Development of amplicon deep sequencing markers and data analysis pipeline for genotyping multi-clonal malaria infections

Table 2 Detectability of the minority clone in defined ratios of P. falciparum strains HB3 and 3D7

Ratios in mixtures	cpmp					csp					Minimum Coverage HaplotypR^c
HB3:3D7	3D7^a %	HB3^a %	PCR artefacts %	Back-ground^b %	Coverage	3D7^a %	HB3^a %	PCR artefacts %	Back-ground^b %	Coverage	Minimum Coverage HaplotypR^c
1:1	34.6	57.4	0.48	7.53	40,768	34.7	50.5	5.79	9.01	9009	6
1:10	75.6	16.4	0.40	7.59	13,037	76.1	10.1	5.63	8.08	3341	30
1:50	88.8	3.15	0.06	7.95	4953	82.7	2.88	6.23	8.16	14,711	150
1:100	90.9	1.53	0.36	7.26	13,311	83.5	2.25	5.41	8.88	11,975	300
1:500	90.8	0.48	0.27	8.44	5649	84.0	0.46	4.76	10.8	3508	1500
1:1000	91.5	0.23	0.03	8.26	3039	85.7	0.22	5.09	9.02	1807	3000
1:1500	92.5	0.11	0.48	6.94	55,887	86.3	0.08^d	5.71	7.91	23,619	4500
1:3000	92.5	0.09⁴	0.38	7.00	7417	85.0	0.04^d	5.87	9.10	2318	9000

^a Percent of reads that cluster with 3D7 and HB3 reference sequences
^b Singleton reads and reads that failed to cluster with 3D7 or HB3 haplotypes
^c Theoretical minimum required coverage needed to detect minority clone by software HaplotypR with default cut-off values
^d Haplotypes considered as noise by software HaplotypR (default cut-off: ≥3 reads per haplotype and a minority clone detection limit of 1:1000)

ISSN: 1471-2164