How do I track and manage sample mixtures for combination screening?


With the need to find potential drugs faster and more effectively, the pharmaceutical industry test mixtures or ‘pools’ of tens to hundreds of compounds per assayed well. As well as providing process efficiencies, testing mixtures can improve error-tolerance by reducing false negatives and positives [1]. More recently, biotechnology companies have started studying mixtures of 2 or 3 compounds with varying concentrations per assayed well.

Testing mixtures is particularly relevant to combination therapies, as it allows companies to make sure that the combined compounds don't interact negatively or have undesirable effects. Alternatively, the genetic complexity of many diseases means that focusing on a single target may not produce a sustained effect because of pathway redundancy and/or resistance mechanisms. In order to reach effective and sustained clinical responses, companies are increasingly performing combination screening focussed on multi-targeted drugs or drug combinations. The importance of testing mixtures in environmental studies is also growing, due to the need to assess combined exposures to multiple chemicals.

For mixture testing in both pharma and biotech, it is critical for the scientist to track the components in the well to associate the right compound(s) with the right data so that the assay results can be reliably and properly analysed.

mixtures

How do you track compound mixtures?

Accurate tracking of mixtures presents challenges. Consider how you would record the following:

  • Mixtures can comprise hundreds of substances, each with its own properties such as substance type, sample ID etc
  • Mixtures can include multiple solvents, each with its own data
  • The proportions and concentrations of each component in a mixture vary in each well
  • Mixtures can be added to other mixtures
  • Plates or vials of mixtures can be replicated or stored for use in subsequent assays

The number of variables to be tracked are outside the capacity of most spreadsheets and may be too complex for many sample tracking or LIMS systems. So what other options are there?

An industry-standard software solution

Titian’s Mosaic, the industry standard software for sample tracking, has developed tools and capabilities to accurately track pools of substances. This enables researchers to easily:

  • Identify and re-test the individual substances from the mixture hits
  • Test each substance in multiple distinct mixtures to infer the hits
  • Ensure mixture constituents have different molecular weights to allow LC-MS to identify the hits using Affinity Selection Mass Spectrometry (ASMS)

Mosaic software guides the user from the moment mixtures are created, through all transfers, to when the sample mixture is shipped. It allows researchers to track and view the components of the mixtures they are handling any time. Mosaic also keeps an audit trail of the whole life cycle of the sample mixture.

Users can easily register mixtures in Mosaic individually or using its bulk file import.

All the details about each mixture are conveniently displayed on the user interface, including identification and concentration of each mixture component.

In the example screenshot below, the selected well (G02) contains two different substances at different concentrations (listed in Substances) in a total volume of 3 µL of a mixture of solvents (listed in Solvent). It also indicates the specific containers that were used as sources for the selected mixture (listed in Parents).

mixtures-screenshot

Mosaic can track mixtures:

  • With large numbers of substance constituents, each with their specific substance type, concentration, concentration unit (e.g. mixture of biological substance and small molecule)
  • With multiple solvent constituents

Users can also record and track transfers from multiple sources into one output container (to create a mixture), or transfers of mixtures from one plate to another plate(s) (replication), or from a vial to another vial(s) (aliquotting).

Mosaic software also tracks mixtures as they are stored or retrieved from manual stores or in automated stores integrated with Mosaic. Researchers can place orders for whole samples or aliquots. The operator is then guided by Mosaic through the retrieval of the samples from the store and processing.
Mosaic logs all sample transfers and moves as labware is sorted or scanned on various devices. Every operation is recorded in Mosaic’s detailed 21 CFR Part 11 compliant audit trail.

mixtures-screenshot-audit

Finally, Mosaic can also track the dispatch and shipping of mixtures to other sites. The data associated with the mixtures can also be transferred to external systems, for example: IDBS ActivityBase or Genedata Screener.

Making combination screening easy

The purpose of combination screening is to see if the effect of the combination of two compounds is greater or less than the sum of their individual effects. One way to test this is to run a cross-titration with one compound arrayed across the plate, and another down the plate, looking for synergistic or antagonistic effects.

One integrated and effective solution for combination screening and analysis combines Mosaic software with Beckman Coulter’s Echo (previously Labcyte) and Genedata Screener. These three products work very tightly together so that:

  • The design of screen is created in the Echo Combination Screen application[2]
  • The substances to test are allocated to layers of the screen and the Echo protocol created in Mosaic, which also manages tracking the substances from storage through the screen
  • The resulting data is fed directly into Genedata Screener for analysis[3]

Using these three market-leading products together:

  • Provides a clear picture of results
  • Automates the rapid and accurate creation of combination screens
  • Ensures every component and quantity is automatically tracked and traceable in a 21 CFR Part 11 compliant audit trail

These features contribute to making Mosaic sample management software the most convenient and powerful tool for tracking inventories of any type of samples, including mixtures. With its reliable and comprehensive audit trail, it offers confidence in all the samples that are being handled and tested.

References
[1] Pooling in high throughput drug screening (Curr Opin Drug Discov Devel, May 2009)
[2] Web page: Echo Combination Screen  
[3] Web page: Genedata Screener for combination screening

Want to know more?

Titian Software offer a free white paper to download: "The Essential Guide to Managing Laboratory Samples"

 

Tags: News, combination screening, sample management