Molecular basis of a linkage peak: exome sequencing and family-based analysis identify a rare genetic variant in the ADIPOQ gene in the IRAS Family Study

Abstract

Family-based linkage analysis has been a powerful tool for identification of genes contributing to traits with monogenic patterns of inheritance. These approaches have been of limited utility in identification of genes underlying complex traits. In contrast, searches for common genetic variants associated with complex traits have been highly successful. It is now widely recognized that common variations frequently explain only part of the inter-individual variation in populations. 'Rare' genetic variants have been hypothesized to contribute significantly to phenotypic variation in the population. We have developed a combination of family-based linkage, whole-exome sequencing, direct sequencing and association methods to efficiently identify rare variants of large effect. Key to the successful application of the method was the recognition that only a few families in a sample contribute significantly to a linkage signal. Thus, a search for mutations can be targeted to a small number of families in a chromosome interval restricted to the linkage peak. This approach has been used to identify a rare (1.1%) G45R mutation in the gene encoding adiponectin, ADIPOQ. This variant explains a strong linkage signal (LOD > 8.0) and accounts for ∼17% of the variance in plasma adiponectin levels in a sample of 1240 Hispanic Americans and 63% of the variance in families carrying the mutation. Individuals carrying the G45R mutation have mean adiponectin levels that are 19% of non-carriers. We propose that rare variants may be a common explanation for linkage peaks observed in complex trait genetics. This approach is applicable to a wide range of family studies and has potential to be a discovery tool for identification of novel genes influencing complex traits.

Figure 1.

Pedigrees of families 2010 (A) and 1008 (B) from the IRASFS. Generations are denoted to the left. Genotyped individuals are noted as ‘G’ (homozygous for G45) and ‘R’ (heterozygotes carrying both G45 and R45 alleles). Below each individual is the measured plasma adiponectin concentration in µg/ml.

Figure 2.

Linkage analysis of plasma adiponectin on chromosome 3 in IRASFS Hispanic families. Maximum LOD score is shown on the y-axis and centiMorgans position on chromosome 3 is shown in the x-axis. Blue line is linkage analysis of all families using age, gender, recruitment center and BMI as covariates. Green line is linkage analysis of all families using age, gender, recruitment center, BMI and G45R genotype as covariates.