AS666 - A multi-omics resource for sickle cell trait in African Americans from the Women’s Health Initiative

Investigator Names and Contact Information

Alexander Reiner (apreiner@uw.edu)

Charles Kooperberg

Introduction/Intent

SPECIFIC AIMS

The NHLBI's TransOmics for Precision Medicine (TOPMed) program seeks to apply whole genome sequencing (WGS) and other -omics technologies to various heart, lung, and blood (HLB) disorders -- generating large volumes of omics data and making those datasets accessible to the broad research community to stimulate discovery research. While samples funded through prior TOPMed X01s have largely supported the production of omics data (RNA, methylation, metabolites, and proteins) related to heart and lung diseases and their risk factors, there has been relatively little multi-omics data generated in the following two major research areas: (1) sickle cell and other hematologic conditions and disorders of hematopoiesis; (2) RNA-seq, DNA methylation, metabolite and protein profiling from under-represented minority samples such as African Americans (AAs).

Though the genetic basis of sickle cell disease (SCD) has been known for decades, the phenotypic heterogeneity of SCD is poorly understood. Moreover, the clinical sequelae and public health implications of the carrier state (sickle cell trait or SCT), a condition that affects nearly 10% of AAs, have only begun to be elucidated. Individuals with SCT (previously thought of as a benign condition) are at increased risk for exertional sudden death, chronic kidney disease (CKD), and venous thromboembolism (VTE). However, the molecular mechanisms for SCT-related complications are poorly understood. The TOPMed Hematology & Hemostasis Working Group has shown that SCT is associated with differences in hematologic and immune cell parameters and that genetic modifiers of SCT (e.g., a regulatory variant of α-globin) impact risk of related complications We have also identified several novel African ancestry-specific genetic variants associated with quantitative blood cell counts (such as DARC-associated “ethnic neutropenia”) or hematologic conditions, including a novel TET2 germline regulatory variant associated with clonal hematopoiesis of indeterminate potential (CHIP) in AA. Not only for sickle cell, but also for other HLB conditions and phenotypes which disproportionately impact AA, there is a paucity of gene expression, methylation, metabolomic, and clinical data to perform mechanistic follow-up of implicated genetic variants and to determine their full phenomic or clinical spectrum.

The prospective, multi-ethnic Women’s Health Initiative (WHI) cohort study has been a major contributor to TOPMed. WHI has additional biospecimens on a large number of AAs that have not yet been utilized by TOPMed and can contribute to the scientific focus areas described above. These include high-quality genomic DNA, RNA, and plasma, along with SCT and α-globin genotypes and CHIP somatic mutation status derived from WGS and/or targeted sequencing. The high quality of specimens from the WHI biorepository has been demonstrated repeatedly through prior work. Importantly, all omics and related phenotypic data are consented for sharing with the broader research community through a public database such as dbGaP and other related databases supported by NIH, consistent with the goals of the TOPMed program.

Here we propose to measure additional omics data (WGS, RNA-seq, DNA methylation, metabolite and protein profiling) which, together with the clinical, hematologic phenotypic, and environmental data already available in the same WHI AAs, can be used to inform the molecular pathobiology of SCT and other conditions (hematologic and non-hematologic) that disproportionately affect AAs and identify important disease modifiers of sickle cell including gene-gene and gene-environment interactions. We propose to apply innovative statistical approaches and to collaborate with other TOPMed investigators with additional participants with SCT or SCD. The ultimate goal is to transform sickle cell and hematopoietic genomic science from simple genetic locus-trait associations to comprehensive understanding of complex disease pathobiology at a multi-omics, systems level. We propose the following series of phased projects utilizing both TOPMed and non-TOPMed WHI biospecimens:

• 1. Perform methylation, metabolomic, and protein profiling on 1,000 SCT carriers and 1000 AA SCT non-carriers using genomic DNA and plasma samples collected at the WHI baseline exam. This will allow analysis of the mechanism and genetic modifiers of SCT associations on CKD, thrombosis, and white blood cell traits. Through our close collaboration with the TOPMed SCD Working Group, we will integrate multi-omic analyses to test genetic variants that modify the clinical severity of SCT as potential modifiers of SCD.
• 2. Perform RNAseq, methylation, metabolite, and protein profiling on 1000 AA with genomic DNA, plasma, and RNA available at the WHI 2012-2013 Long Life Study (LLS) exam. These individuals have or will have blood cell counts and CHIP measurements at LLS exam. The generation of WGS and multi-omic data in these AA individuals at the LLS exam will enable integrative omics and mediation or mechanistic analysis of African-specific germline genetic variants associated with hematologic quantitative traits (blood cell counts and indices) identified through TOPMed H&H, including longitudinal analysis of a recently identified African-specific TET2 CHIP-associated variant and other multi-omics analyses.
• 3. Perform WGS at the baseline exam on 800 WHI AA samples of Aim 1 and 2 who currently do not have WGS as part of TOPMed or the CCDG.