. 2023 Sep 22;12:e85023. doi: 10.7554/eLife.85023

Table 4. DHODH genotype and corresponding dose-response phenotype for representative in vitro TCMDC-125334 + DSM265 selected lines.

Table 4—source data 1. Individual bioreplicates of EC50 values (nM) obtained from dose-response assays.

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Table 4—source data 2. Copy number variation (CNV) analysis based on whole-genome sequencing.

Denoised log₂ copy ratios were calculated across the genic intervals of the full genome for all sequenced samples. Values were calculated using the GATK4.0 CNV detection pipeline.

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Table 4—source data 3. Homozygous variants identified from in vitro selections by whole-genome sequencing.

Each entry represents a single clonal mutation that is present in the drug-selected clone but not in the matched parent line (i.e. arose during the drug selection process). Note we conducted whole-genome sequencing for two representative clones from each flask. The others were characterized via Sanger sequencing of the dhodh locus (see Source Data 4).

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Table 4—source data 4. Sanger sequencing of in vitro selected clones selected with DSM265 + TCMDC-125334.

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Clone ID	DHODH mutation(s)	DHODH CNV	TCMDC-125334 EC50 (nM)	DSM265EC50 (nM)	IDI-6273 EC50 (nM)	Genz669178 EC50 (nM)
3D7 A10	WT	1	140±42.6	4.5±1.6	502±209	6.9±2.2
DT-F1-C1	WT^*	2	260±79.5	8.6±1.6	1190±276	15.9±3.61*
DT-F1-C2	WT^†	1	153±21.0	6.1±0.88	628±117	7.74±1.23
DT-F2-C1	V532A^*	1	661±145**	79.2±19.0*	1320±368*	11.4±3.08
DT-F2-C2	V532A^*	1	536±54.4	82.4±23.1*	881±185	8.69±2.35
Overall p-value (approximate)			<0.0001	<0.0001	0.0019	0.0091
Kruskall-Wallis statistic			35.72	35.80	27.85	23.50

The parasite lines are each designated with a unique identifier; for example, DT-F1-C1 was selected with DSM255 and TCDC-125334 (DT) came from flask 1 (F1), and is designated as ‘C1’ for ‘Clone 1’. Data is shown as mean EC₅₀ ± standard deviation. Statistical significance was determined by a Kruskal-Wallis test, with post hoc multiple comparisons (Dunn’s) of each clone to 3D7 A10. *p≤0.05; **p≤0.01. Overall statistics are reported for each comparison group. Each dose-response assay was performed with triplicate technical replicates, and average EC₅₀’s were obtained from 3 independent biological replicates. WT = wildtype.

DHODH genotype determined by whole-genome sequencing.

^†

DHODH genotype determined by Sanger sequencing.