Terms and Conditions

Sample quality is the single most important factor in the success of a sequencing performance!

1. 1. Keck Genomics Platform accepts samples as either tissue, isolated nucleic acids, or completed libraries. Although Keck Genomics Platform will accept tissues and can perform isolation of nucleic acids, it will not guarantee performance. Customer will assume all risk of down-stream performance of any samples that is below recommended quality.
   2. Samples submitted to Keck Genomics Platform should:
      1. If appropriate, be de-identified;
      2. Have proper consents in place;
      3. Have all necessary service approvals and agreements in place;
      4. No obligations of specific identification of the samples;
      5. Must be safe and non-hazardous.
   3. All Samples must meet KGP’s Requirements, otherwise customer will assume all risks:
      1. KGP performs thorough quality control before each application. Therefore, it is critical to provide enough volume to allow for 2-5uL (varies with concentration) to be utilized in quality control assessment.

1. 1. Samples that contain either lower than recommended concentration or quality may impact overall quality of the final library. KGP cannot guarantee performance of any sample that is below the recommended quality and thus will flag any such sample for a discussion with the customer prior to pooling for sequencing.
   2. Low-quality libraries are very unpredictable and in many cases, the true displeasure can only be revealed in the final sequencing data. The poor performance can be a result of high duplication rates, variation of insert size, poor probe hybridization, and decreased complexities. Due to the unpredictable nature of low quality samples, costumer will assume any risk of the overall performance.
   3. Due to the overall poor-quality nature of FFPE samples, KGP has developed workflows designed to maximize the success when working with such samples; however, we cannot guarantee performance of library preparation or final data quality, as vast numbers of samples are considered poor-quality and will not pass our standard quality control. KGP does understand the value of subpar FFPE samples and will continue pushing the boundaries in developing better protocols to maximize the quality of data, but the customer must assume the risks involved and provide payment for services regardless of outcome when working with samples that do not meet our QC specifications.
   4. The general rule of thumb when considering downstream assays for FFPE (DNA) samples is that FFPE tends to generate better WES data than WGS data. In addition, FFPE (RNA) are too degraded for a polyA selection and need to follow the ribosomal degradation protocol. Generally, when working with highly degraded poor-quality samples increase in overall quantity, can occasionally compensate for poor-quality that may influence better results.

Please contact us prior to isolation and sample preparation, as any sample that is submitted that does not meet the requirements will be subjected to a $30/sample handling fee.

1. 1. Blood should be stored in lavender tubes (EDTA-coated) or Trizol and should not be stored in heparin-tubes as heparin is a potent amplification inhibitor.
   2. Nucleic acids should be stored in buffers such as 10mM Tris, ddWater, or Elusion Buffer with concentration of EDTA not to exceed 0.1mM.
   3. 5mL tubes are accepted for storage, but we prefer samples to be submitted in 96-well full-skirt plates that can withstand -80C temperatures. The samples should be sealed properly to withstand shipment.
   4. We recommend submission of RNA samples on dry-ice.
   5. We recommend a minimal volume of 15uL to allow us to perform thorough quality control and have enough material for down-stream processing.

1. 1. All samples that do not meet quality requirements may be submitted for sequencing by customer’s written consent, but KGP cannot guarantee quality of the data and all the expenses will be the responsibility of the customer.
   2. Any sample that is below recommended quality will be treated as a low-quality sample. The customer will have the opportunity to provide KGP with a brand-new sample with handling fees applied. The new sample will be assigned a new ID and will be treated as a new sample.
   3. At the customer’s request, any unused samples can be returned to the customer with applicable shipping and handling fees.
   4. Any sample that is mislabeled or does not meet KGP’s submission guidelines will be subject to a $30/sample fee.
   5. 16 or more samples should be submitted in full-skirt PCR plate. Failure to comply will result in a sample handling fee of $30/sample.
   6. Customer is responsible for performance and full cost of the sequencing services performed on submitted libraries.
   7. Customer will be notified by email upon receiving of samples.
   8. Customer is responsible to provide KGP with proof of BUA or IRB that is associated with every sample that is submitted.
   9. We recommend submission of the samples to be timed between Monday and Wednesday to avoid potential weekend deliveries. In addition, please provide additional business days around any holiday seasons.

Sample Submission Address:
Attention: Keck Genomics Platform
Keck School of Medicine of University of Southern California
1450 Biggy Street, NRT 2501
Los Angeles, CA 90033
Tel:(323)442–0288​

1. 1. Nucleic Acids Quality Control
      1. DNA
         1. Qubit, Bioanalyzer, TapeStation are recommended standards
         2. DIN > 5
         3. Nanodrop, although informative is not recommended
      2. RNA
         1. Qubit, Bioanalyzer, Tapestation are recommended
         2. RIN (RNA integrity Number) > 7
         3. On FFPE we also calculate DV200 and follow Illumina’s guidelines of > 30% to be considered into library preparation.
      3. Library
         1. Qubit, Bioanalyzer, Tapestation are recommended
         2. Kapa qRT-PCR on a 5nM dilution is recommended to determine the final concentration
         3. KGP cannot guarantee performance of libraries that are not generated in-house and therefore an advance payment is required prior to the initiation of the sequencing run.

1. 1. KGP will perform sequencing on all samples as agreed by the customer’s quote.
   2. Sequencing is to be performed within 6 weeks after arrival of all samples and each sample either passes quality control or KGP has given consent by customer to proceed.
   3. The customer will not be charged additional cost for any added sequencing depth.
   4. Any sample that has at least 85% or greater target coverage is considered a success and will not be subject to re-sequencing.
   5. It is important to note that inclusion of a poor-performing sample may not only result in poor performance of the sample itself, but may also impact the entire run and as a result, affect target coverage across all samples. KGP cannot guarantee agreed performance of the entire run if customer desires not to exclude a flagged low-quality library.

1. 1. Deliverables of sequencing data are raw reads .fastq files, aligned to a genome .bam files, in case of DNA copy number files, variant files .vcf, for RNA expression files, and general stats file. Any analysis beyond basic informatics becomes collaborative in nature with a possibility of additional fees that may apply.
   2. Any data stored on our server that is older than 3 months will be subject to deletion without notification.
   3. Data will be distributed through sftp or via external drive per customer request. KGP will only be responsible for copying the data to single location and any additional data movement will be subject to additional fees. Due to increased risk of malicious codes, KGP will not accept external drives provided by customer.

1. 1. Keck Genomics Platform requires proof of account prior to the release of any data.
   2. Customer will only be invoiced for services that were actually performed.
   3. If customer decides not to sequence a poor-quality sample, the customer will only be charged $30/sample for sample handling.

For payment details please contact:

Kendra L. Bergen
Budget/Business Analyst
(323) 442-7823
kendra.bergen@med.usc.edu

Ashley Jauregui
Research Laboratory Technician III/ Supervisor of Laboratory Operations
(323) 442-0859
ashleyj2@usc.edu