Table 1

Tumor heterogeneity methods compared

Method	Summary	Input data type	Output	Publication	Tissue/blood
PyClone	Allele read counts ->cellular prevalence estimation	.tsv file containing variant allele frequency and copy number variability	Clusters	Roth et al40	ctDNA and tDNA
SciClone	Like PyClone, but takes a narrow selection of genes (copy number neutral and loss of heterozygosity free)	.tsv file containing variant allele frequency, copy number variability, and common LOH site to exclude	Clusters	Miller et al44	tDNA
AFH	VAF/MSAF	VAF and MSAF	AFH Score	Liu et al47	ctDNA and tDNA
MATH	Width of the VAF distribution	VAF	MATH Score	Mroz and Rocco48	tDNA
Shannon’s Diversity Index	The negative sum of the natural log of the probability distribution of VAF for all mutated loci within a sample.	VAF	Diversity Index Score	Oh et al53	tDNA

AFH, allele frequency heterogeneity; ctDNA, circulating tumor DNA; LOH, loss of heterogeneity; MATH, mutant allele tumor heterogeneity; MSAF, maximum somatic allele frequency; tDNA, tumor DNA; VAF, variant allele frequency.