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    High throughput mutation detection
Liquid handling
Standardisation of PCR Optimisation and Design Specification (SPODS)
Mutation screening
LIMS/process interface
CSCE
DNA extraction
MALDI-TOF
Home > Technologies > High throughput > Liquid handling
The information in this section relates to the period from summer 2003 to summer 2008. Whilst this project is no longer ongoing we are happy to receive feedback and answer any queries arising from it.
High throughput mutation detection strategy
Liquid Handling  

Project Leader: Chris Mattocks

A key component of the strategy is the use of robotics for liquid handling. This not only speeds up the process of setting up reactions but also increases consistency and reduces the chance of error. The project examined the particular characteristics of the methodology that were required to facilitate the use of robotics and necessary scale-up for high throughput, and how these affected the design of individual processes (e.g. PCR). These can be summarised as follows:

Consumables
The decision as to what particular methodology was used at each stage was based largely on cost; this is a function of the consumables required. For example sequencing cleanup can be performed on either 96 or 384 well filter plates (among other methods) but the cost is not proportionate to the number of wells. Consequently it is about three times cheaper to use a 384 well plate format.
Simplicity
The aim was to distil each stage of the process down to the most simple and automation friendly form. This facilitated standardisation and increased robustness both in terms of hardware operation and user interaction with the system.
Standardisation
It is desirable to standardise as many processes as possible across the range of processes to be carried out by the system. This reduces the number of different protocols that are required simplifies set-up, maintenance and user interaction with the system and increases robustness.
Multiplexable
In comparison with the capacity of the latest analysis platforms (e.g. ABI 3730) the current and foreseeable throughput requirements for diagnostic genetics was considered relatively modest. In view of this multiplexing was kept to a minimum maximise robustness. However, post PCR multiplexing for analysis by CSCE was used as this was not seen to adversely affect the system as a whole.
Flexibility

The processes were designed to be as flexible as possible, particularly with respect to batch sizes. This enables the system to cope with batching regimes suitable for backlogs as well as day to day testing.

Robustness

Quality of results and Reproducibility are crucial considerations in design and implementation of a high throughput pipeline for mutation detection. Re-testing for failed or poor quality results requires time consuming re-selection of samples as well as non-standard batches and procedures. This can be very and disruptive to a high throughput system. In general sequencing due to failed primary screen is now running at <5%.

 

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Last Updated:28 May, 2004 by G. Watkins.
 
© 2006 National Genetics Reference Laboratory (Wessex), Salisbury District Hospital, Salisbury SP2 8BJ; Tel: +44 (0)1722 429080; E-mail:ncpc@soton.ac.uk