Thousands of variables come in to play throughout the lifecycle of a pathology sample. Due to the sensitive nature of NGS any or all of these could effect the final sequencing quality.Using a suitable LIMS we can track as many or as few variables and feed it back into the system to continuously improve sequencing quality.
Example
For a certain assay we track the following information:
- Time between blood collection and extraction
- Temperature in instrument/lab at each workflow point
- Concentration of sample
- White cell count
- Time of day extracted
- Storage temperature data
- Age of index lot
- Clustering
- Q scores
Target metrics
- On target reads
By using various data & spatial analysis techniques we can correlate variations in environmental changes to post alignment mapped reads & QC scores. Not only can we use this to adjust parts of workflows we can use it as a training set to train future workflow decisions to optimize sequencing quality
Software Development & Bioinformatics 