Genotypic tropism testing by massively parallel sequencing: qualitative and quantitative analysis

Table 3 Tropism results from different assays

isolate	phenotype(trofile)	prediction from bulk-sequence, predicted as X4 at FPR ^a of:	MPS, proportion. predicted as X4 ^b
1	X4	2.5%	85.3%
2	X4	5%	87.0%
3	X4	10%	14.2%
4	X4	15%	5.4%
5	X4	15%	48.0%
6	X4	---^c	68.5%
7	X4	---	1.0%
8	R5	10%	1.4%
9	R5	---	3.4%
10	R5	---	0.3%
11	R5	---	0.5%
12	R5	---	1.6%
13	R5	---	1.8%
14	R5	---	2.4%

Tropism results from different approaches used: phenotype (trofile), coreceptor usage prediction from bulk-genotype, and coreceptor usage prediction from massively parallel sequencing.
FPR: false-positive-rate of geno2pheno.
^athe displayed value is the highest cutoff at which an isolate would have been predicted as X4
^bdefault geno2pheno[coreceptor]-cutoff of 10% FPR used
^c '---' if predicted FPR, was above the highest cutoff tested (20%)

ISSN: 1472-6947