Review articleSuccesses and challenges of using whole exome sequencing to identify novel genes underlying an inherited predisposition for thoracic aortic aneurysms and acute aortic dissections
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).
Section snippets
Approach
The commercial human exome capture arrays and next generation sequencing technologies are designed to capture and sequence approximately 97–99% of the exons and flanking introns that are in current genomic databases (Reinhardt et al., 1996), although in practice, performance can fall modestly short of this (Clark et al., 2011). Additionally, computer programs have been developed to map sequence reads to the reference human genome, identify genetic variants, annotate amino acid changes, predict
Identification of novel FTAAD genes encoding proteins in the TGF-β pathway
The “low hanging fruits” as far as using WES and large pedigrees to identify novel genes for FTAAD were rare variants in genes encoding proteins in the canonical TGF-β signaling pathways, specifically SMAD3 and TGFB2, encoding Smad3 and TGF-β2, respectively (Boileau et al., 2012, Regalado et al., 2011b). Sequencing first cousins once removed in family TAA549 rapidly narrowed down the number of potentially disease-causing rare variants to 11 variants, one of which was a novel frameshift
Identification of novel FTAAD genes encoding proteins involved in SMC contraction
Similar to the identification of rare variants in genes encoding proteins in the canonical TGF-β pathway, we also rapidly identified mutations in another gene regulating SMC contraction as a cause of FTAAD. We and others had previously identified mutations in genes encoding the major proteins forming the thin and thick filaments of smooth muscle: α-actin (ACTA2) and myosin heavy chain (MYH11) (Guo et al., 2007, Zhu et al., 2006). In addition, we identified mutations in MYLK encoding the myosin
Identification of further genes for FTAAD: Where are we?
Whole exome sequencing of affected relative pairs, followed by validation of putative genes by sequencing additional families, has successfully identified novel genes for FTAAD. The genes reported to date have disrupted known pathways to thoracic aortic disease and were easily confirmed with minimal additional molecular, cellular, or animal studies. Although we have genetic evidence to strongly support some additional genes as disease-causing for FTAAD, these genes are predicted to disrupt new
Future directions
Our research group has successfully used an approach involving WES and large families to identify defective genes resulting in disruption of known disease pathways associated with FTAAD. The identification of further genes for FTAAD highlights the genetic heterogeneity and complexity of identifying causative genes for this disease. Going forward, there are some hurdles to overcome to identify causative mutations for FTAAD. First, there is significant genetic heterogeneity for FTAAD and the vast
Acknowledgments
We are extremely grateful to the families who participated in these studies. We would like to acknowledge the following sources that provided support for these studies: RO1 HL62594 (D.M.M.), P50HL083794-01 (D.M.M.), UL1 RR024148 (UTHealth), Vivian L. Smith Foundation (D.M.M.), TexGen Foundation (D.M.M.), the Richard T. Pisani Funds (D.M.M.), the Lung Cohorts Sequencing Project (HL-102923), the WHI Sequencing Project (HL-102924), the Heart Cohorts Sequencing Project (HL-103010), the Broad
References (43)
- et al.
Familial thoracic aortic aneurysms and dissections—incidence, modes of inheritance, and phenotypic patterns
Annals of Thoracic Surgery
(2006) - et al.
Familial thoracic aortic dilatations and dissections: a case control study
Journal of Vascular Surgery
(1997) - et al.
Signaling processes for initiating smooth muscle contraction upon neural stimulation
Journal of Biological Chemistry
(2009) - et al.
Discovery and statistical genotyping of copy-number variation from whole-exome sequencing depth
American Journal of Human Genetics
(2012) - et al.
Mutations in smooth muscle alpha-actin (ACTA2) cause coronary artery disease, stroke, and moyamoya disease, along with thoracic aortic disease
American Journal of Human Genetics
(2009) Challenges in medical applications of whole exome/genome sequencing discoveries
Trends in Cardiovascular Medicine
(2012)- et al.
Mutations in KCTD1 cause scalp-ear-nipple syndrome
American Journal of Human Genetics
(2013) - et al.
Reduced penetrance and variable expressivity of familial thoracic aortic aneurysms/dissections
American Journal of Cardiology
(1998) - et al.
Fibrillin-1 and fibulin-2 interact and are colocalized in some tissues
Journal of Biological Chemistry
(1996) - et al.
Mutations in Myosin light chain kinase cause familial aortic dissections
American Journal of Human Genetics
(2010)
TGFB2 mutations cause familial thoracic aortic aneurysms and dissections associated with mild systemic features of Marfan syndrome
Nature Genetics
Performance comparison of exome DNA sequencing technologies
Nature Biotechnology
Familial patterns of thoracic aortic aneurysms
Archives of Surgery
A Gly1127Ser mutation in an Egf-like domain of the Fibrillin-1 gene is a risk factor for ascending aortic-aneurysm and dissection
American Journal of Human Genetics
Mechanisms of disease: hypertrophic cardiomyopathy
Nature Reviews. Cardiology
An FBN1 pseudoexon mutation in a patient with Marfan syndrome: confirmation of cryptic mutations leading to disease
Journal of Human Genetics
Mutations in smooth muscle alpha-actin (ACTA2) lead to thoracic aortic aneurysms and dissections
Nature Genetics
Familial thoracic aortic aneurysms and dissections: identification of a novel locus for stable aneurysms with a low risk for progression to aortic dissection
Circulation. Cardiovascular Genetics
Deaths: final data for 1999
National Vital Statistics Reports
TGFBR2 mutations alter smooth muscle cell phenotype and predispose to thoracic aortic aneurysms and dissections
Cardiovascular Research
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