Browsing by Author "Schubert, Jeffrey A."

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    Clinically relevant variants identified in thoracic aortic aneurysm patients by research exome sequencing
    (Wiley Blackwell (John Wiley & Sons), 2016-05) Schubert, Jeffrey A.; Landis, Benjamin J.; Shikany, Amy R.; Hinton, Robert B.; Ware, Stephanie M.; Department of Pediatrics, IU School of Medicine
    Thoracic aortic aneurysm (TAA) is a genetically heterogeneous disease involving subclinical and progressive dilation of the thoracic aorta, which can lead to life-threatening complications such as dissection or rupture. Genetic testing is important for risk stratification and identification of at risk family members, and clinically available genetic testing panels have been expanding rapidly. However, when past testing results are normal, there is little evidence to guide decision-making about the indications and timing to pursue additional clinical genetic testing. Results from research based genetic testing can help inform this process. Here we present 10 TAA patients who have a family history of disease and who enrolled in research-based exome testing. Nine of these ten patients had previous clinical genetic testing that did not identify the cause of disease. We sought to determine the number of rare variants in 23 known TAA associated genes identified by research-based exome testing. In total, we found 10 rare variants in six patients. Likely pathogenic variants included a TGFB2 variant in one patient and a SMAD3 variant in another. These variants have been reported previously in individuals with similar phenotypes. Variants of uncertain significance of particular interest included novel variants in MYLK and MFAP5, which were identified in a third patient. In total, clinically reportable rare variants were found in 6/10 (60%) patients, with at least 2/10 (20%) patients having likely pathogenic variants identified. These data indicate that consideration of re-testing is important in TAA patients with previous negative or inconclusive results.
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    Exome Sequencing Identifies Candidate Genetic Modifiers of Syndromic and Familial Thoracic Aortic Aneurysm Severity
    (Springer Nature, 2017-08) Landis, Benjamin J.; Schubert, Jeffrey A.; Lai, Dongbing; Jegga, Anil G.; Shikany, Amy R.; Foroud, Tatiana; Ware, Stephanie M.; Hinton, Robert B.; Pediatrics, School of Medicine
    Thoracic aortic aneurysm (TAA) is a genetic disease predisposing to aortic dissection. It is important to identify the genetic modifiers controlling penetrance and expressivity to improve clinical prognostication. Exome sequencing was performed in 27 subjects with syndromic or familial TAA presenting with extreme phenotypes (15 with severe TAA; 12 with mild or absent TAA). Family-based analysis of a subset of the cohort identified variants, genes, and pathways segregating with TAA severity among three families. A rare missense variant in ADCK4 (p.Arg63Trp) segregated with mild TAA in each family. Genes and pathways identified in families were further investigated in the entire cohort using the optimal unified sequence kernel association test, finding significance for the gene COL15A1 (p = 0.025) and the retina homeostasis pathway (p = 0.035). Thus, we identified candidate genetic modifiers of TAA severity by exome-based study of extreme phenotypes, which may lead to improved risk stratification and development of new medical therapies.
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    Genetic Causes of Cardiomyopathy in Children: First Results From the Pediatric Cardiomyopathy Genes Study
    (American Heart Association, 2021-05-04) Ware, Stephanie M.; Wilkinson, James D.; Tariq, Muhammad; Schubert, Jeffrey A.; Sridhar, Arthi; Colan, Steven D.; Shi, Ling; Canter, Charles E.; Hsu, Daphne T.; Webber, Steven A.; Dodd, Debra A.; Everitt, Melanie D.; Kantor, Paul F.; Addonizio, Linda J.; Jefferies, John L.; Rossano, Joseph W.; Pahl, Elfriede; Rusconi, Paolo; Chung, Wendy K.; Lee, Teresa; Towbin, Jeffrey A.; Lal, Ashwin K.; Bhatnagar, Surbhi; Aronow, Bruce; Dexheimer, Phillip J.; Martin, Lisa J.; Miller, Erin M.; Sleeper, Lynn A.; Razoky, Hiedy; Czachor, Jason; Lipshultz, Steven E.; Pediatrics, School of Medicine
    Pediatric cardiomyopathy is a genetically heterogeneous disease with substantial morbidity and mortality. Current guidelines recommend genetic testing in children with hypertrophic, dilated, or restrictive cardiomyopathy, but practice variations exist. Robust data on clinical testing practices and diagnostic yield in children are lacking. This study aimed to identify the genetic causes of cardiomyopathy in children and to investigate clinical genetic testing practices. Methods and Results Children with familial or idiopathic cardiomyopathy were enrolled from 14 institutions in North America. Probands underwent exome sequencing. Rare sequence variants in 37 known cardiomyopathy genes were assessed for pathogenicity using consensus clinical interpretation guidelines. Of the 152 enrolled probands, 41% had a family history of cardiomyopathy. Of 81 (53%) who had undergone clinical genetic testing for cardiomyopathy before enrollment, 39 (48%) had a positive result. Genetic testing rates varied from 0% to 97% between sites. A positive family history and hypertrophic cardiomyopathy subtype were associated with increased likelihood of genetic testing (P=0.005 and P=0.03, respectively). A molecular cause was identified in an additional 21% of the 63 children who did not undergo clinical testing, with positive results identified in both familial and idiopathic cases and across all phenotypic subtypes. Conclusions A definitive molecular genetic diagnosis can be made in a substantial proportion of children for whom the cause and heritable nature of their cardiomyopathy was previously unknown. Practice variations in genetic testing are great and should be reduced. Improvements can be made in comprehensive cardiac screening and predictive genetic testing in first-degree relatives. Overall, our results support use of routine genetic testing in cases of both familial and idiopathic cardiomyopathy.
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    The genetic architecture of pediatric cardiomyopathy
    (Elsevier, 2022) Ware, Stephanie M.; Bhatnagar, Surbhi; Dexheimer, Phillip J.; Wilkinson, James D.; Sridhar, Arthi; Fan, Xiao; Shen, Yufeng; Tariq, Muhammad; Schubert, Jeffrey A.; Colan, Steven D.; Shi, Ling; Canter, Charles E.; Hsu, Daphne T.; Bansal, Neha; Webber, Steven A.; Everitt, Melanie D.; Kantor, Paul F.; Rossano, Joseph W.; Pahl, Elfriede; Rusconi, Paolo; Lee, Teresa M.; Towbin, Jeffrey A.; Lal, Ashwin K.; Chung, Wendy K.; Miller, Erin M.; Aronow, Bruce; Martin, Lisa J.; Lipshultz, Steven E.; Pediatric Cardiomyopathy Registry Study Group; Pediatrics, School of Medicine
    To understand the genetic contribution to primary pediatric cardiomyopathy, we performed exome sequencing in a large cohort of 528 children with cardiomyopathy. Using clinical interpretation guidelines and targeting genes implicated in cardiomyopathy, we identified a genetic cause in 32% of affected individuals. Cardiomyopathy sub-phenotypes differed by ancestry, age at diagnosis, and family history. Infants < 1 year were less likely to have a molecular diagnosis (p < 0.001). Using a discovery set of 1,703 candidate genes and informatic tools, we identified rare and damaging variants in 56% of affected individuals. We see an excess burden of damaging variants in affected individuals as compared to two independent control sets, 1000 Genomes Project (p < 0.001) and SPARK parental controls (p < 1 × 10-16). Cardiomyopathy variant burden remained enriched when stratified by ancestry, variant type, and sub-phenotype, emphasizing the importance of understanding the contribution of these factors to genetic architecture. Enrichment in this discovery candidate gene set suggests multigenic mechanisms underlie sub-phenotype-specific causes and presentations of cardiomyopathy. These results identify important information about the genetic architecture of pediatric cardiomyopathy and support recommendations for clinical genetic testing in children while illustrating differences in genetic architecture by age, ancestry, and sub-phenotype and providing rationale for larger studies to investigate multigenic contributions.