Genetics of human cardiovascular disease

Abstract

Cardiovascular disease encompasses a range of conditions extending from myocardial infarction to congenital heart disease, most of which are heritable. Enormous effort has been invested in understanding the genes and specific DNA sequence variants that are responsible for this heritability. Here, we review the lessons learned for monogenic and common, complex forms of cardiovascular disease. We also discuss key challenges that remain for gene discovery and for moving from genomic localization to mechanistic insights, with an emphasis on the impact of next-generation sequencing and the use of pluripotent human cells to understand the mechanism by which genetic variation contributes to disease.

Figure 1. Overlap of genetic loci causing Mendelian dyslipidemic syndromes, those targeted by lipid lowering therapies, and those identified by GWAS

Each GWAS locus is named according to a plausible biologic candidate in the locus or the gene nearest to the lead single nucleotide polymorphism (SNP). Note that for most GWAS loci, the causal gene is not yet proven. Of 19 genes previously implicated in Mendelian lipid disorders, 16 of the genes underlying these Mendelian disorders lie within 100 kilobases of one of the lead SNPs mapped by GWAS, including nine that lie within 10 kilobases of the nearest lead SNP (Teslovich et al., 2010).

Figure 2

Association signals arising from rare variants. A. and B. Each line represents DNA sequence from a different individual and each circle represents a DNA sequence variant. Each color denotes a DNA sequence variant allele at a different nucleotide site. A. “Low-frequency” variants can be defined as variants in frequency between 1:1000 and 1:20. Each variant can be assayed typically by genotyping and tested for association individually using single marker tests of association. B. “Very Rare” variants can be defined as variants in frequency less than 1:1000 frequency and often the variant may be seen only in a single person (i.e., a singleton). Variants in this frequency range need to be grouped together and tested in aggregate. Association signals from a burden of such very rare variants are typically best validated using re-sequencing of the same genomic interval in additional individuals. Figure adapted from (Manolio et al., 2009)

Figure 3. Estimate of sample sizes required for gene discovery in exome sequencing studies of complex traits

Extrapolations were performed using gene re-sequencing counts from published candidate gene studies. Fisher exact test was performed for gene burden testing on mutation carrier status within each study. The red horizontal line indicates the genome-wide P-value threshold (P = 2.5 × 10⁻⁶) for gene burden of rare variants with minor allele frequencies < 1%. The extrapolations show that thousands of samples are needed to exceed statistical significance at a genome-wide level. Rare variant counts for ANGPTL3, ANGPTL4 and ANGPTL5 for plasma triglycerides were obtained from Romeo and colleagues (Romeo et al., 2009); APOA5, APOB, GCKR and LPL for hypertriglyceridemia from Johansen and colleagues (Johansen et al., 2010); SLC12A3/SLC12A1/KCNJ1 from Ji and colleagues (Ji et al., 2008).

Figure 4. Modeling human genetic disease in reprogrammed cells

Reprogrammed cells derived from skin fibroblasts or blood cells of individuals with genetic variants associated with disease can be used for disease modeling, drug discovery, and to determine the impact of sequence variants on cellular biology. Reprogramming to induced pluripotent stem (iPS) cells and subsequent directed differentiation to relevant cell types can yield large numbers of human disease-related cell types for investigation. Specific genetic variants can also be engineered into human pluripotent stem cells using zinc-finger nucleases or TALENs to generate iPS or embryonic stem (ES) cells harboring disease-associated variants. Future approaches involving transdifferentiation may allow for a more direct approach to generate relevant cell types for study of CVD. In some cases diseases will be cell autonomous, but in others may require co-culture of two or more cell types to recapitulate the disease process.