Multi-omics Studies of Childhood Complex Traits in Diverse Populations

National Human Genome Research Institute

Investigators

Linked publications, trials & patents

Abstract

The overall approach of the lab is to apply modern-day human genomics and genetics tools to population-based childhood disease cohorts in order to better understand the pathophysiology of disease. This approach includes the recruitment of cohorts through international, national, and internal collaborators; the application of DNA sequencing technologies, including whole genome-, whole exome-, RNA-, bisulfite-, long-read, and single cell sequencing; and the development of analytical frameworks that span genetic epidemiology, population genetics, and computational biology. Associations derived from this approach are then functionally validated to develop therapeutic hypotheses for the diseases in question. The 12 months covered by this annual report have included varying applications of the above in three main contexts: Childhood Severe Acute Malnutrition (SAM) Our previous studies identified DNA hypomethylation in children with the more-deadly edematous form of SAM (known as ESAM) relative to the non-edematous form (NESAM). We developed a systematic way of assessing correlation between neighboring sites of DNA methylation, through which we were able to demonstrate a previously unrecognized highly organized structure of correlated DNA methylation across the genome that reflects reported patterns of gene regulation and is disrupted during ESAM. We also reported differences in one-carbon metabolism (OCM) between children with ESAM and those with NESAM. In this last reporting period: - We showed that sequence variants at genes involved in OCM are more commonly found on east-African genetic backgrounds and are significantly associated with ESAM - We conducted single variant genotyping of OCM-associated loci in over 400 samples using cell-free DNA obtained from previously collected serum samples used to assess OCM in ESAM and NESAM. - We refined our cellular model of starvation-induced fatty liver begun in the previous reporting period. This model recapitulates liver fat accumulation over time - a major pathological feature that is seen more often in ESAM. - We initiated the Kwashiorkor Study Network (KwashNet) to facilitate a multinational sample repository of clinically well-phenotyped ESAM cases and NESAM controls. KwashNet has met both virtually and in-person (Gaborone, Botswana, June 2023), to refine study design, recruitment, data sharing and governance, budget, and institutional agreements in the context of individual site IRB regulations. We received a Non-Human Subjects Research waiver to collate data from deidentified samples, and developed protocols for patient recruitment across the sites. Modifiers of Sickle Cell Disease We have been focused on identifying two classes of disease modifiers a) cis-modifiers of fetal-hemoglobin (HbF) production and b) modifiers of transfusions reponses in sickle cell disease. HbF is well known to reduce the severity of SCD and its production is modified by genetic variants in the beta-globin cluster on chromosome 11. We used long-read sequencing to identify and validate novel structural- (SVs) and single-nucleotide variants (SNVs) in the beta-globin cluster by aligning data to the newly published telomere-to-telomere (T2T) human genome reference and comparing this to the previous human genome build (hg38). We found that the T2T reference reveals previously unrecognized genetic variants and reduces false positives in complex genomic regions. The manuscript describing these findings is in preparation. We previously published a genome-wide association of large-effect alloimmunization risk loci in which we identified a genome-wide significant association between an intergenic locus on chromosome 5q33 and being a transfusion responder; we replicated this in a second cohort. In this reporting period, we developed a translational protocol that will allow for fine mapping the putative functional role of this variant. We worked with collaborators in NHLBI and the NIH Clinical Center to identify individuals with the 5q33 risk variant and developed a clinical protocol to recontact and recruit these individuals for molecular and clinical phenotyping. We have also optimized the application of single cell technologies to determine the effect of the variant on the expression and regulation of near-by genes in patient samples. Genomic characterization of African populations Through our interactions with the H3Africa Consortium, we continue to contribute to efforts to delineate the full landscape of African genetic variation. In the most recent reporting period, our external collaborators have agreed upon and executed detailed protocols for patient recruitment, sample acquisition and shipping, as well as data dissemination and analysis. Sequencing of samples is expected to be completed by the time of the next reporting period, with analyses to follow. We continue to demonstrate expertise in this are by co-authorship of manuscripts that speak to the complex genetic and ethical issues raised.