Abstract In sub-Saharan Africa (SSA), many pediatric patients with Burkitt lymphoma (BL) perish because of diagnostic delays. About 95% of pediatric BL cases in SSA are Epstein-Barr virus (EBV) positive. We assessed plasma EBV DNA in 400 pediatric patients with BL and 400 controls, frequency-matched on sex, age, and country, enrolled in the Epidemiology of Burkitt Lymphoma in East African Children and Minors study in Uganda, Kenya, and Tanzania (2010-2016). EBV was measured using a digital droplet polymerase chain reaction assay targeting EBV BamHI-W internal repeats, duplexed with RPP30 human housekeeping gene. The study population was predominantly male (63% of cases of BL, and 64% of controls), with an average age of ∼7.5 years. EBV DNA was detected in 309 (77.3%) cases of BL, and 62 (15.5%) controls. The mean plasma EBV DNA levels were 5.00 (standard deviation [SD] 1.63) log10 copies per mL for cases with BL vs 1.94 (SD 1.35) for controls (P < .0001). Excluding 50 cases with BL and 61 controls with indeterminate (RPP30 and EBV negative) samples, the maximum sensitivity of plasma EBV DNA detection to discriminate cases with BL from controls was 88.3% (95% confidence interval [CI], 84.4-91.5), with 81.7% (95% CI, 77.2-85.7) specificity, and area under the curve 91.9% (95% CI, 89.7-93.9). A specificity of 100% was achieved at a threshold of 4.19 log10 EBV copies per mL, which reduced sensitivity to 66.6%. Assay accuracy varied from 83% to 87.4% at different thresholds. Testing for EBV DNA could facilitate the recognition of BL earlier in SSA, a critical step in improving BL cure rates in the region.

Burkitt lymphoma (BL) is responsible for many childhood cancers in sub-Saharan Africa, where it is linked to recurrent or chronic infection by Epstein-Barr virus or Plasmodium falciparum . However, whether human leukocyte antigen ( HLA ) polymorphisms, which regulate immune response, are associated with BL has not been well investigated, which limits our understanding of BL etiology. Here we investigate this association among 4,645 children aged 0-15 years, 800 with BL, enrolled in Uganda, Tanzania, Kenya, and Malawi. HLA alleles are imputed with accuracy >90% for HLA class I and 85-89% for class II alleles. BL risk is elevated with HLA-DQA1*04:01 (adjusted odds ratio [OR] = 1.61, 95% confidence interval [CI] = 1.32-1.97, P = 3.71 × 10 −6 ), with rs2040406(G) in HLA-DQA1 region (OR = 1.43, 95% CI = 1.26-1.63, P = 4.62 × 10 −8 ), and with amino acid Gln at position 53 versus other variants in HLA-DQA1 (OR = 1.36, P = 2.06 × 10 −6 ). The associations with HLA-DQA1*04:01 (OR = 1.29, P = 0.03) and rs2040406(G) (OR = 1.68, P = 0.019) persist in mutually adjusted models. The higher risk rs2040406(G) variant for BL is associated with decreased HLA-DQB1 expression in eQTLs in EBV transformed lymphocytes. Our results support the role of HLA variation in the etiology of BL and suggest that a promising area of research might be understanding the link between HLA variation and EBV control.

Introduction: Burkitt lymphoma (BL) is an aggressive B-cell lymphoma with hallmark somatic IG::MYC chromosomal translocations. BL is responsible for a significant proportion of childhood cancers in equatorial Africa, where exposure to Epstein Barr Virus (EBV) and P. falciparum are established risk factors. Host genetic factors are suspected to modify risk but are currently undefined, with exception of the sickle cell trait that is protective against severe malaria and childhood BL in Africa. Discovery of novel host genetic susceptibility in BL would suggest new directions to understand the biology of BL, particularly the link between host and environmental cofactors. Methods: We conducted the first genome-wide association study (GWAS) of BL among 4,645 children (800 with BL) aged 0–15 years enrolled in the Epidemiology of Burkitt lymphoma in East African Children and Minors (EMBLEM) study in Uganda, Kenya, and Tanzania (2010–2016) and the Childhood Infections and Cancer case-control study in Malawi (2005–2008). Genotypes at approximately 4.6 million sites were determined using the Infinium Omni5Exome-4 v1.3 BeadChip (Illumina) and imputation was performed using the African Genome Resources reference panel (Sanger Imputation Service), with rigorous quality control to filter unreliable calls. GWAS based on logistic mixed model was performed in SAIGE, adjusting for age, sex, and ancestry using population-specific principal components, and country of origin. Additional analyses were performed using genomic, epigenomic and expression data from the BL and ICGC MMML-Seq genome sequencing projects to provide insight into the potential mechanisms by which the novel loci may influence BL risk in African children. Results: Considering variants with a minor allele frequency threshold of ≥5%, we identified one genome-wide significant locus at 21q22.12 (Figure 1A) upstream of RUNX1. The index SNP (rs111457485, ref/effect: C/T, effect size: −0.57; p-value = 5.7 × 10−9; Figure 1B) is common in Africans (frequency of allele T: 10.2%) and rare in Europeans (allele frequency of T: 0.7%) in the 1000 Genomes populations. Fine mapping in this locus using the Sum of Single Effects (SuSiE) model revealed a credible set of 17 variants spanning 76 kb including the causal variant at the locus with 95% probability (Figure 1C). This associated region contains enhancer elements linked to RUNX1 expression that are differentially methylated in BL as compared to follicular lymphoma. Moreover, mining of RNA-seq data identified a novel spliced transcript expressed in BL and germinal center B cells. In secondary transcriptome-wide analyses in whole blood and spleen, we identified statistically significant association with additional loci at 19p13.2 in region previously identified to harbor somatic mutations in BL. The research was funded by: National Cancer Institute, National Institutes of Health, US Department of Health and Human Services Keywords: Aggressive B-cell non-Hodgkin lymphoma, Cancer Health Disparities, Genomics, Epigenomics, and Other-Omics No conflicts of interests pertinent to the abstract.

Endemic Burkitt lymphoma (eBL) is a pediatric cancer coendemic with malaria in sub-Saharan Africa, suggesting an etiological link between them. However, previous cross-sectional studies of limited geographic areas have not found a convincing association. We used spatially detailed data from the Epidemiology of Burkitt Lymphoma in East African Children and Minors (EMBLEM) study to assess this relationship. EMBLEM is a case–control study of eBL from 2010 through 2016 in six regions of Kenya, Uganda, and Tanzania. To measure the intensity of exposure to the malaria parasite, Plasmodium falciparum , among children in these regions, we used high-resolution spatial data from the Malaria Atlas Project to estimate the annual number of P. falciparum infections from 2000 through 2016 for each of 49 districts within the study region. Cumulative P. falciparum exposure, calculated as the sum of annual infections by birth cohort, varied widely, with a median of 47 estimated infections per child by age 10, ranging from 4 to 315 infections. eBL incidence increased 39% for each 100 additional lifetime P. falciparum infections (95% CI: 6.10 to 81.04%) with the risk peaking among children aged 5 to 11 and declining thereafter. Alternative models using estimated annual P. falciparum infections 0 to 10 y before eBL onset were inconclusive, suggesting that eBL risk is a function of cumulative rather than recent cross-sectional exposure. Our findings provide population-level evidence that eBL is a phenotype related to heavy lifetime exposure to P. falciparum malaria and support emphasizing the link between malaria and eBL.

Interferon lambda 4 (IFN-λ4) is a novel type-III interferon that can be expressed only by carriers of the genetic variant rs368234815-dG within the first exon of the IFNL4 gene. Genetic inability to produce IFN-λ4 (in carriers of the rs368234815-TT/TT genotype) has been associated with improved clearance of hepatitis C virus (HCV) infection. The IFN-λ4-expressing rs368234815-dG allele (IFNL4-dG) is most common (up to 78%) in West sub-Saharan Africa (SSA), compared to 35% of Europeans and 5% of individuals from East Asia. The negative selection of IFNL4-dG outside Africa suggests that its retention in African populations could provide survival benefits, most likely in children. To explore this hypothesis, we conducted a comprehensive association analysis between IFNL4 genotypes and the risk of childhood Burkitt lymphoma (BL), a lethal infection-associated cancer most common in SSA. We used genetic, epidemiologic, and clinical data for 4,038 children from the Epidemiology of Burkitt Lymphoma in East African Children and Minors (EMBLEM) and the Malawi Infections and Childhood Cancer case-control studies. Generalized linear mixed models fit with the logit link controlling for age, sex, country, P. falciparum infection status, population stratification, and relatedness found no significant association between BL risk and 3 coding genetic variants within IFNL4 (rs368234815, rs117648444, and rs142981501) and their combinations. Because BL occurs in children 6-9 years of age who survived early childhood infections, our results suggest that additional studies should explore the associations of IFNL4-dG allele in younger children. This comprehensive study represents an important baseline in defining the health effects of IFN-λ4 in African populations.

Burkitt lymphoma (BL) is an aggressive B-cell lymphoma that significantly contributes to childhood cancer burden in sub-Saharan Africa. Plasmodium falciparum, which causes malaria, is geographically associated with BL, but the evidence remains insufficient for causal inference. Inference could be strengthened by demonstrating that mendelian genes known to protect against malaria-such as the sickle cell trait variant, HBB-rs334(T)-also protect against BL. We investigated this hypothesis among 800 BL cases and 3845 controls in four East African countries using genome-scan data to detect polymorphisms in 22 genes known to affect malaria risk. We fit generalized linear mixed models to estimate odds ratios (OR) and 95% confidence intervals (95% CI), controlling for age, sex, country, and ancestry. The ORs of the loci with BL and P. falciparum infection among controls were correlated (Spearman's ρ = 0.37, p = .039). HBB-rs334(T) was associated with lower P. falciparum infection risk among controls (OR = 0.752, 95% CI 0.628-0.9; p = .00189) and BL risk (OR = 0.687, 95% CI 0.533-0.885; p = .0037). ABO-rs8176703(T) was associated with decreased risk of BL (OR = 0.591, 95% CI 0.379-0.992; p = .00271), but not of P. falciparum infection. Our results increase support for the etiological correlation between P. falciparum and BL risk.

In high-income countries, mosaic chromosomal alterations in peripheral blood leukocytes are associated with an elevated risk of adverse health outcomes, including hematologic malignancies. We investigate mosaic chromosomal alterations in sub-Saharan Africa among 931 children with Burkitt lymphoma, an aggressive lymphoma commonly characterized by immunoglobulin- MYC chromosomal rearrangements, 3822 Burkitt lymphoma-free children, and 674 cancer-free men from Ghana. We find autosomal and X chromosome mosaic chromosomal alterations in 3.4% and 1.7% of Burkitt lymphoma-free children, and 8.4% and 3.7% of children with Burkitt lymphoma ( P -values = 5.7×10 −11 and 3.74×10 −2 , respectively). Autosomal mosaic chromosomal alterations are detected in 14.0% of Ghanaian men and increase with age. Mosaic chromosomal alterations in Burkitt lymphoma cases include gains on chromosomes 1q and 8, the latter spanning MYC , while mosaic chromosomal alterations in Burkitt lymphoma-free children include copy-neutral loss of heterozygosity on chromosomes 10, 14, and 16. Our results highlight mosaic chromosomal alterations in sub-Saharan African populations as a promising area of research.

Epstein-Barr virus (EBV) is associated with endemic Burkitt lymphoma (eBL), but the contribution of EBV variants is ill-defined. Studies of EBV whole genome sequences (WGS) have identified phylogroups that appear to be distinct for Asian versus non-Asian EBV, but samples from BL or Africa, where EBV was first discovered, are under-represented. We conducted a phylogenetic analysis of EBV WGS and LMP-1 sequences obtained primarily from BL patients in Africa and representative non-African EBV from other conditions or regions using data from GenBank, Sequence Read Archive, or Genomic Data Commons for the Burkitt Lymphoma Genome Sequencing Project (BLGSP) to generate data to support the use of a simpler biomarker of geographic or phenotypic associations. We also investigated LMP-1 patterns in 414 eBL cases and 414 geographically matched controls in the Epidemiology of Burkitt Lymphoma in East African children and minors (EMBLEM) study using LMP-1 PCR and Sanger sequencing. Phylogenetic analysis revealed distinct genetic patterns of African versus Asian EBV sequences. We identified 281 single nucleotide variations (SNVs) in LMP-1 promoter and coding region, which formed 12 unique patterns (A to L). Nine patterns (A, AB, C, D, F, I, J, K and L) predominated in African EBV, of which four were found in 92% of BL samples (A, AB, D, and H). Predominant patterns were B and G in Asia and H in Europe. EBV positivity in peripheral blood was detected in 95.6% of EMBLEM eBL cases versus 79.2% of the healthy controls (odds ratio [OR] =3.83; 95% confidence interval 2.06-7.14). LMP-1 was successfully sequenced in 66.7% of the EBV DNA positive cases but in 29.6% of the controls (ORs ranging 5-11 for different patterns). Four LMP-1 patterns (A, AB, D, and K) were detected in 63.1% of the cases versus 27.1% controls (ORs ranges: 5.58-11.4). Dual strain EBV infections were identified in WGS and PCR-Sanger data. In conclusion, EBV from Africa is phylogenetically separate from EBV in Asia. Genetic diversity in LMP-1 formed 12 patterns, which showed promising geographic and phenotypic associations. Presence of multiple strain infection should be considered in efforts to refine or improve EBV markers of ancestry or phenotype. Lay Summary:Epstein-Barr virus (EBV) infection, a ubiquitous infection, contributes to the etiology of both Burkitt Lymphoma (BL) and nasopharyngeal carcinoma, yet their global distributions vary geographically with no overlap. Genomic variation in EBV is suspected to play a role in the geographical patterns of these EBV-associated cancers, but relatively few EBV samples from BL have been comprehensively studied. We sought to compare phylogenetic patterns of EBV genomes obtained from BL samples in Africa and from tumor and non-tumor samples from elsewhere. We concluded that EBV obtained from BL in Africa is genetically separate from EBV in Asia. Through comprehensive analysis of nucleotide variations in EBV's LMP-1 gene, we describe 12 LMP-1 patterns, two of which (B and G) were found mostly in Asia. Four LMP-1 patterns (A, AB, D, and F) accounted for 92% of EBVs sequenced from BL in Africa. Our results identified extensive diversity of EBV, but BL in Africa was associated with a limited number of variants identified, which were different from those identified in Asia. Further research is needed to optimize the use of PCR and sequencing to study LMP-1 diversity for classification of EBV variants and for use in epidemiologic studies to characterize geographic and/or phenotypic associations of EBV variants with EBV-associated malignancies, including eBL.

Background Burkitt lymphoma (BL) is an aggressive B-cell lymphoma that accounts for 50-75% of childhood cancers in sub-Saharan Africa. Recurrent infection with Plasmodium (P.) falciparum is hypothesized to be causally linked to BL, but the epidemiological evidence is limited because it is based on exposures measured after BL onset. The prolonged period before BL onset makes traditional cohort studies impractical. To circumvent this problem, it was proposed that genetic variants that confer genetic resistance to P falciparum, such as heterozygotes for the HBB sickle allele (rs334), could be used to demonstrate a causal link with malaria. However, results from six studies have been conflicting, perhaps, reflecting effects of small sample size, design flaws in the studies or confounding. For example, co-inheritance with other genetic variants, such as a-thalassemia, have been reported to confound the epidemiological associations of severe malaria with rs334. Additionally, resistance against P. falciparum due to "premunition", defined as anti-clinical and anti-parasite resistance due to acquired immunity, could confound genetic associations with BL. To address the hypothesis of whether resistance to malaria protects against BL, we investigated the associations between BL and rs334 and 31 other single nucleotide polymorphisms (SNPs) plus α-thalassemia (hereafter, index malaria resistance SNPs/variants), and premunition, defined as P. falciparum positivity at enrollment, in cases enrolled in Uganda, Tanzania, Kenya, and Malawi, all designated as high malaria burden countries by the World Health Organization. Methods The study cohort consisted of 800 children (<16 years) with BL and 3845 children without BL enrolled in the Epidemiology of Burkitt Lymphoma in East African Children and Minors (EMBLEM) study (2010-2016) and the Infections and Childhood Cancer case-control study conducted in Malawi (2005-2010). P falciparum status was determined by thick-film microscopy, malaria antigen (HRP2/pLDH) rapid diagnostic test, or PCR at enrollment. Malaria protective SNPs were extracted from genome-wide data measured using Infinium Omni5Exome-4 v1.3 BeadChip (Illumina, San Diego, CA, USA). Genotyping for α3.7-thalassemia deletions (/-α3.7)utilized droplet digital polymerase chain reaction. We tested for associations between BL and the malaria index SNPs, a genotypes, and P. falciparum positivity using generalized linear mixed models, controlling for age, sex, and the first 3 population-specific principal components as fixed effects and for genetic relatedness (calculated from genome-wide data) as a random effect. We considered a p-value < 0.05 for statistical significance for malaria index SNPs. Results The mean age was similar for BL cases and controls (7.19 years versus 7.43 years, p= 0.07), but BL cases were more likely to be males (63.2% versus 52.1%, p£0.0001). P. falciparum positivity was lower in BL cases than controls (35.2% versus 48.3%, p<0.0001). Figure 1 shows the associations between 32 malaria index SNPs with BL and with P. falciparum positivity. Odds of BL were significantly decreased in presence of HBB rs334 (odds ratio [OR]= 0·687, 95% CI 0·533-0·885; p=0·0037) and ABO rs8176703 (0·591, 0·379-0·922; p=0.0203). Results for α-genotypes included the normal genotype (αα/αα), triplication (ααα/αα), -α3.7/αα, -α3.7/-α3.7deletions and unknown. Using αα/αα as the reference, the ORs for BL were 1.82, p=0.06 for ααα/αα; 1.07, p=0.469 for -α3.7/αα; and 0.78, p=0.15 for -α3.7/-α3.7. The odds of BL were significantly decreased with P. falciparum positivity in analyses without the two significant index SNPs (OR= 0.526, 95% CI 0.428-0.633, p=9.64x10-12) and changed minimally when the two SNPs were included (OR= 0·524, 0·435-0·630, p=7·291x10-12) . Conclusion Based on 4,581 children in four high malaria burden countries, we found reduced odds of BL among carriers of malaria index variants in HBB and ABO genes which suggests that these variants may protect against BL as well. Additionally, our findings of decreased odds of BL with P. falciparum positivity at enrollment suggest premunition may be protective against BL, independent of the significant associations with SNPs in HBB and ABO. Together, our findings further enhance the evidence of a causal role of malaria in BL; coordination between malaria and BL programs in countries with high malaria/BL burden should be strengthened. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Background Endemic Burkitt lymphoma (eBL), which occurs at a disproportionately high rate among children in Africa, is associated with Plasmodium falciparum (Pf) malaria and Epstein-Barr virus (EBV). Genetic factors, including Human leukocyte antigen (HLA) system, are hypothesized to play a role in eBL by modulating the immune response or susceptibility to associated pathogens. However, the association between HLA and eBL has not been comprehensively evaluated to-date. Methods We investigated the association between HLA variants and eBL among 800 cases and 3,845 controls aged 0-15 years enrolled in two studies: the Epidemiology of Burkitt lymphoma in East African children and minors (EMBLEM) study conducted in Uganda, Tanzania and Kenya (2010-2016) and the Infections and Childhood Cancer Study conducted in Malawi (2005-2008). HLA alleles from eight classical HLA genes were imputed from genome wide data (Illumina 5 M array) with the SNP2HLA program using an updated multi-ancestry HLA reference panel (n=21,456). We demonstrated accurate imputation at 2-field resolution by comparing the imputed HLA alleles against HLA alleles obtained by sequence-based typing of 600 EMBLEM participants (200 cases and 400 controls) from Uganda. We performed country-specific association tests using generalized linear mixed models (GLMMs), adjusting for sex (genetic confirmed), age, falciparum positivity, and population structure using the top 3 principal components and accounting for genetic relatedness. Odds ratios (OR) were used to estimate the effect size for each HLA variant and significance was assessed by Wald tests. Meta-analyses were performed to obtain summary effects across countries. For 12 HLA alleles with previously reported associations with severe malaria (e.g., HLA-B*53), EBV antibodies (e.g., HLA-DRB1*15:01) or eBL (e.g., HLA-A*02), were hypothesized, apriori, that we would observe associations with eBL mirroring biologic effects of prior associations. Thus, a P value of 0.05 was considered sufficient for statistical significance. For all other associations, we adjusted for multiple testing with P<2.7×10-4 (correction for 187 tested HLA alleles) used to determine statistical significance for classical HLA alleles at 1- and 2-field resolution and P<1.1×10-6 (correction for 46,350 HLA variants) for all other variants in the HLA region. Conditional analyses were performed to identify HLA variants that independently influence eBL susceptibility. Results We found high concordance rates (>85%) of HLA imputation at all HLA class I and class II alleles of 2-field resolution. The frequency distribution of imputed HLA alleles was similar to that based on sequencing-based HLA typing in a subset of Ugandan participants (Pearson r=0.97). The expected associations between eBL and HLA alleles were only observed for HLA-A*02 and -B*41 based on a nominal p<0.05. More importantly, we found significant associations between eBL and HLA-DQA1*04:01 (adjusted odds ratio [aOR]= 1.61, 95% confidence interval [CI]=1.32 to 1.97, P=3.71×10-6) and SNP rs2040406, located in the HLA-DQA1 region (aOR=1.43 (95%CI=1.26 to 1.63), P=4.62×10-8) (Figure 1). No other HLA alleles or non-allele variants were significantly associated with eBL in conditional analysis on HLA-DQA*04:01 or rs2040406. The novel association with SNP rs2040406 corresponds to a single residue Gln53 within the HLA-DQA1 peptide-binding groove that tracks with rs2040406 (r2 = 0.88) and showed the strongest association among all residues (aOR=1.36, P=2.06×10-6). Conclusions We present a comprehensive investigation of the associations between eBL and HLA variants utilizing imputed HLA data. Consistent associations were observed for two eBL-based apriori-stipulated hypotheses (HLA-A*02 and-B*41); however, contrary to our expectations, the malaria-based apriori hypotheses were not confirmed. Our agnostic analysis identified new associations between eBL and variants in the HLA-DQB1/DQA1 region, thereby providing new directions to explore the underlying relationship between HLA, immunity and eBL risk. In particular, the association of eBL with rs2040406 was attributed to residue Gln53 within the HLA-DQA1 peptide-binding groove. These associations hint at functional effects, perhaps mediated by stronger binding of EBV glycoproteins. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Introduction: Burkitt lymphoma (BL) is an aggressive B-cell lymphoma with reciprocal IG∷MYC translocations and accounts for 50-75% of childhood cancers in sub-Saharan Africa. Mosaic chromosomal alterations (mCAs) are large, somatically acquired structural chromosomal alterations that are clonal and observed in detectable fractions of circulating mononuclear cells. mCAs have been linked to increased hematologic cancer risk, but their association with BL, a mononuclear B cell tumor, is unknown. We hypothesized that the frequency and distribution of mCAs in peripheral leukocytes would be elevated in children with BL, potentially serving as a biomarker of chromosomal instability relevant to BL risk. Methods: We investigated peripheral leukocyte DNA extracted from children enrolled in the Epidemiology of Burkitt Lymphoma in East African Children and Minors (EMBLEM) study (2010-2016) and the Infections and Childhood Cancer case-control study conducted in Malawi (2005-2010). We used genome-wide single nucleotide polymorphism (SNP) array data to investigate the frequency, type, and distribution of mCAs >2Mb in size detected in peripheral leukocytes of 931 pediatric BL cases with 3,645 healthy children in Uganda, Tanzania, and Kenya, and with 177 non-BL pediatric cancers in Malawi. Eagle2 and SHAPEIT4 software were used for phasing to infer haplotypes for SNP array data and WGS data. MoChA (v2014-05-14) was used to detect mCAs. Parallel analysis using similar methods was performed on whole genome sequences (WGS) from paired tumor-normal blood samples from two Ugandan BL patients from the BL Genome Sequencing Project (BLGSP) and from paired BL- and lymphoblastoid-derived cell lines. Results: Most samples (92%) were from the EMBLEM study, whereas 8% were from Malawi. The mean age of the BL cases and controls was similar (~7.4 years in both, P=0.60). Table 1 shows detected autosomal mCAs for BL cases and controls by country. Overall, a total of 250 autosomal mCAs were detected in 78 (8.4%) of the 931 BL cases. By comparison, a total of 188 autosomal mCAs were detected in 131 (3.4%) of the 3822 controls. Autosomal mCAs were detected in cell fractions ranging from 0.5% to 99.2% (Figure S1). The average number of autosomal mCAs per person (i.e., total of mCAs detected/number of individuals with mCAs detected) was higher in the BL cases compared to controls (3.21 [SD 3.24] versus 1.44 [SD 2.31], P-value=4.50×10-5. The higher frequency of mCAs in blood samples of children with BL compared to controls was independent of age, sex, P falciparum status, and country (OR=2.8, 95% CI=2.06-3.81, P-value=5.70×10-11, Table 1. mCAs on the X chromosome in girls were also associated with BL (5% versus 1.7%, OR=3.12, 95% CI=1.47-6.29, P-value=1.65×10-3). We did not observe an association for mCAs on the Y chromosome in boys. Analysis of paired tumor-normal samples confirmed the presence of the IG∷MYC translocation in tumor, but the same pipelines did not detect the translocation in the corresponding normal blood sample. In informative tumor-normal cases, some mCAs were only detected in tumor, others were detected in both tumor and normal blood, whereas others were detected mCAs in normal only suggesting some mCAs in blood could arise from pre-BL clones. mCAs only observed in BL cases were predominantly gains on chromosome 1q and 8 (Figure 1) which contain major drivers of Burkitt lymphomagenesis including PLEKHO1, MCL1, PSMB4, ILF2, HAX1, ATP8B2 and CKS1B.Conclusion: We report a high frequency of mCAs in healthy sub-Saharan African children and even higher frequency in pediatric BL cases. The mCAs in children with BL clustered on chromosomes 1q and 8 in regions that overlap with several significantly mutated BL genes, suggesting that mCAs may be potential biomarkers important in the natural history of BL. Using paired tumor-normal sample WGS data, we report both similar and unique mCAs in the paired samples suggesting pre-BL clones in blood. These methods are scalable to large cohorts with SNP array data to investigate health effects associated with mCAs in Africa. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Intussusception is a common cause of intestinal obstruction in infants and toddlers. Uncommon presentation with a mass protruding from the anus is often misdiagnosed as rectal prolapse when a high index of suspicion is not maintained, with the likelihood of worse outcomes. We report the successful management of an 8 month old infant with prolapsed ileo-colic intussusception at the Moi Teaching and Referral Hospital (MTRH) which had been mistaken for rectal prolapse. We discuss how to differentiate trans-anal protrusion of intussusception (TAPI) from other prolapsing conditions and highlight the common challenges encountered in managing an infant with delayed presentation.

Background Endemic Burkitt lymphoma (eBL) is an aggressive B cell non-Hodgkin lymphoma associated with antigenic stimulation from Plasmodium falciparum malaria. Whether eBL risk is related to malaria parasite density is unknown. To address this issue, children with eBL, asymptomatic and clinical malaria, as a surrogate of malaria parasite density, were assessed. Methods Malaria-related laboratory results (parasite density, haemoglobin, platelet count, and white cell count [WBC]) count) were compiled for 4019 eBL cases and 80,532 subjects evaluated for asymptomatic malaria or clinical malaria (severe malaria anaemia, hyperparasitaemia, cerebral malaria, malaria prostration, moderate malaria, and mild malaria) in 21 representative studies published in Africa (mostly East Africa) and 850 eBL cases and 2878 controls with primary data from the Epidemiology of Burkitt Lymphoma in East African Children and Minors (EMBLEM) case–control study in Uganda, Tanzania, and Kenya. The average values of malaria-related laboratory results were computed by condition and trends across single-year age groups were assessed using regression and spline models. Results Overall, malaria infection or malaria was diagnosed in 37,089 of children compiled from the literature. Children with eBL and asymptomatic parasitaemia/antigenaemia, but not those with clinical malaria, were closest in their mean age (age 7.1–7.2 vs. 7.4–9.8 years), haemoglobin level (10.0–10.4 vs. 11.7–12.3 g/dL), malaria parasite density (2800 vs. 1827–7780 parasites/µL), platelet count (347,000–353,000 vs. 244,000–306,000 platelets/µL), and WBC count (8180–8890 vs. 7100–7410 cells/µL). Parasite density in these two groups peaked between four to five years, then decreased steadily thereafter; conversely, haemoglobin showed a corresponding increase with age. Children with clinical malaria were markedly different: all had an average age below 5 years, had dramatically elevated parasite density (13,905–869,000 parasites/µL) and dramatically decreased platelet count (< 159,000 platelets/µL) and haemoglobin (< 7 g/dL). Conclusions eBL and asymptomatic parasitaemia/antigenaemia, but not clinical malaria, were the most similar conditions with respect to mean age and malaria-related laboratory results. These results suggest that children with asymptomatic parasitaemia/antigenaemia may be the population at risk of eBL.

Summary Platelet counts are decreased in Plasmodium falciparum malaria, which is aetiologically linked with endemic Burkitt lymphoma (eBL). However, the pattern of platelet counts in eBL cases is unknown. We studied platelet counts in 582 eBL cases and 2 248 controls enrolled in a case‐control study in Uganda, Tanzania and Kenya (2010–2016). Mean platelet counts in controls or eBL cases with or without malaria‐infection in controls versus eBLcases were compared using Student’s t ‐test. Odds ratios (ORs) and two‐sided 95% confidence intervals (95% CIs) were estimated using multiple logistic regression, controlling for age, sex, haemoglobin and white blood cell counts. Platelets were decreased with malaria infection in the controls [263 vs. 339 × 10 9 platelets/l, P < 0·0001; adjusted OR (aOR) = 3·42, 95% CI: 2·79–4·18] and eBL cases (314 vs. 367 × 10 9 platelets/l, P ‐value = 0·002; aOR = 2·36, 95% CI: 1·49–3·73). Unexpectedly, platelets were elevated in eBL cases versus controls in overall analyses (mean: 353 vs. 307 × 10 9 platelets/l, P < 0·0001; aOR = 1·41; 95% CI: 1·12–1·77), and when restricted to malaria‐positive (mean 314 vs. 263 × 10 9 platelets/l, P < 0·0001; OR = 2·26; 95% CI: 1·56–3·27) or malaria‐negative (mean 367 vs. 339 × 10 9 platelets/l, P < 0·001; OR = 1·46; 95% CI: 1·17–1·83) subjects. Platelets were decreased with malaria infection in controls and eBL cases but elevated with eBL.

Endemic Burkitt lymphoma (eBL) is the most common childhood cancer in sub‐Saharan African countries, however, few epidemiologic studies have been undertaken and none attempted enrolling cases from multiple countries. We therefore conducted a population‐based case–control study of eBL in children aged 0–15 years old in six regions in Northern Uganda, Northern Tanzania and Western Kenya, enrolling 862 suspected cases and 2,934 population controls (response rates 98.5–100%), and processing ~40,000 vials of samples using standardized protocols. Risk factor questionnaires were administered, and malaria period prevalence was measured using rapid diagnostic tests (RDTs). A total of 80.9% of the recruited cases were diagnosed as eBL; 61.4% confirmed by histology. Associations with eBL risk were computed using logistic regression models adjusted for relevant confounders. Associations common in at least two countries were emphasized. eBL risk was decreased with higher maternal income and paternal education and elevated with history of inpatient malaria treatment >12 months before enrollment. Reporting malaria‐attributed fever up to 6 months before enrollment and malaria‐RDT positivity at enrollment were associated with decreased eBL risk. Conversely, reporting exposure to mass malaria suppression programs (e.g., indoor residual insecticide) was associated with elevated risk. HIV seropositivity was associated with elevated eBL risk, but the relative impact was small. The study shows that it is feasible to conduct networked, multisite population‐based studies of eBL in Africa. eBL was inversely associated with socioeconomic status, positively associated with inpatient malaria treatment 12 months ago and with living in areas targeted for malaria suppression, which support a role of malaria in eBL.

The burden of Plasmodium falciparum (Pf) malaria in Kenya is decreasing; however, it is still one of the top 10 causes of morbidity, particularly in regions of western Kenya. Between April 2015 and June 2016, we enrolled 965 apparently healthy children aged 0-15 years in former Nyanza and Western Provinces in Kenya to characterize the demographic, geographic, and household risk factors of asymptomatic malaria as part of an epidemiologic study to investigate the risk factors for endemic Burkitt lymphoma. The children were sampled using a stratified, multistage cluster sampling survey design. Malaria was assessed by rapid diagnostic test (RDT) and thick-film microscopy (TFM). Primary analyses of Pf malaria prevalence (pfPR) are based on RDT. Associations between weighted pfPR and potential risk factors were evaluated using logistic regression, accounting for the survey design. Plasmodium falciparum malaria prevalence was 36.0% (27.5%, 44.5%) by RDT and 22.3% (16.0%, 28.6%) by TFM. Plasmodium falciparum malaria prevalence was positively associated with living in the lake-endemic area (adjusted odds ratio [aOR] 3.46; 95% confidence interval [95% CI] 1.63, 7.37), paternal occupation as peasant farmer (aOR 1.87; 1.08, 3.26) or manual laborer (aOR 1.83; 1.00, 3.37), and keeping dogs (aOR 1.62; 0.98-2.69) or cows (aOR 1.52; 0.96-2.40) inside or near the household. Plasmodium falciparum malaria prevalence was inversely associated with indoor residual insecticide spraying (IRS) (aOR 0.44; 0.19, 1.01), having a household connected to electricity (aOR 0.47; 0.22, 0.98), and a household with two (aOR 0.45; 0.22, 0.93) or ≥ three rooms (aOR 0.41; 0.18, 0.93). We report high but geographically heterogeneous pfPR in children in western Kenya and significant associations with IRS and household-level socioeconomic factors.

The co-authors were omitted from the article, they have now been added.Background: Gastroschisis is an anterior abdominal wall defect occurring in up to 4 babies per 10,000 live births. Though the anomaly is rarely associated with other disorders, it poses serious pathophysiological challenges that negatively affect outcome. Review of the management of gastroschisis at Moi Teaching & Referral Hospital (MTRH) from 2013-2016 was done to determine the outcome.Materials and Methods: A four year (2013-2016) retrospective review of gastroschisis management at MTRH was undertaken. Theatre records were used to track all files of babies admitted and operated on. The primary outcome of data analysis was survival. Secondary outcomes analyzed were age at admission, maternal age, birth order, associated anomalies and complications.Results: Records that were available for analysis were 107. Males were 58 (54%). Male to female ratio was 1.1:1. Mean age at admission was 1.35 ± 0.06 days. Weight ranged from 1250-3800 gm with a mean of 2330 gms. Majority were first born. Mean maternal age was 21.25 ± 3.62 years. Complex gastroschisis occurred in 12 (11%). Overall survival was 43%. However, of those who reached the stage of definitive treatment of containment (either primary closure or staged silo placement), had 48% survival rate. Survival rate was highest in the group who weighed 2500 gms and above. Poor outcomes were noted in the premature and low birth weight neonates, and those with complications. Sepsis was the leading cause of mortality. Length of hospital stay was an average of 24 days for the survivors.Conclusions & Recommendations: Prematurity, low birth weight, and complications negatively influenced survival. Improving obstetric care, establishment of paediatric surgical centres and neonatal support services are key to turning around the survival of neonates with this severe surgical anomaly.

PURPOSE:Wilms tumor is the commonest renal malignancy in childhood. Survival in high-income countries is approximately 90%, whereas in low-income countries, it is less than 50%. This study assessed treatment outcomes of patients with Wilms tumor at a Kenyan academic hospital.PATIENTS AND METHODS:We conducted a retrospective medical record review of all children diagnosed with Wilms tumor between 2010 and 2012. Data on treatment outcomes and various sociodemographic and clinical characteristics were collected.RESULTS:Of the 39 patients with Wilms tumor, 41% had event-free survival, 31% abandoned treatment, 23% died, and 5% had progressive or relapsed disease. Most patients presented at an advanced stage: stage I (0%), II (7%), III (43%), IV (40%), or V (10%). The most likely treatment outcome in patients with low-stage (I to III) disease was event-free survival (67%), whereas in those with high-stage (IV to V) disease, it was death (40%). No deaths or instances of progressive or relapsed disease were recorded among patients with low-stage disease; their only reason for treatment failure was abandonment of treatment. Stage of disease significantly affected treatment outcomes (P = .014) and event-free survival estimates (P < .001). Age at diagnosis, sex, duration of symptoms, distance to hospital, and health insurance status did not statistically significantly influence treatment outcomes or event-free survival estimates.CONCLUSION:Survival of patients with Wilms tumor in Kenya is lower compared with that in high-income countries. Treatment abandonment is the most common cause of treatment failure. Stage of disease at diagnosis statistically significantly affects treatment outcomes and survival.

Background: Methicillin-resistant Staphylococcus aureus (MRSA) are pathogens that have major negative impact in all aspects of patient care and are increasingly being recognized as troublesome pathogens in the community. The MRSA are multi-drug resistant bacteria responsible for higher morbidity, mortality and cost of treatment in the affected patients. Research on MRSA antimicrobial susceptibility and resistance in developing countries is limited; hence accurate burden is not certain. Objective: To determine the prevalence and susceptibility pattern of MRSA in S. aureus isolates from patients treated in various units at Moi Teaching and Referral Hospital. Study Design: Cross-sectional design was used to conduct the study. Methods and Materials: Staphylococcus aureus stored isolates from patients at various units at Moi Teaching and Referral Hospital (MTRH) were identified by laboratory conventional methods. Methicillin resistant Staphylococcus aureus was determined using cefoxitin and oxacillin, discs and confirmed by Penicillin Binding Protein (PBP2a’) latex agglutination test. Susceptibility testing was performed according to the Clinical Laboratory Standards Institute procedures. Control strains used were: ATCC 43300 for Methicillin resistant S. aureus (MRSA) strains and ATCC 29213 for methicillin susceptible S. aureus (MSSA) strains. Nine anti-microbials (Erythromycin, Gentamycin, Tetracycline, Vancomycin, Rifampin, Linezolid, Ciprofloxacin, Clindamycin and Fucidicacid) were used to test the anti-microbial susceptibility patterns. Control organisms were run along with the isolates for quality Assurance. The data was analyzed using STATA version 11. Categorical variables were summarized as frequencies and the corresponding percentages. Results were presented using tables and graphs. Results: A total of 107 isolates of S. aureus were obtained, of which 39 (37%) were MRSA. Most of the MRSA, 13 (33%) and 7 (17%), were found in pus and tracheal aspirate samples respectively. Majority of the MRSA isolates were from surgical wards and intensive care unit. The MRSA isolates were highly resistant to erythromycin (92%; 36/39) and tetracycline (92% 36/39) and moderately susceptible to linezolid (77% 30/39), Vancomycin (75% 29/39) and fucidic acid (67% 26/39). A total of 28 (74.4%) MRSA isolates were Clindamycin inducible resistant. Conclusions and Recommendations: This study showed that MRSA is a significant pathogen at MTRH. The MRSA were most detected in pus specimens and least in peritoneal aspirates. Routine Screening of S. aureus isolates for MRSA strains at MTRH is therefore imperative. Infection control measures should be put in place to reduce prevalence and prevent the spread of MRSA at MTRH.

The management of esophageal atresia in a resource-limited environment is plagued with challenges that often lead to poor outcome. The diagnosis and management of babies with long-gap esophageal atresia adds a new dimension to these challenges. We report the success of esophageal replacement surgery for a baby with long-gap esophageal atresia in a resource-limited setting. One year after surgery, she was eating well and her weight gain was appropriate.