Contract for sample tracking system for NHS Scotland Whole Genome Sequencing Service

The NHS in Scotland is setting up a National Sequencing Services to carry out Whole Genome Sequencing (WGS) as part of the development of this Service the need for a sample tracking system has been identified, to ensure a managed, quality assured automated service is delivered with a high sequencing capacity.

Initial focus on the service will be to increase SARS-CoV-2 WGS capacity to approximately 5k samples per week, delivered in 2 NHS Laboratories, from 2 separate Health boards by end of September 2021.

The Service will be delivered though the adoption of automation for key process steps for sample processing as the current WGS laboratory process includes manual steps, and a mixture of systems are used across the 2 sites to document the processing of the samples.

IT systems are in place to facilitate the logistics of submission of samples, and subsequently to manage the raw data outputs for subsequent bioinformatics analysis and ultimate result reporting.

This contract notice is for a sample tracking system to facilitate sample management and tracking within the WGS process only.

The requirement covers the workflow after documented receipt of the sample in the WGS processing laboratories until the point of generation of raw sequencing data.

The automation of the processing of the samples will be delivered by liquid handling systems (which may be from multiple suppliers), these are yet to be configured.

Detailed below is the potential steps (although not exclusive) that we will require data acquisition by the sample tracking system include:

a) Liquid handler cDNA preparation (automated in 96 well plate, sample and well ID from NPex, plate identifier, time stamp, reagent batches, operators and instruments used).

b) Liquid handler for PCR amplification (sample/well ID, plate identifier, time stamp, reagent batches, operators and instruments used).

c) Liquid handler for DNA quantitation (e.g. fluorimeter or bead based quantitation for concentration measurement for each sample recorded in WGS LIMS, and automated concentration adjustment if not bead based).

d) Possible repeat of steps 3 and 4 above, with new concentration measurements and automated calculation of water quantities added for each well if fluorimeter based).

e) Liquid handler for tagmentation (sample/well ID, plate identifier, time stamp, reagent batches, operators and instruments used).

f) Liquid handler for Library amplification (sample/well ID, plate identifier, assignment of indices, time stamp, reagent batches, operators and instruments used)

g) Liquid handler Library clean up (Beads) sample/well ID, plate identifier, time stamp, reagent batches, operators and instruments used)

h) Liquid liquid handler Library quality check (Bioanalyzer/Tapestation – connected as needs to communicate with WGS LIMS re library quality)

i) Liquid handler Normalise libraries (bead based or fluorimetric quantitation as above)

j) Liquid handler for library pooling.

k) Sample sheet generation for Sequencer