Table 1.

Overview of possible contamination types, their consequences and suitable filtering options. PC-AF: pool-complement allelic fraction.

Contamination type	Cause (the type of co-multiplexed samples)	Possible somatic variant calling artefacts	Prevalence of given contamination type in affected datasets	Suitable post-sequencing filtering options
a) Contaminant germline variants in a tumour sample	Any samples from other individuals	False positive somatic variants in the form of germline variation from other individuals	The most likely contamination type to occur; Contamination targets are expected to be more affected in copy number loss regions*	A variant filter based on an appropriate germline variant database or a relevant panel of normal samples; A filter based on PC-AF values (if a more discriminative solution is necessary)
b) Contaminant somatic variants in a tumour sample	Other tumour samples	False positive “recurrent” somatic variants in the form of somatic variation from other tumour samples – whether from other individual(s) or the same individual	Expected to be relevant in tumour sample pools enriched** for specific somatic variants; Contamination targets are expected to be more affected in copy number loss regions*	A filter based on PC-AF values (non-discriminative filtering might lead to false negatives of high importance)
c) Contaminant germline variants in a control sample	Any samples from other individuals	False negatives/missed somatic variant calls – only concerning somatic variants that also occur as germline variants	Dependent on the occurrence of important variants as both germline and somatic in a given project’s setting	Review of calls not classified as somatic, adjustment of the variant caller parameters
d) Contaminant somatic variants in a control sample	Any tumour samples	False negatives/missed somatic variant calls – concerning all somatic variants	Elevated relevancy when matched samples are co-multiplexed; Prevalence dependent on the enrichment** of potential contaminant variants in a given sample pool; Consequences dependent on variant caller’s tendency to reject a somatic variant candidate due to evidence of its presence in the matched control	Review of calls not classified as somatic, adjustment of the variant caller parameters

*Copy number loss regions of high-purity tumour samples will be especially affected.

**The enrichment will increase together with given variant’s recurrence, as well as with purity of tumour samples that carry the variant.