis and storage. After sufficient time has elapsed for the investigator to analyze the data, Dr. Dressman follows up again to offer any needed assistance with submitting data to public repositories such as GEO and Dryad.
Policies for scheduling instrument time are based on a model of continuous (24/7) operations in order to maximize throughput, as most of the instrument platforms are capable of processing multiple samples without constant direct supervision. Priorities for sample processing are as follows: DCI members' research; other research conducted by investigators at Duke University; research from investigators at neighboring institutions (University of North Carolina at Chapel Hill, North Carolina State University, North Carolina Central University); and research from investigators at other institutions.
Initial consultation and any routine discussions are free of charge to DCI members. While the Shared Resource normally charges $60/hr for consultations and for assistance with manuscript and grant proposal preparation, this fee is waived for DCI members.