SGT Policies

The Sequencing and Genomic Technologies Core Facility has established the following policies to ensure the efficient and responsible operations of generating high-quality next generation sequencing data. To maintain a smooth workflow and facilitate collaborative research efforts for all clients, we kindly ask clients of the facility to follow these policies:

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1. Service Request

  1. Clients must request a quote for all service requests through SGT’s LIMS SeqLIMS. We highly recommend a scientific consultation for new clients.
    View detailed instructions
     
  2. Clients must receive an approved quote before placing an order.
     
  3. Clients must provide accurate and complete information about the project, including sample details, experimental design, required services in our requested format. We strongly recommend a consultation for new clients.
     
  4. Duke clients must provide a fund code before we will begin to work on an order.
     
  5. External clients must provide a PO before we begin to work on an order. Alternatively, external clients may pay us via wire transfer. We will release data upon receipt of wire transfer.

2. Sample Submission and Preparation

  1. Clients must submit samples following the guidelines provided by the Core Facility, including proper labeling and relevant documentation. We will return samples that do not follow the guidelines. If we need to replate samples for any reason, charges will be incurred for replating, and SGT is not responsible for any mislabeling of samples.

  2. Clients are responsible for ensuring the quality and integrity of the samples they submit for analysis. Clients are responsible for paying for any troubleshooting due to sample problems.

  3. If samples do not pass QC according to vendor guidelines, SGT may still build and/or sequence libraries per client request. However, SGT will not guarantee the results, and the client is responsible for paying the charges. If the client opts to resubmit a sample, charges will be incurred for extra QC measurements. SGT does not guarantee the results of any low input, FFPE, or degraded samples.

3. Custom Sequencing Orders and Client Provided Libraries

  1. SGT will run sequencing protocols with client-provided custom Illumina primers but does not guarantee the sequencing results with custom primers (i.e. the client is responsible for the costs of sequencing runs and requested troubleshooting sequencing with custom primers). Custom primers can only be run on a full flow cell (i.e. client must purchase a full flow cell for custom primer runs).
  2. SGT will run client-built libraries but does not guarantee the sequencing results (i.e. the client is responsible for the costs of a sequencing runs and troubleshooting sequencing of client prepared libraries).
  3. Before SGT will work on a client-built library, the client must acknowledge on the order form that SGT is not responsible for the sequencing results and have read the SGT policies.

4. Service Prioritization

  1. Orders are prioritized in order of sample receipt. Samples enter the queue once QC is passed (i.e. resubmissions move the order to the end of the queue). If a backlog would occur for any reason, SGT prioritizes Duke orders, external orders paying by wire transfer, and external orders paying by check.

  2. SGT’s average turn-around-times are listed here. We do not guarantee the turn-around-time for a lane order.

  3. Unforeseen circumstances (e.g., equipment failure, supply shortages) may cause delays.

5. Data Deliver, Storage, and Retention

  1. SGT’s internal data management plan can be found here.

  2. The client is the owner and responsible for the data produced.

  3. SGT delivers demultiplexed FASTQ files via SFTP server for most sequencing protocols. To demultiplex client-built libraries, we will ask for index information. If incorrect information is provided and requires extra demultiplexing, clients are responsible for paying an hourly rate. By default, we deliver bcl files for 10x Genomics data. Clients can request delivery of demultiplexed 10x Genomics data in the comments of their order in SeqLIMS

  4. Clients are responsible for the retrieval of their data within 30 days from the SFTP server after the delivery email is sent from SGT. Clients are also responsible for ensuring the integrity of their download, and we strongly recommend verifying MD5 checksums.

  5. After 30 days, data will be removed from SGT storage and archived. Clients are responsible for cost of retrieval of data after 30 days.

6. Bioinformatics Analyses

  1. An order separate from a sequencing order is required for bioinformatic services. We highly recommend a consultation for those unfamiliar with bioinformatics.

  2. SGT offers pipelines for many analyses. Requests outside the scope of those pipelines are subjected to an hourly rate.

7. Publication and Acknowledgment

  1. SGT kindly requests authorship for staff who provide any the following to a manuscript (authorship requirements defined by the Association of Biomolecular Resource Facilities):

    • Conception, design of project, critical input, or original ideas

    • Acquisition of data, analysis and interpretation, beyond routine practices

    • Draft the article or revise it critically for intellectual content

    • Write a portion of the paper (not including Materials and Methods section)

    • Intellectual contribution

    • Final authority for the approval of article

  2. We kindly remind all clients to acknowledge the SGT in any resulting publications or presentations that utilize data generated by the facility:

    • We thank the School of Medicine for use of the Sequencing and Genomics Technologies Core Facility for [insert service here].

  3. All PacBio Revio results must include the NIH grant that was used to purchase the Revio:

                - We thank the School of Medicine for the use of the Sequencing and Genomics Core Facility for [insert service here]. Purchase of the PacBio Revio was funded by the NIH (1S10OD034222-01).

  4. SGT may request notification of publications for record-keeping and reporting purposes.

8. Compliance and Ethics

  1. Clients must comply with all applicable institutional, local, state, and federal regulations concerning the use of NGS technology and data. It is the responsibility of the client to acquire all IRB and/or other regulatory approvals before sequencing.

  2. Ethical considerations related to sample acquisition, data sharing, and patient privacy must be strictly adhered to.

  3. SGT only accepts de-identified samples from human subjects and does not work with samples containing PHI. SGT is not CLIA certified.

  4. All SGT faculty, staff, and clients are expected to adhere to the School of Medicine’s Code of Professional Conduct. Bullying, disrespect, harassment, and other unprofessional behaviors will not be tolerated.  

9. Fee Structure and Payment

  1. Service fees will be charged based on the established fee structure, subject to annual review and approval by Duke University School of Medicine’s Office of the Vice Dean for Basic Research.

  2. Per institutional policy, SGT does not offer any discounts. Any client concerns about sequencing data must be brought to the attention of SGT within 30 days of data delivery via email to sequencing@duke.edu.  

  3. External clients may provide their own reagents, which will be subjected to a 10% handling fee.