Dataset 1: Genotyping results for 111 single nucleotide polymorphisms (SNPs) typed in 2486 Plasmodium falciparum samples collected from primary school children during a parasitological survey in western Kenya in 2009 and 2010.

The columns contain the following information: sample_id, unique sample identifier; admin1, provincial location of school; district_name, district location of school; date_visit, date of sample collection; assay_code, name of assay; allele1 and allele2, alternative alleles at a specific SNP position; result, genotype call after processing; allele_ratio1, proportion of allele 1; allele_ratio2, proportion of allele 2; pass_fail, coding of SNP based on availability of valid genotype (pass=1) or lack of a valid genotype (fail=0). Geospatial data for individual school locations is considered sensitive data and therefore cannot be made open access. However, it can be accessed through a request to our data governance committee at [email protected]. The criteria for such access is specified in detail in the data sharing guidelines under which the DGC operates, and relates to a) addressing health research, b)operating within the bounds of informed consent, c)complying with confidentiality procedures, d) mitigating potential harm to participants in research

Dataset 2: Single nucleotide polymorphisms (SNPs) and distance differences between Plasmodium falciparum parasite pairs sampled during a parasitological survey of primary school children in western Kenya.

Differences were computed for all parasite pairwise comparisons. Sample_id and sample_id_x are unique sample identifiers; snps represent the number of SNP differences between parasite pairs; distance represents geographical distance, in kilometres, between parasite pairs

Drop in Haemoglobin Level during the Malaria Season according to HbAS, G6PD Deficiency, and Haptoglobin Genotype

<p>Haemoglobin levels at the start and end of the malaria season are shown by haptoglobin genotype ( <i>Hp^2/2</i> versus <i>Hp^1/1</i> and <i>Hp^1/2</i> combined), HbAS compared to HbAA and G6PD (A type) deficiency, wild-type, heterozygotes, and homozygotes/hemizygotes. Error bars denote standard error of the mean. </p

Sample Construction

<p>At the start of the malaria season, 780 children (aged 2–6 y) were recruited from ten rural Gambian villages, of these, 61 children were lost to follow-up (of whom four died). At the end of the malaria season, 707 children were surveyed. A total of 671 children had complete haemoglobin, malaria blood film, and haptoglobin genotype data. After biochemical assays and further genotyping, 565 children had complete data for multivariate regression analysis.</p

Genes and transcribed Single Nucleotide Polymorphisms (SNP) used in ASE assay.

a<p>Different transcribed SNPs were used to obtain ASE data for the CEU/CHB and YRI datasets due to MAF differences in the populations used.</p>b<p>Only the CEU population was analysed due to the low MAF observed for transcribed SNPs in the YRI and CHB populations.</p

<i>Cis</i>-association of SNPs with ASE data.

<p>Hapmap populations used: CEU (blue), CHB (green) and YRI population (yellow) unrelated individuals. Dots represent the results using a LM and crosses represent SNPs associated with ASE data which are in complete LD with the transcribed SNP (T-test results). Coordinates are in NCBI Build 35. Horizontal lines reflect a multiple testing adjusted gene-wide statistical significance threshold of 5%. Vertical lines represent the 5′ prime (grey) and 3′ prime(black) of the gene.</p

Multi-population <i>cis</i>-mapping (CEU, CHB, YRI).

<p>For the CHI3L2 gene, only CEU and CHB populations were pooled. Horizontal lines reflect a multiple testing adjusted gene-wide statistical significance threshold of 5%.</p

MOESM1 of Whole genome sequencing of Plasmodium falciparum from dried blood spots using selective whole genome amplification

Additional file 1: Figure S1. A plot of primers (probes) and their binding distribution on the P. falciparum genome. The topmost panel show cumulating binding positions and distribution profile of all the 28 primers. Black dots (1) show positions where the primer binds and Red (0) dots shows positions with no primer binding. Probes are ordered from bottom to top; the first 10 primers is Probe_10, followed by Probe_20 then Probe_28. Figure S2. Coverage depths frequencies of samples with different parasitaemia levels. Figure S3. Coverage of genes associated with drug resistance. Colours reflect the percentage of genome covered, ranging from 5x (grey) to 30x or more (red). Table S1. Non-reference allele frequencies (NRAF) of major drug resistance genes for venous blood (VB; leucodepleted and unamplified) and dried blood spots (DBS; sWGA) samples. Gene name, chromosome number, position, mutation name, mutation type and the NRAF found in West Africa populations (MalariaGen https://www.malariagen.net/apps/pf/4.0/ ) are shown. Notably, the studied populations have high dhfr mutation frequencies and rare crt mutations. Presumably because the use of SP was widespread and is still being used (e.g. pregnancy prophylaxis), whereas enough time has passed since chloroquine was widely used [26–28]. Table S2. Probe_10. sWGA primers for Plasmodium falciparum

Dataset 1. Information on the 276 SNPs genotyped in 177 genes in P. falciparum parasite populations from The Gambia, Kilifi and Rachuonyo South

<p><b>Dataset 1:</b> <b>Information on the 276 SNPs genotyped in 177 genes in <i>P. falciparum </i>parasite populations from The Gambia, Kilifi and Rachuonyo South. </b>The columns contain the following information: study_location, site of sample collection; sample_id, unique sample identifier; gene_symbol, gene name (if available); chr_valid, chromosome; coord_valid= base position of SNP on chromosome; sequence_code, SNP name; assay_code, name of assay; rsnumber, unique SNP identifier in dbSNP; reference_allele, 3D7 reference allele, alternative_allele, alternative allele; single letter code, IUPAC code for SNPs; result, genotype call after processing; allele1, IUPAC code for allele 1; allele2, IUPAC code for allele 2; allele_ratio1, proportion of allele 1; allele_ratio2, proportion of allele 2; pass_fail, coding of SNP based on availability of valid genotype (pass) or lack of a valid genotype (fail). Geospatial data for homestead location is considered sensitive data and therefore cannot be made open access. However, it can be accessed through a request to our data governance committee, using the email address mmunene@uat/newsite. </p

Dataset 1: Information on the 276 SNPs genotyped in 177 genes in P. falciparum parasite populations from The Gambia, Kilifi and Rachuonyo South

<p><b>Dataset 1:</b> <b>Information on the 276 SNPs genotyped in 177 genes in <i>P. falciparum </i>parasite populations from The Gambia, Kilifi and Rachuonyo South. </b>The columns contain the following information: study_location, site of sample collection; sample_id, unique sample identifier; gene_symbol, gene name (if available); chr_valid, chromosome; coord_valid= base position of SNP on chromosome; sequence_code, SNP name; assay_code, name of assay; rsnumber, unique SNP identifier in dbSNP; reference_allele, 3D7 reference allele, alternative_allele, alternative allele; single letter code, IUPAC code for SNPs; result, genotype call after processing; allele1, IUPAC code for allele 1; allele2, IUPAC code for allele 2; allele_ratio1, proportion of allele 1; allele_ratio2, proportion of allele 2; pass_fail, coding of SNP based on availability of valid genotype (pass) or lack of a valid genotype (fail). Geospatial data for homestead location is considered sensitive data and therefore cannot be made open access. However, it can be accessed through a request to our data governance committee, using the email address mmunene@uat/newsite. </p