Pilots and trial experiments
We are happy to help investigators conduct proof-of-principle studies for new assay types and pilot studies using standard assays with challenging or unfamiliar sample types.
For higher-risk projects, we generally recommend beginning with a pilot of approximately 4–8 samples, with representation from the major biological conditions whenever possible. Very small pilots can be difficult to interpret: a failure may reflect a sample-specific problem rather than the assay, while success with one or two samples may not predict performance across a larger cohort. Pilot studies are intended to evaluate feasibility and optimize the workflow; they are not necessarily designed to provide statistically definitive biological conclusions.
Depending on the assay and project, we may be able to reduce pilot costs by:
- Sharing compatible reagent or processing costs across projects
- Separating CoLab labor charges from investigator-provided reagents
- Batching compatible samples with other projects
- Performing a reduced-scale workflow
- Completing an intermediate QC or limited sequencing for validation only
The pilot plan, success criteria, expected deliverables, and decision to proceed to the full study should be agreed upon before work begins.
Failed experiments and refunds
The Genomics CoLab has extensive experience with the standard assays we support, but no genomic assay is guaranteed to succeed. Failures or low-quality results may arise from sample-specific or project-wide issues, including RNA or DNA quality, cell viability, tissue preservation, antibody performance, sample composition, reagent or instrument problems, sequencing performance, or human error.
We provide assay-specific sample requirements and use intermediate quality-control checks whenever possible to limit failures and limit the cost once failures happen. If a sample does not meet recommended criteria, we will discuss the risks and available alternatives with the investigator before proceeding. If the investigator asks us to continue with material that does not meet the recommended criteria, the investigator generally assumes the financial risk of an unsuccessful or lower-quality result.
When a documented CoLab error causes an assay to fail, we will take responsibility for the affected CoLab work. When sufficient material remains and a rerun is technically possible, we will repeat the affected work without additional CoLab labor or reagent charges. The appropriate remedy will depend on the stage and cause of failure and does not necessarily include repeating unaffected portions of a project while recognizing the requirement to control for additional batch variables.
The CoLab cannot replace or reimburse investigators for lost or consumed biological material. Investigators should retain backup material whenever possible, particularly for valuable or irreplaceable samples.
When failure results from sample quality, sample biology, investigator-provided materials, an inherent limitation of the assay, or another cause not attributable to a CoLab error, the completed work and consumed reagents remain billable. We will review the available QC information with the investigator and recommend whether to stop, modify, or repeat the experiment.
In some circumstances, a manufacturer may provide replacement reagents following a documented failure. When replacement reagents are available, a rerun may be possible with limited charges not covered by the manufacturer. Replacement reagents and waived charges cannot be guaranteed.
Billing
The Genomics CoLab bills monthly for work completed during the previous billing period. Charges may be issued by project stage rather than only after the entire project is complete, particularly when a project includes separately completed sample preparation, library preparation, sequencing, or bioinformatic analysis.
For internal UCSF billing, investigators are responsible for providing a valid SpeedType and confirming that it will remain active through the expected billing period. Please notify us before work begins if the proposed SpeedType has an approaching expiration date.
Requests to charge soon-to-expire funds in advance can be considered only when permitted by applicable UCSF recharge and financial policies. If advance billing is not permitted, investigators must provide another valid SpeedType before work proceeds.
Project-specific estimates are based on the information available when the project is approved. Changes in sample number, assay configuration, sequencing requirements, analysis scope, or investigator-requested work may require a revised estimate.
Turn around times
Turn around times are subject to change based on staff member availability for the assay in questions and the machine or sequencing queue times. We will contact investigators if projects are expected to take longer than the discussed turn around times due to changes in these areas as the project is progressing. We also can not reimburse clients due to delays in returning data.
Sample retention
We will store your samples, any back up samples submitted to us, as well intermediate and final products of the assay until the completion of the project and provide you the ability to pick up any left over materials. We do not have a strict window of time when samples/libraries are thrown away, but we will contact you and give you a 'last chance' to pick them up before doing so.
Data retention
Data generated in the Genomics CoLab or analyzed by our team will be available for at least 1 year following the completion of the project.
Libraries that are sent to the CAT core for sequencing will have CAT data ready emails forwarded to the investigators for download. If no data processing or analysis is being done by the Genomcis CoLab this is your only mechanism to recover data. Please see the CAT website for their data policy details, but this data is typically only available for ~3 months.
Acknowledgment/authorship
We always appreciate co-authorship in manuscripts we are involved in should the lead and senior authors believe our contributions to the study are significant, but we do not mandate it. We do ask our group be mentioned in the acknowledgments when ever possible.