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:

1. Service Request

  1. Clients must request a quote for all service requests through SGT’s LIMS DUGSIM. We highly recommend a scientific consultation for new clients.
  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, there is a $5 charge for each sample, 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.

  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 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).
  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).

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.

  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 FASTQ files via SFTP server for most sequencing protocols. 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 DUGSIM.

  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.

  5. After 90 days, data will be removed from SGT storage and archived. Clients are responsible for cost of retrieval of data after 90 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 users should acknowledge funding from 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.

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