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Start Over Author "DePalma, Steven" Journal nature genetics
4 results on '"DePalma, Steven"'

1. Genomic analyses implicate noncoding de novo variants in congenital heart disease

Author

Richter, Felix, Morton, Sarah U, Kim, Seong Won, Kitaygorodsky, Alexander, Wasson, Lauren K, Chen, Kathleen M, Zhou, Jian, Qi, Hongjian, Patel, Nihir, DePalma, Steven R, Parfenov, Michael, Homsy, Jason, Gorham, Joshua M, Manheimer, Kathryn B, Velinder, Matthew, Farrell, Andrew, Marth, Gabor, Schadt, Eric E, Kaltman, Jonathan R, Newburger, Jane W, Giardini, Alessandro, Goldmuntz, Elizabeth, Brueckner, Martina, Kim, Richard, Porter, George A, Bernstein, Daniel, Chung, Wendy K, Srivastava, Deepak, Tristani-Firouzi, Martin, Troyanskaya, Olga G, Dickel, Diane E, Shen, Yufeng, Seidman, Jonathan G, Seidman, Christine E, and Gelb, Bruce D

Subjects
Biological Sciences, Genetics, Human Genome, Congenital Structural Anomalies, Congenital Heart Disease, Heart Disease, Pediatric, Cardiovascular, Rare Diseases, 2.1 Biological and endogenous factors, Adolescent, Adult, Animals, Female, Genetic Predisposition to Disease, Genetic Variation, Genomics, Heart, Heart Defects, Congenital, Humans, Male, Mice, Middle Aged, Open Reading Frames, RNA, Untranslated, RNA-Binding Proteins, Transcription, Genetic, Young Adult, Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology
Abstract

A genetic etiology is identified for one-third of patients with congenital heart disease (CHD), with 8% of cases attributable to coding de novo variants (DNVs). To assess the contribution of noncoding DNVs to CHD, we compared genome sequences from 749 CHD probands and their parents with those from 1,611 unaffected trios. Neural network prediction of noncoding DNV transcriptional impact identified a burden of DNVs in individuals with CHD (n = 2,238 DNVs) compared to controls (n = 4,177; P = 8.7 × 10-4). Independent analyses of enhancers showed an excess of DNVs in associated genes (27 genes versus 3.7 expected, P = 1 × 10-5). We observed significant overlap between these transcription-based approaches (odds ratio (OR) = 2.5, 95% confidence interval (CI) 1.1-5.0, P = 5.4 × 10-3). CHD DNVs altered transcription levels in 5 of 31 enhancers assayed. Finally, we observed a DNV burden in RNA-binding-protein regulatory sites (OR = 1.13, 95% CI 1.1-1.2, P = 8.8 × 10-5). Our findings demonstrate an enrichment of potentially disruptive regulatory noncoding DNVs in a fraction of CHD at least as high as that observed for damaging coding DNVs.

Published
2020

2. Contribution of rare inherited and de novo variants in 2,871 congenital heart disease probands

Author

Jin, Sheng Chih, Homsy, Jason, Zaidi, Samir, Lu, Qiongshi, Morton, Sarah, DePalma, Steven R, Zeng, Xue, Qi, Hongjian, Chang, Weni, Sierant, Michael C, Hung, Wei-Chien, Haider, Shozeb, Zhang, Junhui, Knight, James, Bjornson, Robert D, Castaldi, Christopher, Tikhonoa, Irina R, Bilguvar, Kaya, Mane, Shrikant M, Sanders, Stephan J, Mital, Seema, Russell, Mark W, Gaynor, J William, Deanfield, John, Giardini, Alessandro, Porter, George A, Srivastava, Deepak, Lo, Cecelia W, Shen, Yufeng, Watkins, W Scott, Yandell, Mark, Yost, H Joseph, Tristani-Firouzi, Martin, Newburger, Jane W, Roberts, Amy E, Kim, Richard, Zhao, Hongyu, Kaltman, Jonathan R, Goldmuntz, Elizabeth, Chung, Wendy K, Seidman, Jonathan G, Gelb, Bruce D, Seidman, Christine E, Lifton, Richard P, and Brueckner, Martina

Subjects
Biological Sciences, Genetics, Pediatric, Congenital Structural Anomalies, Congenital Heart Disease, Cardiovascular, Heart Disease, Clinical Research, Rare Diseases, Human Genome, 2.1 Biological and endogenous factors, Adult, Autistic Disorder, Cardiac Myosins, Case-Control Studies, Child, Exome, Female, Gene Expression, Genetic Predisposition to Disease, Genome-Wide Association Study, Growth Differentiation Factor 1, Heart Defects, Congenital, Heterozygote, High-Throughput Nucleotide Sequencing, Homozygote, Humans, Male, Mutation, Myosin Heavy Chains, Pedigree, Risk, Vascular Endothelial Growth Factor Receptor-3, Medical and Health Sciences, Developmental Biology, Agricultural biotechnology, Bioinformatics and computational biology
Abstract

Congenital heart disease (CHD) is the leading cause of mortality from birth defects. Here, exome sequencing of a single cohort of 2,871 CHD probands, including 2,645 parent-offspring trios, implicated rare inherited mutations in 1.8%, including a recessive founder mutation in GDF1 accounting for ∼5% of severe CHD in Ashkenazim, recessive genotypes in MYH6 accounting for ∼11% of Shone complex, and dominant FLT4 mutations accounting for 2.3% of Tetralogy of Fallot. De novo mutations (DNMs) accounted for 8% of cases, including ∼3% of isolated CHD patients and ∼28% with both neurodevelopmental and extra-cardiac congenital anomalies. Seven genes surpassed thresholds for genome-wide significance, and 12 genes not previously implicated in CHD had >70% probability of being disease related. DNMs in ∼440 genes were inferred to contribute to CHD. Striking overlap between genes with damaging DNMs in probands with CHD and autism was also found.

Published
2017

3. Genomic analyses implicate noncoding de novo variants in congenital heart disease

Author

Richter, Felix, Morton, Sarah U, Kim, Seong Won, Kitaygorodsky, Alexander, Wasson, Lauren K, Chen, Kathleen M, Zhou, Jian, Qi, Hongjian, Patel, Nihir, DePalma, Steven R, Parfenov, Michael, Homsy, Jason, Gorham, Joshua M, Manheimer, Kathryn B, Velinder, Matthew, Farrell, Andrew, Marth, Gabor, Schadt, Eric E, Kaltman, Jonathan R, Newburger, Jane W, Giardini, Alessandro, Goldmuntz, Elizabeth, Brueckner, Martina, Kim, Richard, Porter, George A, Bernstein, Daniel, Chung, Wendy K, Srivastava, Deepak, Tristani-Firouzi, Martin, Troyanskaya, Olga G, Dickel, Diane E, Shen, Yufeng, Seidman, Jonathan G, Seidman, Christine E, and Gelb, Bruce D

Subjects
Adult, Heart Defects, Congenital, Male, RNA, Untranslated, Adolescent, Transcription, Genetic, Cardiovascular, Medical and Health Sciences, Congenital, Mice, Open Reading Frames, Young Adult, Genetic, Genetics, 2.1 Biological and endogenous factors, Animals, Humans, Genetic Predisposition to Disease, Aetiology, Heart Defects, Pediatric, Human Genome, Untranslated, Genetic Variation, RNA-Binding Proteins, Heart, Genomics, Biological Sciences, Middle Aged, Heart Disease, Congenital Structural Anomalies, RNA, Female, Transcription, Developmental Biology
Abstract

A genetic etiology is identified for one-third of patients with congenital heart disease (CHD), with 8% of cases attributable to coding de novo variants (DNVs). To assess the contribution of noncoding DNVs to CHD, we compared genome sequences from 749 CHD probands and their parents with those from 1,611 unaffected trios. Neural network prediction of noncoding DNV transcriptional impact identified a burden of DNVs in individuals with CHD (n = 2,238 DNVs) compared to controls (n = 4,177; P = 8.7 × 10-4). Independent analyses of enhancers showed an excess of DNVs in associated genes (27 genes versus 3.7 expected, P = 1 × 10-5). We observed significant overlap between these transcription-based approaches (odds ratio (OR) = 2.5, 95% confidence interval (CI) 1.1-5.0, P = 5.4 × 10-3). CHD DNVs altered transcription levels in 5 of 31 enhancers assayed. Finally, we observed a DNV burden in RNA-binding-protein regulatory sites (OR = 1.13, 95% CI 1.1-1.2, P = 8.8 × 10-5). Our findings demonstrate an enrichment of potentially disruptive regulatory noncoding DNVs in a fraction of CHD at least as high as that observed for damaging coding DNVs.

Published
2019

4. De novo copy number variants identify new genes and loci in isolated sporadic tetralogy of Fallot

Author

Greenway, Steven C, primary, Pereira, Alexandre C, additional, Lin, Jennifer C, additional, DePalma, Steven R, additional, Israel, Samuel J, additional, Mesquita, Sonia M, additional, Ergul, Emel, additional, Conta, Jessie H, additional, Korn, Joshua M, additional, McCarroll, Steven A, additional, Gorham, Joshua M, additional, Gabriel, Stacey, additional, Altshuler, David M, additional, de Lourdes Quintanilla-Dieck, Maria, additional, Artunduaga, Maria Alexandra, additional, Eavey, Roland D, additional, Plenge, Robert M, additional, Shadick, Nancy A, additional, Weinblatt, Michael E, additional, De Jager, Philip L, additional, Hafler, David A, additional, Breitbart, Roger E, additional, Seidman, Jonathan G, additional, and Seidman, Christine E, additional

Published
2009
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