Genomics Research Center Policies
Terms and Conditions
Subject to the following terms and conditions, the Genomics Research Center (GRC) agrees to perform, and the Client agrees to pay for, services rendered as set forth in the order submitted by Client through the GRC submission process. The order shall be accepted upon receipt of properly submitted samples meeting requirements outlined below. Payment will be rendered upon Client receipt of data and results as outlined, and agreed upon, in the order submission process.
Through submission of samples to the GRC, you acknowledge and agree to the following policies:
General Sample Handling and Submission
1. All samples are to be submitted to the GRC drop-off location (G-7814) located near the biological supply center GRC Drop-off Location Map. In order to prevent distractions to GRC staff, samples must not be brought directly to the GRC unless otherwise discussed with GRC leadership. RNA samples must be placed in the -80C Ultra Low freezer only. Guidelines for proper storage of other sample types can be found on our website. The GRC will not accept samples exposed to hazardous (i.e. radioactive isotopes) or infectious agents (HIV, Influenza, etc...) without proper documentation and discussion about health risks.
2. All samples must be properly stored in a secure secondary container (i.e. sealed Ziploc bag or sample box) clearly labeled with Principal Investigator (PI) and drop-off date. The appropriate submission form must be completed, printed and placed submitted along with samples. In addition, an electronic version of the completed submission form must be sent to the GRC (New Sample Submission Drop-Off Email) the same day as sample drop-off. **Importantly, email of the submission form does not constitute sample submission. Only receipt of actual samples and the appropriate completed submission form to the GRC constitutes "sample submission". Sample tube or plate labels must match the IDs provided on the sample submission form exactly. If a discrepancy is found, samples will not be processed further and will be returned.
3. All samples must be de-identified and contain no personal health information (PHI) or any other information that could be used to identify a human subject. All GRC services are for research purposes only and are not to used for diagnosis or treatment decisions. Proper informed consent, if required, should be obtained prior to sample submission and proper documentation of such consent must be provided to the GRC before samples will be accepted.
4. All samples submitted for GRC services, must adhere to GRC submission guidelines or samples will not be accepted and will be returned to the PI/submittor.
5. Samples submitted to GRC must be assessed for quality and quantity. Current quality control guidelines and requirements for GRC services can be found here. In the event that the client proceeds without QC or with samples that fail GRC QC, the GRC cannot be responsible for the quality of data produced or any results obtained and all costs associated with rendered service are due and must be paid in a timely manner.
6. The GRC offers micro array processing, however, all work for this service is not performed "on-site". Samples submitted for micro array service will be assessed for quantity and quality and subsequently shipped to third-party provider for processing. GRC does not take responsibility for any sample loss after shipment. We follow high quality packaging/shipping guidelines but cannot guarantee receipt and handling at third-party provider. While the GRC only partners with vetted high quality third-party providers with documented expertise, we are unable to provide any guarantees of success and data quality. We routinely evaluate third-party performance and identify alternatives if necessary.
7. While the GRC accepts client prepared sequence-ready libraries, we cannot guarantee performance or data quality. The client is responsible for all sequencing costs associated with submitted non-GRC prepared libraries. GRC will not offer any guarantee of any work not performed "in-house" by GRC trained staff. In addition, barcode/index information must be provided for all submitted libraries on the submission form. The GRC offers 3 QC options for non-GRC sequence-ready libraries (Sample Submission Guidelines). Please be sure to indicate on the submission form the preferred option.
8. The GRC offers numerous diverse services. It is crucial to use the correct submission form for the service requested. All samples must be submitted along with the correct submission form to avoid miscommunication as to the desired service requested. For example, samples submitted for "Bioanalyzer Only" processing will not be processed for RNA-seq as part of the same submission. A new submission, specific for RNA-seq, must be provided to GRC before any additional work will be performed.
9. The GRC's Quantstudio 12K FLEX Real-Time PCR instrument is open to the UR community. A PPMS is required for all "run ready" qPCR plates setup by Client. Users must confirm instrument availability through PPMS reservation calendar prior to submitting. Any plates submitted without machine availability will not be processed and will be returned to GRC drop-off location.
10. cDNA samples submitted to GRC's qPCR setup service must be accurately quantified and concentrations provided on submission form. Any cDNA samples submitted lacking concentrations will not be processed and returned to GRC drop-off location.
Data handling and Deliverables
1. The deliverables for RNA-seq projects are fastq files (raw reads and quality filtered reads), fastQC reports, BAM alignment files for the appropriate reference genome, differential expression analysis result outputs (DeSeq2 and CuffDiff2), PCA plot of all samples, sample distance matrix of all samples, heatmap of top 50 significant differentially expressed genes per comparison, and volcano plot for each comparison. Additionally, a project summary report is generated that includes summary metrics/statistics for each sample as well as a summary of software used in the analysis. Any analysis beyond these basic deliverables become collaborative in nature, but analysis fees still apply.
2. DNA-seq data will be provided as fastq files (raw reads and quality filtered reads), fastQC reports, BAM alignment files for the appropriate reference genome, and variant call files (VCF) for SNP/InDel identification versus the reference genome or suitable control sample if provided. Any analysis beyond these basic deliverables become collaborative in nature, but analysis fees still apply.
3. All data/results are transferred via BH2 (internal) or secure weblink (external) to the individuals listed on the submission form. The Principal Investigator is required to also received the deliverables. If external hard disks are desired, these must be provided to GRC for data transfer or GRC will provide this for an additional fee. Although we routinely screen for viruses, the GRC makes no warranty as to absence of viruses or other malicious code that may harm software or systems.
4. GRC will maintain archived (backed up) copies of all data/analysis files generated for a period of 5 years, after which the data will be deleted from GRC servers. It is important that all clients maintain a appropriately managed copy of all project data and files to ensure long-term access/use. If necessary, data/result file re-distribution is provided and may be subject to additional fees.
5. Additional analyses or repeat analyses are subject to additional analysis fees.
Payment and Invoicing
1. PPMS is the system used by GRC for billing/invoicing. It is required that all internal GRC clients obtain a valid PPMS ID in order to submit samples for GRC services. There is no pre-payment required or allowed for services per URMC Finance and NIH guidelines. If a quote was provided, it should be included with the sample submission paper work to ensure billing accuracy.
2. All external clients must setup a purchase order (PO) as method of payment and provide the PO number before any work will be performed. External wire transfers are also accepted. Credit cards are not a valid form of payment.
All work performed by the University of Rochester Genomics Research Center (GRC) should be acknowledged in scholarly publications, posters, and oral presentations. Proper recognition allows us to measure the impact of our work and supports our initiatives in obtaining sponsored funding. In addition, any GRC personnel who make a substantial intellectual or experimental contribution are deserving of further recognition as co-author on any published material at the discretion of the Director and Principal Investigator.