Successes and challenges of using whole exome sequencing to identify novel genes underlying an inherited predisposition for thoracic aortic aneurysms and acute aortic dissections

Abstract

Thoracic aortic aneurysms involving the aortic root and/or ascending aorta can lead to acute aortic dissections. Approximately 20% of patients with thoracic aortic aneurysms and dissections (TAAD) have a family history of the disease, referred to as familial TAAD (FTAAD) that can be inherited in an autosomal dominant manner with variable expression with respect to disease presentation, age of onset and associated features. Whole exome sequencing (WES) has been used to identify causative mutations in novel genes for TAAD. The strategy used to reduce the large number of rare variants identified using WES is to sequence distant relatives with TAAD and filter for heterozygous rare variants that are shared between the relatives, predicted to disrupt protein function and segregate with the TAAD phenotype in other family members. Putative genes are validated by identifying additional families with a causative mutation in the genes. This approach has successfully identified novel genes for FTAAD.

Introduction

Thoracic aortic aneurysms leading to acute aortic dissections (TAAD) are a common cause of premature deaths, ranking as high as the 15th leading cause of death in the United States (Hoyert et al., 2001). If an individual is known to have a genetic predisposition to TAAD, clinical management can be initiated to prevent premature death due to aortic dissection. We and others have determined that up to 20% of TAAD patients without a genetic syndrome have a family history of TAAD, referred to as familial TAAD (FTAAD), indicating the disease has a significant genetic component (Biddinger et al., 1997, Coady et al., 1999). Analysis of FTAAD pedigrees showed TAAD is primarily inherited in families as an autosomal dominant condition with reduced penetrance, indicating that a single gene mutation is the most likely cause of the disease in these families (Albornoz et al., 2006, Milewicz et al., 1998). The disease presentation is variable, not only in the age of onset and aortic disease presentation, but also in the presence of other cardiovascular features that segregate with TAAD, such as congenital defects [e.g., bicuspid aortic valve (BAV) and patent ductus arteriosus (PDA)] and vascular diseases elsewhere (e.g., intracranial aneurysms, coronary artery disease, and occlusive cerebrovascular disease) (Guo et al., 2011, Loscalzo et al., 2007, Regalado et al., 2011a, Tran-Fadulu et al., 2009). The clinical heterogeneity of FTAAD suggests that there are multiple genes involved in the disease and genetic heterogeneity for FTAAD has been confirmed through the identification of genes for this condition.

Multiple genes for FTAAD have been identified using different genetic techniques. Positional cloning successfully identified mutations in three genes causing FTAAD: TGFBR2, encoding transforming growth factor-β receptor type II, and ACTA2 and MYH11, encoding the smooth muscle specific isoforms of α-actin and β-myosin, respectively (Guo et al., 2007, Pannu et al., 2005, Pannu et al., 2007, Zhu et al., 2006). A candidate gene approach was also used to identify FTAAD genes: TGFBR1 encoding transforming growth factor-β receptor type I, FBN1 encoding fibrillin, and MYLK encoding myosin light chain kinase (Francke et al., 1995, Milewicz et al., 1996, Tran-Fadulu et al., 2009, Wang et al., 2010). Thus far, the genes implicated for FTAAD highlight disruption of two distinct molecular pathways involved in the etiology of the thoracic aortic disease: TGF-β signaling and smooth muscle cell (SMC) contractile function (Milewicz et al., 2008). Furthermore, specific clinical manifestations associated with mutations in these genes help explain the clinical heterogeneity observed for this condition (Guo et al., 2009, Loeys et al., 2005, van de Laar et al., 2011, Zhu et al., 2006).

Despite identifying six genes for FTAAD using these genetic strategies, only about 20% of TAAD families have mutations in these genes. This fact suggests that the search for novel genes containing rare variants leading to disease will be complicated by the possibility that each gene will contribute to disease in only a small proportion of families. We have recently turned to whole exome sequencing (WES) to increase the pace and efficiency of novel gene identification. As recently reviewed (Marian, 2012), WES provides an unbiased assessment of genetic variants in the protein coding regions of the genome. Since approximately 85% of causative mutations for Mendelian diseases are found in the coding regions or in canonical splice sites, WES is an efficient approach to identify causative mutations for these diseases (Ng et al., 2009, Turner et al., 2009). This review will outline the strategy we have used to successfully identify rare gene variants causing familial TAAD using WES, as well as discuss the challenges going forward using this approach (Boileau et al., 2012, Guo et al.,, Regalado et al., 2011b).