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2.  Exome Analysis of a Family with Pleiotropic Congenital Heart Disease 
A number of single gene defects have been identified in patients with isolated or nonsyndromic congenital heart defects (CHD). However, due to significant genetic heterogeneity candidate gene approaches have had limited success in finding high-risk alleles in most cases.
Use exome sequencing to identify high-risk gene variants in a family with highly penetrant pleiotropic CHD.
DNA samples from 2 members of a family with diverse CHD were analyzed by exome sequencing. Variants were filtered to eliminate common variants and sequencing artifacts and then prioritized based upon the predicted effect of the variant and on gene function. The remainder of the family was screened using PCR, high resolution melting analysis and DNA sequencing to evaluate variant segregation.
After filtering, more than 2000 rare variants (including single nucleotide substitutions and indels) were shared by the 2 individuals. Of these, 46 were non-synonymous, 3 were predicted to alter splicing, and 6 resulted in a frameshift. Prioritization reduced the number of variants potentially involved in CHD to 18. None of the variants completely segregated with CHD in the kindred. However, one variant, Myh6 Ala290Pro, was identified in all but one affected individual. This variant was previously identified in a patient with tricuspid atresia and large secundum ASD.
It is likely that next generation sequencing will become the method of choice for unraveling the complex genetics of CHD, but information gained by analysis of transmission through families will be crucial.
PMCID: PMC3329568  PMID: 22337856
Atrial Septal Defects; Exome Sequencing; Myosin Heavy Chain 6; Mutations
3.  Non-synonymous variants in Pre B-cell leukemia homeobox (PBX) genes are associated with congenital heart defects 
Congenital cardiac malformations are one of the most common birth defects and most are believed to be multigenic/multifactorial in nature. Recently mice lacking Pre-B cell leukemia transcription homeobox (PBX) genes were created and found to have a range of ventricular outflow tract (OFT) malformations. Therefore, we screened 95 patients with congenital heart defects, including OFT malformations, for variants in genes encoding PBX proteins, as well as interacting proteins. The coding exons of PBX1-4, PKNOX1, PKNOX2, MEIS1-3, and PBXIP1 were amplified by polymerase chain reaction and the products analyzed on a Lightscanner. Samples with abnormal melting profiles were analyzed by DNA sequencing. Seven non-synonymous variants (6 novel and 1 SNP) were identified in 5 proteins (Pbx3, Pbx4, Meis1, Meis3 and Pknox1). One Pbx3 variant, p.A136V, is located in a highly conserved polyalanine tract and predicted to be deleterious. This variant was present in 5.2% of heart defect patients compared with 1.3% of 380 race- and ethnicity-matched controls (P<0.05). None of the other variants were predicted to be damaging. In conclusion, our results support the Pbx3 Ala136Val variant as a modifier or risk allele for congenital heart defects and implicate PBX-related genes as candidates for CHD, especially those affecting the cardiac outflow tract.
PMCID: PMC3342453  PMID: 22426282
congenital heart disease; genetics; Pre-B cell leukemia transcription factors
4.  Shared Segment Analysis and Next-Generation Sequencing Implicates the Retinoic Acid Signaling Pathway in Total Anomalous Pulmonary Venous Return (TAPVR) 
PLoS ONE  2015;10(6):e0131514.
Most isolated congenital heart defects are thought to be sporadic and are often ascribed to multifactorial mechanisms with poorly understood genetics. Total Anomalous Pulmonary Venous Return (TAPVR) occurs in 1 in 15,000 live-born infants and occurs either in isolation or as part of a syndrome involving aberrant left-right development. Previously, we reported causative links between TAVPR and the PDGFRA gene. TAPVR has also been linked to the ANKRD1/CARP genes. However, these genes only explain a small fraction of the heritability of the condition. By examination of phased single nucleotide polymorphism genotype data from 5 distantly related TAPVR patients we identified a single 25 cM shared, Identical by Descent genomic segment on the short arm of chromosome 12 shared by 3 of the patients and their obligate-carrier parents. Whole genome sequence (WGS) analysis identified a non-synonymous variant within the shared segment in the retinol binding protein 5 (RBP5) gene. The RBP5 variant is predicted to be deleterious and is overrepresented in the TAPVR population. Gene expression and functional analysis of the zebrafish orthologue, rbp7, supports the notion that RBP5 is a TAPVR susceptibility gene. Additional sequence analysis also uncovered deleterious variants in genes associated with retinoic acid signaling, including NODAL and retinol dehydrogenase 10. These data indicate that genetic variation in the retinoic acid signaling pathway confers, in part, susceptibility to TAPVR.
PMCID: PMC4485409  PMID: 26121141
5.  A Family-Based Paradigm to Identify Candidate Chromosomal Regions for Isolated Congenital Diaphragmatic Hernia 
Congenital diaphragmatic hernia (CDH) is a developmental defect of the diaphragm that causes high newborn mortality. Isolated or non-syndromic CDH is considered a multifactorial disease, with strong evidence implicating genetic factors. As low heritability has been reported in isolated CDH, family-based genetic methods have yet to identify the genetic factors associated with the defect. Using the Utah Population Database, we identified distantly related patients from several extended families with a high incidence of isolated CDH. Using high-density genotyping, seven patients were analyzed by homozygosity exclusion rare allele mapping (HERAM) and phased haplotype sharing (HapShare), two methods we developed to map shared chromosome regions. Our patient cohort shared three regions not previously associated with CDH, i.e. 2q11.2-q12.1, 4p13 and 7q11.2, and two regions previously involved in CDH, i.e. 8p23.1 and 15q26.2. The latter regions contain GATA4 and NR2F2, two genes implicated in diaphragm formation in mice. Interestingly, three patients shared the 8p23.1 locus and one of them also harbored the 15q26.2 segment. No coding variants were identified in GATA4 or NR2F2, but a rare shared variant was found in intron 1 of GATA4. This work shows the role of heritability in isolated CDH. Our family-based strategy uncovers new chromosomal regions possibly associated with disease, and suggests that non-coding variants of GATA4 and NR2F2 may contribute to the development of isolated CDH. This approach could speed up the discovery of the genes and regulatory elements causing multifactorial diseases, such as isolated CDH.
PMCID: PMC3507422  PMID: 23165927
congenital diaphragmatic hernia; Utah population database; shared segment analysis; GATA4; NR2F2
6.  Role of Activating FcγR Gene Polymorphisms in Kawasaki Disease Susceptibility and Intravenous Immunoglobulin Response 
A functional polymorphism in the inhibitory IgG-Fc receptor FcγRIIB influences intravenous immunoglobulin (IVIG) response in Kawasaki Disease (KD) a vasculitis preferentially affecting the coronary arteries in children. We tested the hypothesis that the polymorphisms in the activating receptors (Fcγ RIIA, Fcγ RIIIA and Fcγ RIIIB) also influence susceptibility, IVIG treatment response, and coronary artery disease (CAD) in KD patients.
Methods and Results
We genotyped polymorphisms in the activating FcγRIIA, FcγRIIIA and FcγRIIIB genes using pyrosequencing in 443 KD patients, including 266 trios and 150 single parent-child pairs, in northwest US and genetically determined race with 155 ancestry information markers. We used the FBAT program to test for transmission disequilibrium and further generated pseudo-sibling controls for comparisons to the cases. The FcγRIIA-131H variant showed an association with KD (p = 0.001) with ORadditive = 1.51 [1.16–1.96], p = 0.002) for the primary combined population, which persisted in both Caucasian (p = .04) and Asian (p = .01) subgroups and is consistent with the recent genome-wide association study. We also identified over-transmission of FcγRIIIB-NA1 among IVIG non-responders (p = 0.0002), and specifically to Caucasian IVIG non-responders (p = 0.007). Odds ratios for overall and Caucasian non-responders were respectively 3.67 [1.75–7.66], p = 0.0006 and 3.60 [1.34–9.70], p = 0.01. Excess NA1 transmission also occurred to KD with CAD (ORadditive = 2.13 [1.11–4.0], p = 0.02).
A common variation in FcγRIIA is associated with increased KD susceptibility. The FcγRIIIB-NA1, which confers higher affinity for IgG compared to NA2, is a determining factor for treatment response. These activating FcγRs play an important role in KD pathogenesis and mechanism of IVIG anti-inflammatory.
PMCID: PMC3444514  PMID: 22565545
coronary disease; pediatrics; Kawasaki disease; IVIG treatment response; FcγR
8.  Functional FcγRIIB Gene Variants Influence Intravenous Immunoglobulin (IVIG) Response in Kawasaki Disease (KD) Patients 
Capsule Summary
In Kawasaki Disease patients, the authors show associations between high-dose intravenous immunoglobulin (IVIG) response and a polymorphism in the FCγRIIB. This provides basis for defining the IVIG regulatory mechanisms and pharmacogenomic approach to IVIG therapy.
PMCID: PMC3444515  PMID: 21601260
Kawasaki disease; IVIG treatment response; FcγR
9.  Human balanced translocation and mouse gene inactivation implicate Basonuclin 2 in distal urethral development 
We studied a man with distal hypospadias, partial anomalous pulmonary venous return, mild limb-length inequality and a balanced translocation involving chromosomes 9 and 13. To gain insight into the etiology of his birth defects, we mapped the translocation breakpoints by high-resolution comparative genomic hybridization (CGH), using chromosome 9- and 13-specific tiling arrays to analyze genetic material from a spontaneously aborted fetus with unbalanced segregation of the translocation. The chromosome 13 breakpoint was ∼400 kb away from the nearest gene, but the chromosome 9 breakpoint fell within an intron of Basonuclin 2 (BNC2), a gene that encodes an evolutionarily conserved nuclear zinc-finger protein. The BNC2/Bnc2 gene is abundantly expressed in developing mouse and human periurethral tissues. In all, 6 of 48 unrelated subjects with distal hypospadias had nine novel nonsynonymous substitutions in BNC2, five of which were computationally predicted to be deleterious. In comparison, two of 23 controls with normal penile urethra morphology, each had a novel nonsynonymous substitution in BNC2, one of which was predicted to be deleterious. Bnc2−/− mice of both sexes displayed a high frequency of distal urethral defects; heterozygotes showed similar defects with reduced penetrance. The association of BNC2 disruption with distal urethral defects and the gene's expression pattern indicate that it functions in urethral development.
PMCID: PMC3083624  PMID: 21368915
basonuclin 2; hypospadias; birth defects; urethra
10.  Viral Endomyocardial Infection is an Independent Predictor and Potentially Treatable Risk Factor for Graft Loss and Coronary Vasculopathy in Pediatric Cardiac Transplant Recipients 
Evaluate the outcome and prevalence of viral endomyocardial infection after cardiac transplantation.
Viral myocardial infection causes heart failure, but its role after cardiac transplantation is unclear. We hypothesized that viral infection of the cardiac allograft reduces graft survival.
Between 6/1999 and 11/2004, 94 pediatric cardiac transplant patients were screened for the presence of viral genome in serial endomyocardial biopsies (EMBs) using PCR assays. Graft loss, advanced transplant coronary artery disease (TCAD) and acute rejection (AR) were compared in the PCR-positive (PCR+) (n=37) and PCR-negative (PCR−) (n=57) groups, using time dependent Kaplan-Meier and Cox regression analyses. From 11/2002 to 11/2004, intravenous immunoglobulin therapy (IVIG) was administered to patients with PCR+ EMBs. The outcomes of the IVIG-treated, PCR+ patients (n=20) were compared with IVIG-untreated, PCR+ patients (n=17).
Viral genomes were detected in EMBs from 37 (39%) patients; parvovirus B19, adenovirus, & EBV were the most common. The `PCR+ group' (n=37, 25% graft loss at 2.4 years) had decreased graft survival (p<0.001) compared to the `PCR- group' (n=57, 25% graft loss at 8.7 years) and developed advanced TCAD prematurely (p=0.001). The number of AR episodes was similar in both groups. On multivariate analysis, presence of viral genome was an independent risk factor for graft loss (relative risk 4.2, p=0.015). The time to advanced TCAD after becoming PCR+ was longer in the IVIG-treated patients (p=0.03), with a trend towards improved graft survival (p=0.06).
Viral endomyocardial infection is an independent predictor of graft loss in pediatric cardiac transplant recipients. This effect appears to be mediated through premature development of advanced TCAD. IVIG therapy in this subgroup may improve survival and merits further investigation.
PMCID: PMC2963018  PMID: 20688214
Cardiac Transplantation; Virus; Outcome; Graft Vasculopathy; TCAD
Detection of viral genome in rejecting cardiac transplant patients has been reported, with coxsackievirus and adenovirus causing premature graft failure. Recently, parvovirus B19 (PVB19) genome in myocardial samples has been increasingly reported but its role in cardiac pathology and effect on transplant graft survival are unknown. The objectives were to determine if changes in the viruses identified in the myocardium represent an epidemiologic shift in viral myocardial disease and whether PVB19 adversely affects transplant graft survival.
From 9/2002 to 12/2005, 99 children (3 weeks-18 years) with heart transplants had endomyocardial biopsies evaluated for the presence of viral genome utilizing nested PCR. Cellular rejection was assessed by histology of biopsies, while transplant coronary artery disease (TCAD) was diagnosed by coronary angiography or histopathology.
Seven hundred biopsies were evaluated from 99 patients; 121 biopsies had viral genome with 100 (82.6%) positive for PVB19, 24 for Epstein-Barr virus (EBV; 7 positive for PVB19 and EBV), 3 for CMV and 1 for adenovirus. Presence of PVB19 genome did not correlate with rejection score, nor did higher viral copy number. Children with persistent PVB19 infection (>6 months; n=20), had early development of advanced TCAD (p<0.001).
PVB19 is currently the predominant virus detected in heart transplant surveillance biopsies, possibly representing an epidemiologic shift. While cellular rejection does not correlate with the presence or quantity of PVB19 genome in the myocardium, children with chronic PVB19 infection have increased risk for earlier TCAD, supporting the hypothesis that PVB19 negatively affects graft survival.
PMCID: PMC2902647  PMID: 20456978
12.  Nebulette Mutations are Associated with Dilated Cardiomyopathy and Endocardial Fibroelastosis 
Four variants (K60N, Q128R, G202R and A592E) in the nebulette gene (NEBL) were identified in patients with dilated cardiomyopathy (DCM) and endocardial fibroelastosis (EFE). We sought to determine if these mutations cause cardiomyopathy.
Nebulette aligns thin filaments and connects them with the myocardial Z-disk.
We produced transgenic mice with cardiac-restricted over-expression of human wild-type (WT) or mutant nebulette. Chimera and transgenic mice were examined at 4, 6 and 12 months of age by echocardiography and cardiac MRI. The hearts from embryos and adult mice were assessed by histopathologic, immunohistochemical, ultrastructural and protein analyses. Rat H9C2 cardiomyoblasts with transient expression of nebulette underwent cyclic mechanical strain.
We identified lethal cardiac structural abnormalities in mutant embryonic hearts (K60N and Q128R). Founders of the mutant mice lines developed DCM with severe heart failure. An irregular localization pattern for nebulette and impaired desmin expression was noted in the proband and chimera Q128R mice. Mutant G202R and A592E mice exhibited left ventricular dilation and impaired cardiac function accompanied with the specific changes in I-band or Z-disk proteins by 6 months of age, respectively. The mutations modulated distribution of nebulette in the sarcomere and the Z-disks during stretch of H9C2 cells.
NEBL is a new susceptibility gene for EFE and DCM. Different mutations in nebulette trigger specific mechanisms converging to a common pathological cascade leading to EFE and DCM.
PMCID: PMC2957670  PMID: 20951326
nebulette; dilated cardiomyopathy; endocardial fibroelastosis; Z-disk
13.  ANKRD1, the Gene Encoding Cardiac Ankyrin Repeat Protein, Is a Novel Dilated Cardiomyopathy Gene 
We evaluated ankyrin repeat domain 1 (ANKRD1), the gene encoding cardiac ankyrin repeat protein (CARP), as a novel candidate gene for dilated cardiomyopathy (DCM) through mutation analysis of a cohort of familial or idiopathic DCM patients, based on the hypothesis that inherited dysfunction of mechanical stretch-based signaling is present in a subset of DCM patients.
CARP, a transcription coinhibitor, is a member of the titin-N2A mechanosensory complex and translocates to the nucleus in response to stretch. It is up-regulated in cardiac failure and hypertrophy and represses expression of sarcomeric proteins. Its overexpression results in contractile dysfunction.
In all, 208 DCM patients were screened for mutations/variants in the coding region of ANKRD1 using polymerase chain reaction, denaturing high-performance liquid chromatography, and direct deoxyribonucleic acid sequencing. In vitro functional analyses of the mutation were performed using yeast 2-hybrid assays and investigating the effect on stretch-mediated gene expression in myoblastoid cell lines using quantitative real-time reverse transcription–polymerase chain reaction.
Three missense heterozygous ANKRD1 mutations (P105S, V107L, and M184I) were identified in 4 DCM patients. The M184I mutation results in loss of CARP binding with Talin 1 and FHL2, and the P105S mutation in loss of Talin 1 binding. Intracellular localization of mutant CARP proteins is not altered. The mutations result in differential stretch-induced gene expression compared with wild-type CARP.
ANKRD1 is a novel DCM gene, with mutations present in 1.9% of DCM patients. The ANKRD1 mutations may cause DCM as a result of disruption of the normal cardiac stretch-based signaling.
PMCID: PMC2915893  PMID: 19608030
DCM; CARP; ANKRD1; mutations
15.  Mutations in the human δ-sarcoglycan gene in familial and sporadic dilated cardiomyopathy 
Journal of Clinical Investigation  2000;106(5):655-662.
Dilated cardiomyopathy (DCM) is a major cause of morbidity and mortality. Two genes have been identified for the X-linked forms (dystrophin and tafazzin), whereas three other genes (actin, lamin A/C, and desmin) cause autosomal dominant DCM; seven other loci for autosomal dominant DCM have been mapped but the genes have not been identified. Hypothesizing that DCM is a disease of the cytoskeleton and sarcolemma, we have focused on candidate genes whose products are found in these structures. Here we report the screening of the human δ-sarcoglycan gene, a member of the dystrophin-associated protein complex, by single-stranded DNA conformation polymorphism analysis and by DNA sequencing in patients with DCM. Mutations affecting the secondary structure were identified in one family and two sporadic cases, whereas immunofluorescence analysis of myocardium from one of these patients demonstrated significant reduction in δ-sarcoglycan staining. No skeletal muscle disease occurred in any of these patients. These data suggest that δ-sarcoglycan is a disease-causing gene responsible for familial and idiopathic DCM and lend support to our “final common pathway” hypothesis that DCM is a cytoskeletalopathy.
PMCID: PMC381284  PMID: 10974018

Results 1-15 (15)