Gene Coverage Count and Classification (GC3): a locus sequence coverage assessment tool using short-read whole genome sequencing data, and its application to identify and classify histidine-rich protein 2 and 3 deletions in Plasmodium falciparum

Stabler, Thomas C.; Dwivedi, Ankit; Shrestha, Biraj; Joshi, Sudhaunshu; Schindler, Tobias; Ouattara, Amed; García, Guillermo A.; Daubenberger, Claudia; Silva, Joana C.

doi:10.1186/s12936-022-04376-3

Table 2 Agreement between GC₃ deletion assessment results on global samples and hrp2/3-specific qPCR assay^a

From: Gene Coverage Count and Classification (GC₃): a locus sequence coverage assessment tool using short-read whole genome sequencing data, and its application to identify and classify histidine-rich protein 2 and 3 deletions in Plasmodium falciparum

Sample name	Country	Phenotype subgroup	hrp2 ^b	hrp3 ^b	rnr2e2
			hrp2 ^b	hrp3 ^b	(control gene)
			GC₃/PCR	GC₃/PCR	PCR
7G8	Reference (Brazil)	Control	Present/Present	Present/Present	Present
NF54	Reference	Control	Present/Present	Present/Present	Present
Dd2	Reference (Laos)	Control—hrp2 deletion	Absent/Absent	Present/Present	Present
HB3	Reference (Honduras)	Control—hrp3 deletion	Present/Present	Absent/Absent	Present
IGS-BRA-017sA	Brazil	No deletions	Present/Present	Present/Present	Present
IGS-THL-017	Thailand	No deletions	Present/Present	Present/Present	Present
IGS-BRA-021	Brazil	No deletions	Present/Present	Present/Present	Present
IGS-CBD-026	Cambodia	No deletions	Present/Present	Present/Present	Present
IGS-CBD-031	Cambodia	hrp2 deletion (complete)	Absent/Absent	Present/Present	Present
IGS-MLI-036	Mali	hrp3 deletion (complete)	Present/Present	Absent/Absent	Present
IGS-BRA-001sA	Brazil	Double hrp2/3 deletion	Absent/Absent	Absent/Absent	Present
IGS-CBD-008	Cambodia	Low coverage sample	Present/Present	Present/Present	Present
IGS-MWI-254sA	Malawi	Low coverage sample	Present/Present	Present/Present	Present
IGS-MWI-251sA	Malawi	Low coverage sample	Present/Present	Present/Present	Present
IGS-MLI-039	Mali	hrp2 discordant pair	Present/Present	Present/Present	Present
IGS-MLI-031	Mali	hrp3 discordant pair	Present/Present	Present/Present	Present
IGS-CBD-034	Cambodia	hrp2 PCR primer deletion	Present/Present	Present/Present	Present
IGS-CBD-094	Cambodia	hrp3 PCR primer deletion	Present/Present	Present/Present	Present
IGS-CBD-099	Cambodia	hrp3 PCR primer deletion	Present/Present	Absent/Present	Present

^a Cells in purple and blue denote agreement between GC₃ and qPCR results (i.e. "PCR"); red denotes disagreement between methods

Back to article page

ISSN: 1475-2875

Contact us

Submission enquiries: journalsubmissions@springernature.com

Malaria Journal

Contact us