Poster Topical Area: Nutrient-Gene Interactions
Location: Hall D
Poster Board Number: 434
OBJECTIVES: Develop a cost-efficient genetic assay that interrogates extensive genomic regions to identify genetic markers associated with the salt sensitivity (SS) phenotype. The ultimate goal of developing this genetic assay is for future use in cohorts where the SS phenotype has been determined to distinguish responders to low-sodium intake from non-responders.
METHODS: A genetic assay was developed to sequence approximately 124 kb of the genome consisting of 33 genes which have been linked to SS at various levels of evidence (i.e. highly correlated or inconclusively correlated). All coding exons and promoter regions for 13 genes and single nucleotide polymorphisms (SNPs) in 20 genes associated with SS are captured on the assay. The assay utilizes a custom-capture method using molecular inversion probes (MIPs) to generate a library of DNA fragments for next-generation sequencing (NGS) on the Illumina MiSeq platform. Each molecular inversion probe captures 112 nucleotides of the genome and 1,089 MIPs are combined to capture relevant genetic information in targeted genomic regions associated with SS. A minimum sequencing depth of 20x is required for genotyping and haplotype calling, and the concentration of each MIP is optimized to achieve this coverage threshold. The cost of processing one sample includes DNA extraction, library preparation and NGS, and personnel time.
RESULTS: A MiSeq run multiplexing 62 DNA samples from the 1000 Genomes Project was completed using the genetic assay. Average coverage across all genes for the 62 samples was 200x (range: 8x-663x). Four genes had an average of less than 20x average coverage. The cost of processing one sample was $63 or $1.91 per gene. This cost includes DNA extraction ($11), library preparation and NGS costs ($35), and personnel time ($17).
CONCLUSIONS: The results suggest that customized MIPs for NGS can efficiently interrogate extensive genomic regions related to SS. The modest cost makes sequencing for large numbers of people practical and affordable. This low-cost genetic assay holds promise as a practical tool for predicting adverse response to dietary sodium intake and helping health care providers to tailor intervention efforts more effectively to salt sensitive patients.
The UNC Center for Pharmacogenomics and Individualized Therapy and North Carolina Central University provided funding for this project.
University of North Carolina at Chapel Hill
Durham, North Carolina