Copy Number Variation in Congenital Heart Defects

Julie Lander 0 1 2 Stephanie M. Ware 0 1 2 0 S. M. Ware Department of Medical and Molecular Genetics, Indiana University School of Medicine , 1044 W. Walnut, Indianapolis, IN 46202, USA 1 S. M. Ware (&) Department of Pediatrics, Indiana University School of Medicine , 1044 W. Walnut, Indianapolis, IN 46202, USA 2 J. Lander Department of Pediatrics, University of Cincinnati College of Medicine and Cincinnati Children's Hospital , Cincinnati, OH, USA Congenital heart defects (CHDs) are the most common birth defect and a major contributor to mortality, morbidity, and healthcare costs throughout the world. Although improvements in surgical advances and cardiac care have increased the lifespan of individuals with CHDs, the underlying etiologies of disease remain elusive and there have been no interventions that decrease disease incidence. Genetic, epigenetic, and environmental factors all influence the development of CHDs, and an improved understanding of causation is a prerequisite for prevention. Genetic causes of CHDs include both structural chromosome abnormalities and single gene disorders. Copy number variation (CNV), or submicroscopic chromosomal deletions or duplications, has emerged as an important contributor to congenital genetic disorders, including CHDs, and has identified critical dosage sensitive genes important for cardiac development. Common CNVs associated with highly penetrant CHDs were first identified in genomic disorders such as 22q11.2 deletion syndrome and Williams-Beuren syndrome. More recently, research investigations and clinical diagnostic testing support a role for CNVs in CHDs with extracardiac abnormalities (ECAs) - as well as isolated CHD. It is estimated that CNVs contribute to 325 % of CHDs with ECAs and 310 % of isolated CHDs. While somewhat less clear, new evidence suggests that there is an increase in rare, large, genic CNVs in patients with CHDs, indicating that the overall CNV burden may also be an important factor in disease. As genetic testing for CHDs moves forward, CNVs will play an important role in diagnosis and gene discovery. Congenital heart defects (CHDs) are among the most common birth defects, affecting 8 in 1000 live births in the USA [1]. Congenital cardiovascular defects are the most common cause of infant death resulting from birth defects, and 24 % of infants who die of a birth defect have a heart defect [1]. The underlying causes of CHDs are varied and can include chromosome abnormalities, single gene disorders, environmental etiologies, or most commonly, multifactorial etiologies. The full impact of copy number variation (CNV) as a genetic mechanism in CHDs is not known with certainty, but both research investigations and clinical genetic testing indicate an important role that merits further investigation. CHDs can occur as isolated findings, as part of a welldefined syndrome, or in conjunction with additional extracardiac anomalies (ECAs) not formally recognized as a syndrome. The designation of CHDs as isolated can be difficult since many important distinguishing features of syndromic conditions, such as developmental delay or dysmorphic features, may not be apparent at initial evaluation. For the purposes of this review, CHD with ECA is used to describe patients with CHD and additional abnormalities or malformations not delineated as a wellcharacterized genetic syndrome. Likewise, the phrase isolated CHD is used to identify those patients in whom the only major phenotype at the time of diagnosis is a cardiovascular malformation. In a scientific statement from the American Heart Association, Pierpont et al. cite four reasons it is important to determine the genetic cause of a childs congenital heart defect: (1) there may be other important organ system involvement; (2) there may be prognostic information for clinical outcomes; (3) there may be important genetic reproductive risks the family should know about; and (4) there may be other family members for whom genetic testing is appropriate [2]. As the number of individuals with CHD who are living to adulthood increases (about 1 in 150 adults in the USA has a congenital heart defect) [3], the reproductive implications are extended to the patient as well as family members. Thus, it is important to more precisely delineate disease-causing and disease-associated genetic contributions in order to begin to impact the incidence of CHDs. The genetic etiology of CHDs can range from a single nucleotide variant (SNV) to complex genomic rearrangements to inheritance as a complex trait. Genetic copy number variations (CNVs) have emerged over the past two decades as an important cause of disease, including neuropsychiatric disorders [46] and developmental delay [7]. CNVs are generally defined as genetic deletions or duplications that are not identifiable on traditional chromosome analysis. CNVs arise from recombination within the genome. One of the major mechanisms of CNV generation is through nonallelic homologous recombination and may be mediated by flanking low copy repeat regions or repeat regions from similar sequences in highly homologous genes. When this recombination occurs during meiosis, the result can be unequal distribution of genetic elements to the gametes, resulting in CNVs in the offspring. Nonallelic homologous recombination is most highly associated with large CNVs. Recombination can also occur among tandem arrays of variable numbers of tandem repeats (VNTR), typically leading to smaller CNVs [8, 9]. CNVs hold substantial potential to create variation throughout the genome and the de novo mutation rate of CNVs is higher than that of SNVs [10]. As opposed to SNVs, which are limited to four potential variations (A, C, G, T), CNVs can vary in size and gene content, allowing for more extensive genetic changes. CNV Pathogenicity CNVs occur relatively frequent, making up about 12 % of the genome of the average individual [8]. Many CNVs are common among the general population, and likely have little to no contribution to disease. Determining which CNVs contribute to disease has been a matter of intense investigation. Clinicians and researchers have converged on criteria to define CNV pathogenicity. In the context of an individual with a cardiovascular malformation, characteristics of a pathogenic CNV may include: (1) overlap with a known dosage sensitive CHD gene that causes a similar phenotype, (2) overlap with a known diseaseassociated region, (3) de novo CNV or segregation with phenotype within a family, (4) location in a gene-rich region, (5) large deletion or duplication size, and/or (6) rare (occurring in \1 % of healthy controls). Studies prioritize these attributes somewhat differently, but generally agree that pathogenic CNVs share a combination of the above qualities. In 2011, the American College of Medical Genetics (ACMG) released guidelines designed to assist in the clinical interpretation of potentially pathogenic CNVs [11]. It is important to (...truncated)