Table 1.

The nine possible joint genotypes and their associated mappings onto biologically interpretable marginal genotypes

gN\gT	AA	AB	BB
AA	Wild-type	Somatic	Somatic
AB	LOH	Germline	LOH
BB	Errora	Error	Germline

Wild-type [no change: ℙ(AA, AA)], Somatic [wild-type normal and variant tumour: ℙ(AA, AB)+ℙ(AA, BB)], Germline [variant normal and tumour: ℙ(AB, AB)+ℙ(BB, BB)] and loss of heterozygosity [LOH–heterozygous normal and homozygous tumour: ℙ(AB, AA)+ℙ(AB, BB)].

^aWe treat the joint genotypes (BB, AB) and (BB, AA) as errors since this would imply that a homozygous variant mutates back to the reference base, which is a possible, but unlikely event. It is more plausible that these cases are simply errors due to alignment or base calling.