Table 3. Summary of the clinical dataset used to analyse the impact of parasite culturing on gene expression.
RNA-sequencing was performed on 32 malaria-infected German traveller samples (Wichers et al., 2021). The 32 ex vivo samples were used to compare the performance of the var assembly approaches. Parasites from 13 of these ex vivo samples underwent one cycle of in vitro replication, 10 parasite samples were also subjected to a second cycle of replication in vitro, and a single parasite isolate was also analysed after a third cycle of replication. For the ex vivo vs short-term in vitro cultivation analysis only paired samples were used. The number of assembled var contigs represents results per sample using the whole transcript approach, and shows either the number of assembled var contigs significantly annotated as var gene and ≥500 nt in length, or the number of assembled var transcripts identified with a length ≥ 1500 nt and containing at least three significantly annotated var domains*.
| Generation | ||||||
|---|---|---|---|---|---|---|
| Ex vivo (n=32) | 1 (n=13) | 2 (n=10) | 3 (n=1) | |||
| Malaria exposure (n) | Naïve | 15 | 6 | 4 | 1 | |
| Previously exposed | 17 | 7 | 6 | 0 | ||
| Malaria severity (n) | Severe | 8 | 3 | 1 | 0 | |
| Non-severe | 24 | 10 | 9 | 1 | ||
| Number of MSP1 genotypes (number of samples) | 1 | 22 | 9 | 7 | 1 | |
| 2 | 4 | 0 | 0 | 0 | ||
| 3 | 5 | 3 | 0 | 0 | ||
| 4 | 1 | 1 | 0 | 0 | ||
| Number of P. falciparum PE* reads (non-var) (median, IQR) (million of reads) | 34.6 (27.0–36.5) |
17.1 (12.9–18.0) |
17.2 (12.9–19.1) |
15.1 | ||
| Number of non-core P. falciparum PE* reads (median, IQR) (million of reads) | 5.05 (3.62–6.60) |
1.16 (1.07–1.40) |
1.29 (1.04–1.58) |
0.91 | ||
| Number of assembled var contigs in a sample (≥500 nt) (whole transcript approach) (median, IQR) | 53 (44–84) |
61 (38–76) |
71.5 (48.25–79.5) |
75 | ||
| Number of assembled var contigs in a sample (≥1500 nt and 3 sig. domain annotations) (whole transcript approach) (median, IQR) | 20 (7–31) |
15.5 (10–26) |
15 (10.25–23.75) |
18 | ||
PE, paired-end reads.