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1.  Processes and factors involved in decisions regarding return of incidental genomic findings in research 
Studies have begun exploring whether researchers should return incidental findings in genomic studies, and if so, which findings should be returned; however, how researchers make these decisions— the processes and factors involved—has remained largely unexplored.
We interviewed 28 genomics researchers in-depth about their experiences and views concerning the return of incidental findings.
Researchers often struggle with questions concerning which incidental findings to return and how to make those decisions. Multiple factors shape their views, including information about the gene variant (e.g., pathogenicity and disease characteristics), concerns about participants’ well-being and researcher responsibility, and input from external entities. Researchers weigh the evidence, yet they face conflicting pressures, with relevant data frequently being unavailable. Researchers vary in who they believe should decide: participants, principal investigators, institutional review boards, and/or professional organizations. Contextual factors can influence these decisions, including policies governing return of results by institutions and biobanks and the study design. Researchers vary in desires for: guidance from institutions and professional organizations, changes to current institutional processes, and community- wide genetics education.
These data, the first to examine the processes by which researchers make decisions regarding the return of genetic incidental findings, highlight several complexities involved and have important implications for future genetics research, policy, and examinations of these issues.
PMCID: PMC3966970  PMID: 24071801
benefits and risks; decision making; genome sequencing; incidental findings; return of results
2.  High Prevalence of BRCA1 and BRCA2 Germline Mutations with Loss of Heterozygosity in a Series of Resected Pancreatic Adenocarcinoma and Other Neoplastic Lesions 
Pancreatic ductal adenocarcinoma (PDAC) is associated with the breast ovarian cancer syndrome (BRCA1/BRCA2) mutations. It is unknown if this association is causal.
Experimental Design
This is a single-site study of patients who underwent surgical pancreatic tumor resection and self-identified as Ashkenazi Jewish. DNA from normal pancreatic tissue was genotyped for the three Ashkenazi Jewish BRCA1/2 founder mutations BRCA1 185delAG, BRCA1 5382insC, and BRCA2 6174delT, and loss of heterozygosity (LOH) was determined by sequencing DNA from microdissected tumor. When additional tumor tissue was available, p53 immunohistochemistry (IHC) was conducted.
Thirty-seven patients underwent surgery for PDAC, seven for intraductal papillary mucinous neoplasm (IPMN), and 19 for other diseases. A high prevalence of BRCA1/2 mutations was found in the surgical cohort (12/63; 19.0%; P < 0.001), PDAC cohort (8/37; 21.6%; P < 0.001), and IPMN cohort (2/7; 28.6%; P =.01) compared with published control mutation frequency. A high prevalence of BRCA1 185delAG (8.1%; P < 0.001) and BRCA2 6174delT (10.8%; P < 0.001) in Ashkenazi Jewish patients with PDAC was shown. BRCA1/2 LOH was found in 2 of 4 BRCA1-associated PDACs and 3 of 4 BRCA2-associated PDACs. Positive p53 IHC was found in 5 of 8 BRCA1/2 PDACs.
We show a high prevalence of BRCA1/2 mutations with LOH in an Ashkenazi Jewish cohort of surgically resected PDAC and neoplastic lesions, suggesting that these germline mutations are causal in selected individuals.
PMCID: PMC3959126  PMID: 23658460
3.  An Overview of Mongenic and Syndromic Obesities in Humans 
Pediatric blood & cancer  2011;58(1):122-128.
Obesity is increasing in prevalence in the United States with over 65% of adults considered overweight and 16% of children with BMI > 95 percentile. The heritability of obesity is estimated between 40 and 70%, but the genetics of obesity for most individuals are complex and involve the interaction of multiple genes and environment. There are however several syndromic and non-syndromic forms of obesity that are monogenic and oligogenic that provide insight into the underlying molecular control of food intake and the neural networks that control ingestive behavior and satiety to regulate body weight and which may interact with treatment exposures to produce or exacerbate obesity in childhood cancer survivors.
PMCID: PMC3215910  PMID: 21994130
leptin; leptin receceptor; melanocortin 4 receptor; Prader Willi syndrome; Bardet-Biedl syndrome; Alstrom syndrome; 16p11.2 deletion
4.  Variants in GATA4 Are a Rare Cause of Familial and Sporadic Congenital Diaphragmatic Hernia 
Human genetics  2012;132(3):285-292.
Congenital diaphragmatic hernia (CDH) is characterized by incomplete formation of the diaphragm, occurring as either an isolated defect or in association with other anomalies. Genetic factors including aneuploidies and copy number variants are important in the pathogenesis of many cases of CDH, but few single genes have been definitively implicated in human CDH. In this study, we used whole exome sequencing (WES) to identify a paternally inherited novel missense GATA4 variant (c. 754C>T, p. R252W) in a familial case of CDH with incomplete penetrance. Phenotypic characterization of the family included magnetic resonance imaging (MRI) of the chest and abdomen demonstrating asymptomatic defects in the diaphragm in the two “unaffected” missense variant carriers. Screening 96 additional CDH patients identified a de novo heterozygous GATA4 variant (c.848G>A; p.R283H) in a non-isolated CDH patient. In summary, GATA4 is implicated in both familial and sporadic CDH, and our data suggests that WES may be a powerful tool to discover rare variants for CDH.
PMCID: PMC3570587  PMID: 23138528
Congenital diaphragmatic Hernia (CDH); whole exome sequencing (WES); incomplete penetrance; missense variant; GATA4
5.  Whole-exome sequencing identifies novel LEPR mutations in individuals with severe early onset obesity 
Obesity (Silver Spring, Md.)  2013;22(2):576-584.
Obesity is a major public health problem that increases risk for a broad spectrum of co-morbid conditions. Despite evidence for a strong genetic contribution to susceptibility to obesity, previous efforts to discover the relevant genes using positional cloning have failed to account for most of the apparent genetic risk variance.
Design and Methods
Deploying a strategy combining analysis of exome sequencing data in extremely obese members of four consanguineous families with segregation analysis, we screened for causal genetic variants. Filter-based analysis and homozygosity mapping were used to identify and prioritize putative functional variants.
We identified two novel frameshift mutations in the Leptin Receptor (LEPR) in two of the families.
These results provide proof-of-principle that whole-exome sequencing of families segregating for extreme obesity can identify causal pathogenic mutations. The methods described here can be extended to additional families segregating for extreme obesity and should enable the identification of mutations in novel genes that predispose to obesity.
PMCID: PMC3791145  PMID: 23616257
genetics of obesity; leptin receptor
6.  Cancer Genetic Counselor Information Needs for Risk Communication: A Qualitative Evaluation of Interview Transcripts 
Journal of personalized medicine  2013;3(3):10.3390/jpm3030238.
Personalized medicine is a model of healthcare that is predictive, personalized, preventive and participatory (“P4 Medicine”). Genetic counselors are an ideal group to study when designing tools to support cancer P4 Medicine activities more broadly. The goal for this work was to gain a better understanding of the information cancer genetic counselors seek from their patients to facilitate effective information exchange for discussing risk. This was an analysis of a qualitative data set from interviews of eight cancer genetic counselors, recruited from three institutions. Genetic counselors at each site were interviewed using a semi-structured, open-ended questionnaire. A selective coding approach was used to determine major themes associated with genetic counseling information needs for communicating risk. We generated a model for understanding categories of genetic counseling information needs to support risk communication activities. Common activities for risk communication included risk assessment and tailoring communication. Categories of information needs included: (a) clinical patient characteristics, (b) social and cognitive patient characteristics and (c) patient motivation and goals for the genetic counseling session. A logical next step is for this model to inform the design of software systems for pre-visit patient planning and delivering just-in-time educational information to facilitate cancer risk communication activities.
PMCID: PMC3865845  PMID: 24358447
cancer genetic counseling; information exchange; information needs; needs assessment
7.  Researchers’ views on return of incidental genomic research results: qualitative and quantitative findings 
Comprehensive genomic analysis including exome and genome sequencing is increasingly being utilized in research studies, leading to the generation of incidental genetic findings. It is unclear how researchers plan to deal with incidental genetic findings.
We conducted a survey of the practices and attitudes of 234 members of the US genetic research community and performed qualitative semistructured interviews with 28 genomic researchers to understand their views and experiences with incidental genetic research findings.
We found that 12% of the researchers had returned incidental genetic findings, and an additional 28% planned to do so. A large majority of researchers (95%) believe that incidental findings for highly penetrant disorders with immediate medical implications should be offered to research participants. However, there was no consensus on returning incidental results for other conditions varying in penetrance and medical actionability. Researchers raised concerns that the return of incidental findings would impose significant burdens on research and could potentially have deleterious effects on research participants if not performed well. Researchers identified assistance needed to enable effective, accurate return of incidental findings.
The majority of the researchers believe that research participants should have the option to receive at least some incidental genetic research results.
PMCID: PMC3823712  PMID: 23807616
genomic results; incidental findings; return of results; secondary findings; whole-exome sequencing
8.  Novel Association of Early Onset Hepatocellular Carcinoma with Transaldolase Deficiency 
JIMD Reports  2013;12:121-127.
We evaluated a family with a 16-month-old boy with cirrhosis and hepatocellular carcinoma and his 30-month-old brother with cirrhosis. After failing to identify a diagnosis after routine metabolic evaluation, we utilized a combination of RNA-Seq and whole exome sequencing to identify a novel homozygous p.Ser171Phe Transaldolase (TALDO1) variant in the proband, his brother with cirrhosis, as well as a clinically asymptomatic older 8-year-old brother. Metabolite analysis and enzymatic testing of TALDO1 demonstrated elevated ribitol, sedoheptitol, and sedoheptulose-7P, and lack of activity of TALDO1 in the three children homozygous for the p.Ser171Phe mutation. Our findings expand the phenotype of transaldolase deficiency to include early onset hepatocellular carcinoma in humans and demonstrate that, even within the same family, individuals with the same homozygous mutation demonstrate a wide range of phenotypes.
PMCID: PMC3897795  PMID: 24097415
9.  De novo copy number variants are associated with congenital diaphragmatic hernia 
Journal of medical genetics  2012;49(10):650-659.
Congenital diaphragmatic hernia (CDH) is a common birth defect with significant morbidity and mortality. Although the etiology of CDH remains poorly understood, studies from animal models and patients with CDH suggest that genetic factors play an important role in the development of CDH. Chromosomal anomalies have been reported in CDH.
In this study, the authors investigate the frequency of chromosomal anomalies and copy number variants in 256 parent-child trios of CDH using clinical conventional cytogenetic and microarray analysis. The authors also selected a set of CDH related training genes to prioritize the genes in those segmental aneuploidies and identified the genes and gene sets that may contribute to the etiology of CDH.
The authors identified chromosomal anomalies in 16 patients (6.3 %) of the series including 3 aneuploidies, 2 unbalanced translocation, and 11 patients with de novo CNVs ranging in size from 95 kb to 104.6 Mb. The authors prioritized the genes in the CNV segments and identified KCNA2, LMNA, CACNA1S, MYOG, HLX, LBR, AGT, GATA4, SOX7, HYLS1, FOXC1, FOXF2, PDGFA, FGF6, COL4A1, COL4A2, HOMER2, BNC1, BID, and TBX1 as genes that may be involved in diaphragm development. Gene enrichment analysis identified the most relevant gene ontology (GO) categories as those involved in tissue development (p=4.4×10−11) or regulation of multicellular organismal processes (p=2.8×10−10) and “receptor binding” (p = 8.7×10−14) and “DNA binding transcription factor activity” (p= 4.4×10−10).
Our findings support the role of chromosomal anomalies in CDH and provide a set of candidate genes including FOXC1, FOXF2, PDGFA, FGF6, COL4A1, COL4A2, SOX7,BNC1, BID, and TBX1 for further analysis in CDH.
PMCID: PMC3696999  PMID: 23054247
Congenital diaphragmatic hernia (CDH); copy number variant (CNV); chromosomal anomalies; gene priority; gene enrichment
10.  Intragenic Deletion as a Novel Type of Mutation in Wolman Disease 
Molecular genetics and metabolism  2011;104(4):703-705.
Two clinically distinct disorders, Wolman disease (WD) and cholesteryl ester storage disease (CESD), are allelic autosomal recessive disorders caused by different mutations in lysosomal acid lipase (LIPA) which encodes for an essential enzyme involved in the hydrolysis of intracellular cholesteryl esters and triglycerides. We describe a case of lysosomal acid lipase deficiency in an infant with WD and report on a novel mutation type, intragenic deletion.
PMCID: PMC3781170  PMID: 21963785
Wolman disease; LIPA
11.  Fat discrimination: A phenotype with potential implications for studying fat intake behaviors and obesity 
Physiology & behavior  2011;105(2):470-475.
Variations in fat preference and intake across humans are poorly understood in part because of difficulties in studying this behavior. The objective of this study was to develop a simple procedure to assess fat discrimination, the ability to accurately perceive differences in the fat content of foods, and assess the associations between this phenotype and fat ingestive behaviors and adiposity. African-American adults (n=317) were tested for fat discrimination using 7 forced choice same/different tests with Italian salad dressings that ranged in fat-by-weight content from 5–55%. Performance on this procedure was determined by tallying the number of trials in which a participant correctly identified the pair of samples as “same” or “different” across all test pairs (ranging from 1–7). Individuals who received the lowest scores on this task (≤3 out of 7 correct) were classified as fat non-discriminators (n=33) and those who received the highest scores (7 out of 7 correct) were classified as fat discriminators (n=59). These 2 groups were compared for the primary outcome variables: reported food intake, preferences, and adiposity. After adjusting for BMI, sex, age, and dietary restraint and disinhibition, fat non-discriminators reported greater consumption of both added fats and reduced fat foods (p<0.05 for both). Fat non-discriminators also had greater abdominal adiposity compared to fat discriminators (p<0.05). Test-retest scores performed in a subset of participants (n=40) showed moderate reliability of the fat discrimination test (rho=0.53;p<0.01). If these results are replicated, fat discrimination may serve as clinical research tool to identify participants who are at risk for obesity and other chronic diseases due to increased fat intake.
PMCID: PMC3743656  PMID: 21925524
oral fat perception; fat intake; obesity
12.  Common Variants in the CD36 Gene Are Associated With Oral Fat Perception, Fat Preferences, and Obesity in African Americans 
Obesity (Silver Spring, Md.)  2012;20(5):1066-1073.
Animal studies show that CD36, a fatty acid translocase, is involved in fat detection and preference, but these findings have not been reported in humans. The objective of this study was to determine whether human genetic variation in 5 common CD36 polymorphisms is associated with oral fat perception of Italian salad dressings, self-reported acceptance of high-fat foods and obesity in African-American adults (n = 317). Ratings of perceived oiliness, fat content, and creaminess were assessed on a 170-mm visual analogue scale (VAS) in response to salad dressings that were 5%, 35%, and 55% fat-by-weight content. Acceptance of added fats and oils and high-fat foods was self-reported and anthropometric measures were taken in the laboratory. DNA was isolated from saliva and genotyped at 5 CD36 polymorphisms. Three polymorphisms, rs1761667, rs3840546, and rs1527483 were associated with the outcomes. Participants with the A/A genotype at rs1761667 reported greater perceived creaminess, regardless of the fat concentration of the salad dressings (P < 0.01) and higher mean acceptance of added fats and oils (P = 0.02) compared to those with other genotypes at this site. Individuals who had C/T or T/T genotypes at rs1527483 also perceived greater fat content in the salad dressings, independent of fat concentration (P = 0.03). BMI and waist circumference were higher in participants who were homozygous for a deletion (D/D) at rs3840546, compared to I/D or D/D individuals (P < 0.001), but only 2 D/D individuals were tested, so this finding needs replication. This is the first study to demonstrate an association between common variants in CD36 and fat ingestive behaviors in humans.
PMCID: PMC3743670  PMID: 22240721
13.  Genetics and Genomics of Pulmonary Arterial Hypertension 
Pulmonary arterial hypertension (PAH) is a rare disorder that may be hereditable (HPAH), idiopathic (IPAH), or associated with either drug-toxin exposures or other medical conditions. Familial cases have long been recognised and are usually due to mutations in Bone Morphogenetic Protein Receptor type 2 gene (BMPR2), or, much less commonly, 2 other members of the transforming growth factor-beta superfamily, Activin-like Kinase-Type I (ALK1) and Endoglin (ENG), which are associated with hereditary hemorrhagic telangiectasia. In addition, approximately 20% of patients with IPAH carry mutations in BMPR2. We provide a summary of BMPR2 mutations associated with IPAH/HPAH, most of which are unique to each family and are presumed to result in loss of function. We review the finding of missense variants and variants of unknown significance in BMPR2 in IPAH/HPAH, fenfluramine exposure, and PAH associated with congenital heart disease. Clinical testing for BMPR2 mutations is available and may be offered to HPAH and IPAH patients but should be preceded by genetic counselling, since lifetime penetrance is only 10%–20%, and there are currently no known effective preventative measures. Identification of a familial mutation can be valuable in reproductive planning and identifying family members who are not mutation carriers and thus will not require lifelong surveillance. With advances in genomic technology and with international collaborative efforts, genome-wide association studies will be conducted to identify additional genes for HPAH, genetic modifiers for BMPR2 penetrance, and genetic susceptibility to IPAH. In addition, collaborative studies of BMPR2 mutation carriers should enable identification of environmental modifiers, biomarkers for disease development and progression, and surrogate markers for efficacy end points in clinical drug development, thereby providing an invaluable resource for trials of PAH prevention.
PMCID: PMC3725550  PMID: 19555857
Pulmonary Arterial Hypertension; Genetics; Genomics
14.  Polymorphism in the Angiotensin II Type 1 Receptor (AGTR1) is Associated with Age at Diagnosis in Pulmonary Arterial Hypertension 
Pulmonary arterial hypertension (PAH) is a rare, lethal disease associated with single gene disorders, connective tissue disease, exposures to anorexigens, and often idiopathic etiology. There is evidence that genes can modify the risk of PAH: 1) monogenic disorders associated with PAH are incompletely penetrant, and 2) not all patients with associated conditions at increased risk for PAH develop the disease. The renin angiotensin aldosterone system (RAAS) provides a set of candidate genes that could modulate pulmonary vascular disease similar to its effects on renal and peripheral vasculature.
We studied 247 subjects with PAH (177 subjects with idiopathic PAH (IPAH); 63 subjects with PAH/connective tissue disease (CTD); and 7 subjects with PAH associated with anorexigens). Subjects were genotyped for five common polymorphisms in angiotensinogen (AGT), angiotensin converting enzyme (ACE), cardiac chymase A (CMA1), angiotensin II type 1 receptor (AGTR1) and aldosterone synthase (CYP11B2). Genotypes were tested for associations with age at diagnosis, hemodynamic parameters at diagnosis, and/or response to acute pulmonary vasodilator testing at diagnosis.
Associations were demonstrated for AGTR1 and age at diagnosis in IPAH (p=0.005). Homozygotes for the C1166 allele (n=13) were associated with an age at diagnosis 26 years later than subjects with A/A (n=139) or A/C (n=90) genotypes. No associations were demonstrated for AGT, ACE, CMA1, or CYP11B2.
The 1166C polymorphism in AGTR1 appears to be associated with a later age at diagnosis in IPAH suggesting that this pathway could be involved in the biologic variability that is known to occur in PAH.
PMCID: PMC3712279  PMID: 19332265
genetic; pulmonary hypertension; renin; angiotensin; aldosterone
15.  Induced pluripotent stem cells used to reveal drug actions in a long QT syndrome family with complex genetics 
Understanding the basis for differential responses to drug therapies remains a challenge despite advances in genetics and genomics. Induced pluripotent stem cells (iPSCs) offer an unprecedented opportunity to investigate the pharmacology of disease processes in therapeutically and genetically relevant primary cell types in vitro and to interweave clinical and basic molecular data. We report here the derivation of iPSCs from a long QT syndrome patient with complex genetics. The proband was found to have a de novo SCN5A LQT-3 mutation (F1473C) and a polymorphism (K897T) in KCNH2, the gene for LQT-2. Analysis of the biophysics and molecular pharmacology of ion channels expressed in cardiomyocytes (CMs) differentiated from these iPSCs (iPSC-CMs) demonstrates a primary LQT-3 (Na+ channel) defect responsible for the arrhythmias not influenced by the KCNH2 polymorphism. The F1473C mutation occurs in the channel inactivation gate and enhances late Na+ channel current (INaL) that is carried by channels that fail to inactivate completely and conduct increased inward current during prolonged depolarization, resulting in delayed repolarization, a prolonged QT interval, and increased risk of fatal arrhythmia. We find a very pronounced rate dependence of INaL such that increasing the pacing rate markedly reduces INaL and, in addition, increases its inhibition by the Na+ channel blocker mexiletine. These rate-dependent properties and drug interactions, unique to the proband’s iPSC-CMs, correlate with improved management of arrhythmias in the patient and provide support for this approach in developing patient-specific clinical regimens.
PMCID: PMC3536519  PMID: 23277474
16.  Enalapril in Infants with Single Ventricle: Results of a Multicenter Randomized Trial 
Circulation  2010;122(4):333-340.
Angiotensin converting enzyme (ACE) inhibitor therapy improves clinical outcome and ventricular function in adults with heart failure. Infants with single ventricle physiology have poor growth and are at risk for abnormalities in ventricular systolic and diastolic function. The ability of ACE inhibitor therapy to preserve ventricular function and improve somatic growth and outcomes in these infants is unknown.
Methods and Results
The Pediatric Heart Network conducted a double-blind trial involving 230 infants with single ventricle physiology randomized to receive enalapril (target dose 0.4 mg/kg/day) or placebo and followed to 14 months of age. The primary endpoint was weight-for-age z-score at 14 months. The primary analysis was intention-to-treat. A total of 185 infants completed the study. There were 24 and 21 withdrawals/deaths in the enalapril and placebo groups, respectively (P=0.74). Weight-for-age z-score was not different between the enalapril and placebo groups (mean±standard error, −0.62±0.13 vs. −0.42 ±0.13, P=0.28). There were no significant group differences in height-for-age z-score, Ross heart failure class, brain natriuretic peptide concentration, Bayley scores of infant development, or ventricular ejection fraction. The incidence of death or transplantation was 13% and did not differ between groups. Serious adverse events occurred in 88 patients in the enalapril group and 87 patients in the placebo group.
Administration of enalapril to infants with single ventricle physiology in the first year of life did not improve somatic growth, ventricular function, or heart failure severity. The results of this randomized trial do not support the routine use of enalapril in this population.
Clinical Trials Registration Information NCT00113087
PMCID: PMC3692364  PMID: 20625111
trials; angiotensin; heart defects; congenital; heart failure; pediatrics
17.  iPSC-derived β cells model diabetes due to glucokinase deficiency 
The Journal of Clinical Investigation  2013;123(7):3146-3153.
Diabetes is a disorder characterized by loss of β cell mass and/or β cell function, leading to deficiency of insulin relative to metabolic need. To determine whether stem cell–derived β cells recapitulate molecular-physiological phenotypes of a diabetic subject, we generated induced pluripotent stem cells (iPSCs) from subjects with maturity-onset diabetes of the young type 2 (MODY2), which is characterized by heterozygous loss of function of the gene encoding glucokinase (GCK). These stem cells differentiated into β cells with efficiency comparable to that of controls and expressed markers of mature β cells, including urocortin-3 and zinc transporter 8, upon transplantation into mice. While insulin secretion in response to arginine or other secretagogues was identical to that in cells from healthy controls, GCK mutant β cells required higher glucose levels to stimulate insulin secretion. Importantly, this glucose-specific phenotype was fully reverted upon gene sequence correction by homologous recombination. Our results demonstrate that iPSC-derived β cells reflect β cell–autonomous phenotypes of MODY2 subjects, providing a platform for mechanistic analysis of specific genotypes on β cell function.
PMCID: PMC3696557  PMID: 23778137
18.  Severe Dilated Cardiomyopathy in a Patient with Myotonic Dystrophy Type 2 and Homozygous Repeat Expansion in ZNF9 
PMCID: PMC3678523  PMID: 22587749
Dilated cardiomyopathy; Myotonic dystrophy
19.  Mutations in ZIC3 and ACVR2B are a common cause of heterotaxy and associated cardiovascular anomalies 
Cardiology in the young  2011;22(2):194-201.
Heterotaxy syndrome is caused by left-right asymmetry disturbances and is associated with abnormal lateralization of the abdominal and thoracic organs. The heart is frequently involved and the severity of the abnormality usually determines the outcome.
Direct sequence analysis of the coding sequence of genes including Zinc Finger Protein of the Cerebellum 3, Left Right Determine Factor 2, Activin A Receptor Type IIB, and Cryptic was performed in 47 subjects with laterality defects and congenital cardiac disease.
31 (66%) of these subjects had atrioventricular septal defects, 34 (72%) had abnormal systemic venous return, 25 (53%) had transposed or malposed great arteries, and 20 (43%) had pulmonary venous abnormalities. Two novel genetic changes were identified in zinc finger protein of the cerebellum 3 and these variants were not presented in 100 ethnically matched control samples. One previously reported missense mutation in activin A receptor type IIB was identified in 2 unrelated subjects. The genetic changes identified in this study are all located in conserved regions and are predicted to affect protein function in left-right axis formation and cardiovascular development.
Mutations in Zinc Finger Protein of the Cerebellum 3 and Activin A Receptor Type IIB were identified in 4/47 subjects with heterotaxy syndrome for a yield of approximately 8.5%. Our results expand the mutation spectrum of monogenic heterotaxy syndrome with associated cardiac anomalies and suggest that there are other causes of heterotaxy yet to be identified.
PMCID: PMC3678527  PMID: 21864452
left-right asymmetry; congenital heart defect; LEFTYA; CFC1
20.  Identifying interdisciplinary research priorities to prevent and treat pediatric obesity in New York City 
It is well recognized that an interdisciplinary approach is essential in the development and implementation of solutions to address the current pediatric obesity epidemic. In two half-day meetings that included workshops and focus groups, faculty from diverse fields identified critically important research challenges and gaps to childhood obesity prevention. The purpose of this white paper is to describe the iterative, interdisciplinary process that unfolded in an academic health center setting with a specific focus on under-represented minority groups of Black and Hispanic communities, and to summarize the research challenges and gaps related to pediatric obesity which were identified in the process. Although the research challenges and gaps were developed in the context of an urban setting including high risk populations (the northern Manhattan communities of Washington Heights, Inwood, and Harlem), many of the issues raised are broadly applicable. The processes by which the group identified research gaps and methodological challenges that impede a better understanding of how to prevent and treat obesity in children has resulted in an increase in research and community outreach collaborations and interdisciplinary pursuit of funding opportunities across units within the academic health center and overall University.
PMCID: PMC3677023  PMID: 20718818
pediatric obesity prevention; interdisciplinary; research priorities
21.  Genetic Testing for Dilated Cardiomyopathy in Clinical Practice 
Journal of cardiac failure  2012;18(4):296-303.
Familial involvement is common in dilated cardiomyopathy (DCM) and >40 genes have been implicated in causing disease. However, the role of genetic testing in clinical practice is not well defined. We examined the experience of clinical genetic testing in a diverse DCM population to characterize the prevalence and predictors of gene mutations.
Methods and Results
We studied 264 unrelated adult and pediatric DCM index patients referred to 1 reference lab for clinical genetic testing. Up to 10 genes were analyzed (MYH7, TNNT2, TNNI3, TPM1, MYBPC3, ACTC, LMNA, PLN, TAZ, and LDB3), and 70% of patients were tested for all genes. The mean age was 26.6 ± 21.3 years, and 52% had a family history of DCM. Rigorous criteria were used to classify DNA variants as clinically relevant (mutations), variants of unknown clinical significance (VUS), or presumed benign. Mutations were found in 17.4% of patients, commonly involving MYH7, LMNA, or TNNT2 (78%). An additional 10.6% of patients had VUS. Genetic testing was rarely positive in older patients without a family history of DCM. Conversely in pediatric patients, family history did not increase the sensitivity of genetic testing.
Using rigorous criteria for classifying DNA variants, mutations were identified in 17% of a diverse group of DCM index patients referred for clinical genetic testing. The low sensitivity of genetic testing in DCM reflects limitations in both current methodology and knowledge of DCM-associated genes. However, if mutations are identified, genetic testing can help guide family management.
PMCID: PMC3666099  PMID: 22464770
Clinical genetics; heart failure; dilated cardiomyopathy; sarcomere genes; lamin A/C
22.  Copy number variants and infantile spasms: evidence for abnormalities in ventral forebrain development and pathways of synaptic function 
European Journal of Human Genetics  2011;19(12):1238-1245.
Infantile spasms (ISS) are an epilepsy disorder frequently associated with severe developmental outcome and have diverse genetic etiologies. We ascertained 11 subjects with ISS and novel copy number variants (CNVs) and combined these with a new cohort with deletion 1p36 and ISS, and additional published patients with ISS and other chromosomal abnormalities. Using bioinformatics tools, we analyzed the gene content of these CNVs for enrichment in pathways of pathogenesis. Several important findings emerged. First, the gene content was enriched for the gene regulatory network involved in ventral forebrain development. Second, genes in pathways of synaptic function were overrepresented, significantly those involved in synaptic vesicle transport. Evidence also suggested roles for GABAergic synapses and the postsynaptic density. Third, we confirm the association of ISS with duplication of 14q12 and maternally inherited duplication of 15q11q13, and report the association with duplication of 21q21. We also present a patient with ISS and deletion 7q11.3 not involving MAGI2. Finally, we provide evidence that ISS in deletion 1p36 may be associated with deletion of KLHL17 and expand the epilepsy phenotype in that syndrome to include early infantile epileptic encephalopathy. Several of the identified pathways share functional links, and abnormalities of forebrain synaptic growth and function may form a common biologic mechanism underlying both ISS and autism. This study demonstrates a novel approach to the study of gene content in subjects with ISS and copy number variation, and contributes further evidence to support specific pathways of pathogenesis.
PMCID: PMC3230360  PMID: 21694734
infantile spasms; autism; bioinformatics; copy number variation; deletion 1p36 syndrome
23.  Renin-Angiotensin-Aldosterone Genotype Influences Ventricular Remodeling in Infants with Single Ventricle 
Circulation  2011;123(21):2353-2362.
We investigated the effect of polymorphisms in the renin-angiotensin-aldosterone system (RAAS) genes on ventricular remodeling, growth, renal function and response to enalapril in infants with single ventricle.
Methods and Results
Single ventricle infants enrolled in a randomized trial of enalapril were genotyped for polymorphisms in 5 genes: angiotensinogen, angiotensin-converting enzyme, angiotensin II type 1 receptor, aldosterone synthase, and chymase. Alleles associated with RAAS upregulation were classified as risk alleles. Ventricular mass, volume, somatic growth, renal function using estimated glomerular filtration rate (eGFR), and response to enalapril were compared between patients with ≥2 homozygous risk genotypes (high-risk), and those with <2 homozygous risk genotypes (low-risk) at two time points - before the superior-cavopulmonary-connection (pre-SCPC) and at age 14 months. Of 230 trial subjects, 154 were genotyped: 38 were high-risk, 116 were low-risk. Ventricular mass and volume were elevated in both groups pre-SCPC. Ventricular mass and volume decreased and eGFR increased after SCPC in the low-risk (p<0.05) but not the high-risk group. These responses were independent of enalapril treatment. Weight and height z-scores were lower at baseline and height remained lower in the high-risk group at 14 months especially in those receiving enalapril (p<0.05).
RAAS-upregulation genotypes were associated with failure of reverse remodeling after SCPC surgery, less improvement in renal function, and impaired somatic growth, the latter especially in patients receiving enalapril. RAAS genotype may identify a high-risk subgroup of single ventricle patients who fail to fully benefit from volume unloading surgery. Follow-up is warranted to assess longterm impact.
Clinical Trial Registration
Clinical Identifier NCT00113087
PMCID: PMC3137902  PMID: 21576655
24.  Long QT syndrome due to a novel mutation in SCN5A: treatment with ICD placement at 1 month and left cardiac sympathetic denervation at 3 month of age 
We describe the case of a newborn with congenital long QT syndrome, with 2:1 AV block and frequent episodes of Torsades de Pointes (TdP) requiring placement of a dual chamber ICD at 33 days and 3.63 kg, the youngest and smallest patient, thus far reported. Long QT syndrome was diagnosed due to bradycardia in the newborn nursery, with frequent episodes of TdP. The patient was initially treated with magnesium and esmolol then given lidocaine which resulted in dramatic transient normalization of the QTc with 1:1 AV nodal conduction. An attempt to transition to oral sodium channel and beta blockade was unsuccessful. An ICD was placed and dual chamber pacing was initiated which facilitated the transition to an oral medical regimen and ultimate discharge from the hospital. Soon after placement of the ICD, genetic testing revealed a novel F1473C mutation in the SCN5A gene. Episodes of TdP continued and left stellate gangliectomy was performed at 3 months of age. At 30 months follow-up, the patient has occasional, self-limited episodes of TdP and has received rare, successful, and appropriate ICD shocks.
PMCID: PMC3332535  PMID: 19669871
Pediatric; Long QT Syndrome; SCN5A; Implantable cardioverter defibrillator; Sympathectomy
25.  Determinants of extracellular matrix remodelling are differentially expressed in paediatric and adult dilated cardiomyopathy 
European Journal of Heart Failure  2010;13(3):271-277.
The left ventricular phenotype of idiopathic dilated cardiomyopathy (DCM) can appear similar in paediatric and adult patients. However, the aetiology of paediatric DCM is usually idiopathic, and often leads an aggressive clinical course. A structural underpinning of DCM is extracellular matrix changes, which are determined by a balance between matrix metalloproteinases (MMPs) and tissue inhibitors of MMPs (TIMPs). This study tested the hypothesis that different MMP/TIMP profiles occur in paediatric and adult DCM patients.
Methods and results
Left ventricular samples from paediatric (age 9 ± 5 years; n = 10) and adult (age 62 ± 3 years; n = 20) DCM (at time of transplant) were subjected to an MMP/TIMP multiplex array and immunoassay in order to measure the MMP subclasses; collagenases (MMP-8, -13), gelatinases (MMP-2, -9), stromelysin/matrilysin (MMP-3, -7), membrane type (MT1-MMP), as well as for the four known TIMPs. MMP-8 and -9 levels increased by over 150% (P < 0.05), whereas MMP-3 and -7 levels decreased by over 30% (P < 0.05) in paediatric DCM when compared with adult DCM. TIMP-1 and -2 levels increased two-fold (P < 0.05), but TIMP-3 fell by 41% (P < 0.05) in paediatric DCM. Myocardial levels of specific interleukins (IL-1beta, IL-2, IL-8) were increased by approximately 50% in paediatric DCM.
These unique findings demonstrated that a specific MMP/TIMP profile occurs in paediatric DCM when compared with adult DCM, and that local cytokine induction may contribute to this process. These distinct differences in the determinants of myocardial matrix structure and function may contribute to the natural history of DCM in children.
PMCID: PMC3041467  PMID: 21147820
Cardiomyopathy; Extracellular matrix; Matrix metalloproteinase; Paediatrics

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