Table 1 List of methods for tumour phylogeny inference from scDNAseq data, with their main features

Method	SNVs	CNAs	Doublets	SNV Recurrence	SNV loss	Homozygous mutations	Est. max # cells	Est. max # loci
∞SCITE^{7, 8}	Yes	No	Yes	Yes^a	Yes^a	No	10,000	100
SCIΦN^{9, 10}	Yes	No	No	Yes	Yes	No	100	1000
OncoNEM¹¹	Yes	No	No	No	No	No	100	100
SiCloneFit¹²	Yes	No	Yes	Yes	Yes	No	100	100
SPhyr¹³	Yes	No	No	No	Yes	No	100	100
SCICoNE¹⁴	No	Yes	No	–	–	–	100	–
CHISEL¹⁵	Yes^b	Yes	No	–	–	–	1000	–
SCARLET¹⁶	Yes	No^c	No	No	Yes^d	No	100	100
BiTSC²¹⁷	Yes	Yes^e	No	No	Yes	Yes	100	100
COMPASS	Yes	Yes	Yes	No	Yes^f	Yes^f	10,000	100

The maximum number of cells and loci are estimates for reasonable runtimes and performance.
^aHowever model selection is not automated.
^bCan assign SNVs to clones after the CNA-tree is inferred by aggregating all cells assigned to each clone.
^cRequires CNA tree as input, which must be obtained with another method.
^dIf supported by copy-number loss; which could miss CNLOH.
^eAssumes that all loci have the same coverage (in the absence of CNAs), which is not the case for targeted sequencing.
^fWith copy number loss or CNLOH.

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