0
We're unable to sign you in at this time. Please try again in a few minutes.
Retry
We were able to sign you in, but your subscription(s) could not be found. Please try again in a few minutes.
Retry
There may be a problem with your account. Please contact the AMA Service Center to resolve this issue.
Contact the AMA Service Center:
Telephone: 1 (800) 262-2350 or 1 (312) 670-7827  *   Email: subscriptions@jamanetwork.com
Error Message ......
Review |

Genetic Epidemiology and Nonsyndromic Structural Birth Defects:  From Candidate Genes to Epigenetics FREE

Charlotte A. Hobbs, MD, PhD1; Shimul Chowdhury, PhD1; Mario A. Cleves, PhD1; Stephen Erickson, PhD1; Stewart L. MacLeod, PhD1; Gary M. Shaw, DPH2; Sanjay Shete, PhD3; John S. Witte, PhD4; Benjamin Tycko, MD, PhD5
[+] Author Affiliations
1Department of Pediatrics, University of Arkansas for Medical Sciences, College of Medicine, Little Rock
2Department of Pediatrics, Stanford University School of Medicine, Stanford, California
3Department of Epidemiology, University of Texas M. D. Anderson Cancer Center, Houston
4Department of Epidemiology and Biostatistics, University of California, San Francisco
5Department of Pathology and Cell Biology, Institute for Cancer Genetics, Columbia University Medical Center, New York, New York
JAMA Pediatr. 2014;168(4):371-377. doi:10.1001/jamapediatrics.2013.4858.
Text Size: A A A
Published online

Birth defects are a leading cause of infant morbidity and mortality worldwide. The vast majority of birth defects are nonsyndromic, and although their etiologies remain mostly unknown, evidence supports the hypothesis that they result from the complex interaction of genetic, epigenetic, environmental, and lifestyle factors. Since our last review published in 2002 describing the basic tools of genetic epidemiology used to study nonsyndromic structural birth defects, many new approaches have become available and have been used with varying success. Through rapid advances in genomic technologies, investigators are now able to investigate large portions of the genome at a fraction of previous costs. With next-generation sequencing, research has progressed from assessing a small percentage of single-nucleotide polymorphisms to assessing the entire human protein-coding repertoire (exome)—an approach that is starting to uncover rare but informative mutations associated with nonsyndromic birth defects. Herein, we report on the current state of the genetic epidemiology of birth defects and comment on future challenges and opportunities. We consider issues of study design, and we discuss common variant approaches, including candidate gene studies and genome-wide association studies. We also discuss the complexities embedded in exploring interactions between genes and the environment. We complete our review by describing new and promising next-generation sequencing technologies and examining how the study of epigenetic mechanisms could become the key to unraveling the complex etiologies of nonsyndromic structural birth defects.

On April 14, 2003, the Human Genome Project was completed. To celebrate the 10th anniversary of the project, JAMA published a theme issue on genomics on April 10, 2013. In 2002, in a commentary published in the Archives of Pediatrics and Adolescent Medicine,1 we described the basic tools of genetic epidemiology as applied to the study of nonsyndromic structural birth defects. Since that time, many new approaches have become available to discover genetic factors leading to birth defects, and epigenetics has also come to the forefront as an important contributing factor. Herein, we present an updated review of genetic epidemiology and birth defects, focusing on these new approaches.

The prevalence of structural birth defects varies globally,2 ranging from approximately 3% to 6% of all live births. These birth defects are a leading cause of infant mortality and are more prevalent than most chronic diseases of childhood, such as autism,3 pediatric cancers,4 and type 1 diabetes mellitus.5 Most structural birth defects develop early in embryogenesis, during the first 10 weeks of pregnancy, and the majority of these defects occur in isolation and affect only 1 organ system. Despite recent progress in finding highly informative mutations, in some cases, a majority of nonsyndromic birth defects still do not appear to be accounted for by a single gene or chromosomal abnormality. The most prevalent defects are orofacial clefts and heart, neural tube, and limb defects.6 When birth defects are not associated with known multiorgan syndromes, they are referred to as nonsyndromic defects. The etiologies of most nonsyndromic structural birth defects remain incompletely understood, and most are thought to result from a complex interplay between genetic, epigenetic, environmental, and lifestyle factors.7 Maternal lifestyle factors, such as smoking, can alter developmental processes and the expression of key developmental genes, such as GATA4, and the effect of environmental exposures and lifestyle on the developing fetus can, in turn, be influenced by maternal and fetal genetic susceptibilities.

While prior research on nonsyndromic birth defects has focused largely on the independent roles of environmental and/or lifestyle exposures and genetics,8 epigenetic causes have now begun to receive increased attention in this and many other human diseases. As early as 1940, C. H. Waddington, a British embryologist, geneticist, and philosopher of science, defined epigenetics as “the interactions of genes with their environment which bring the phenotype into being.”9 Although studies on epigenetics and birth defects are still limited, they are very important because they may help us to establish the molecular basis for interactions between genes and the environment.8

Embryogenesis requires an intricate coordination of cell migration, proliferation, and death that ultimately determines 3-dimensional events in embryo formation and development. The complexity of embryogenic processes leads us to believe that multiple genes and biological pathways are involved in an intricate series of events that are susceptible to perturbations due to environmental exposures or maternal conditions.10 In the following sections, we will (1) review current approaches to identifying genetic factors associated with birth defects, (2) introduce potential epigenetic approaches, and (3) provide a perspective on the challenges and opportunities for future studies.

Studies to identify etiologies of nonsyndromic birth defects in humans are, for the most part, limited to demonstrating an association between genetic variants and birth defect phenotypes. Such association studies are most readily compared with traditional case-control epidemiologic designs. Population-based samples of cases and controls, small nuclear families (mother, father, and child), or both are enrolled in a study in which the investigator compares the frequencies of specific genetic variants (ie, polymorphisms) in affected and unaffected individuals. Such comparisons could include the index children, as well as 1 or both parents.

Once it has been established that genetic variations effect the occurrence of a particular birth defect, studies are designed to identify and evaluate candidate genes. Candidate genes are those that have been proven or are believed to be associated with the malformation from animal studies, from known or suspected developmental and signaling pathways, or from studying a small number of human pedigrees, and thus need to be confirmed in large, carefully selected, and well-characterized human population samples. The selection of appropriate candidate genes is a key step in such studies. Knowledge of the pathogenesis of the malformation and the function of 1 or more proteins implicated in the disease can facilitate the identification of a suitable candidate gene. Genes that are known to be associated with variations in biologically relevant metabolic processes also may be selected as candidate genes. For example, several studies have demonstrated the protective effect of maternal periconceptional intake of folic acid on the occurrence of orofacial clefts,11 neural tube defects,12 and cardiac defects.13 Subsequently, several studies1416 have investigated the association between genetic polymorphisms in the folate metabolic pathway and the risk of these 3 defect groups.

Single-nucleotide polymorphisms (SNPs) are the most common sources of variation in human genomes.17 Each SNP is a difference in a single nucleotide at a specific site within the genome. For example, a SNP may form by substituting the nucleotide cytosine with the nucleotide thymine at a specific genomic location, annotated as C>T. If both of these variants (alleles) are compatible with life, then they can be present at detectable frequencies in the general population. In fact, we now know that there are approximately 7 million SNPs with a minor allele frequency of more than 5%.18 Until completion of the International HapMap Project in 2009, population- or family-based studies of candidate genes were limited to the detection of associations between phenotypes of interest and only a small number of functional SNPs within candidate genes. By identifying a dense map of common variants and their correlations with each other (ie, linkage disequilibrium), investigations such as the International HapMap Project and the 1000 Genomes Project (Box) have made it possible to test for associations between birth defects and common (minor allele frequency of >5% in the population) or even somewhat rarer genetic variants within each gene.19,20 In the past 5 years, multiple reviews of candidate genes and birth defects have been published. Key pathways that have been implicated in the development of orofacial clefts and neural tube, heart, and kidney defects include the Wnt signaling pathway, the bone morphogenetic protein signaling pathway, the Hedgehog signaling pathway, and variants in genes coding for key enzymes in the folate/homocysteine and oxidative stress pathways.2126

Box Section Ref ID

Box.
Stepping Stones: Projects That Made Genome-Wide Association Studies Possible
  • Genome-wide studies of genetic risk factors for birth defects have only recently been made possible owing to the vast increase in genomic data first provided by the sequencing of the human genome by the Human Genome Project and subsequent studies that identified and measured genetic diversity among human subjects.

  • The Human Genome Project

  • (http://web.ornl.gov/sci/techresources/Human_Genome/index.shtml)

    • Goal: To sequence the entire 3 billion bases in the human genome over a 13-year period. The project was a major international effort including 18 countries.

    • The private company Celera Genomics sequenced the human genome and published its first draft sequence simultaneously with the effort by the National Institutes of Health in Science and Nature, respectively.

  • The International HapMap Project

  • (http://hapmap.ncbi.nlm.nih.gov/)

    • Goal: To identify and catalog patterns of human genetic variation. The project was a collaboration between institutions in the United States, Canada, Japan, China, Nigeria, and the United Kingdom.

  • The 1000 Genomes Project

  • (http://www.1000genomes.org/)

    • Goal: To identify genetic variants with frequencies of 1% or more in populations studied, which include individuals and families from diverse backgrounds around the world.

  • The ENCODE (Encyclopedia of DNA Elements) Project

  • (http://www.genome.gov/10005107)

    • Goal: To identify all functional elements in the human genome.

  • CardioGenomics

  • (http://cardiogenomics.med.harvard.edu/pga-overview)

    • Goal: To advance our understanding of congenital heart defects and genomics research by linking genes to structure, function, dysfunction, and abnormalities.

  • FaceBase Consortium

  • (https://www.facebase.org/)

    • Goal: To provide craniofacial researchers with data repositories, technology, and bioinformatics through a central data management and bioinformatics hub.

  • National Birth Defects Prevention Study

  • (http://www.nbdps.org/)

    • Goal: To find genetic and environmental causes of nonsyndromic birth defects and identify prevention strategies. Over 45 000 case-/control-parental triads entrolled.

  • GENEVA: Gene Environmental Association Studies

  • (http://www.genome.gov/27541319)

    • Goal: To identify genetic variants related to complex disease and identify gene-trait variations associated with environmental exposures.

Candidate gene or pathway approaches are limited by their reliance on preexisting knowledge of relevant pathways and/or mechanisms that may adversely impact embryogenesis. With the completion of the HapMap Project and the advances in technology that provide platforms to genotype a large number of SNPs efficiently, the genome-wide association study (GWAS) was introduced as a popular method for studying common but genetically complex human diseases.27 In contrast to candidate-gene studies, GWASs are not limited by prior knowledge; instead, they take an agnostic approach in which no SNP is considered, a priori, to have a higher likelihood of being associated with the relevant phenotype than any other SNP in the genome.28 Between January 2005 and December 2012, more than 1350 GWASs were reported. With varying success, GWASs have identified common SNPs associated with risks for specific pediatric or adult diseases, but only a few have been completed on birth defects, including one study on hypospadias29 and several studies3033 on nonsyndromic cleft lip with or without cleft palate. Mangold et al30 identified 2 loci, in chromosome bands 17q22 and 10q25.3, that were associated with this type of birth defect, whereas the other 3 studies3133 identified strong associations between a nonsyndromic cleft lip with or without cleft palate and a locus in 8q24.21.

These findings support the use of GWASs for identifying novel chromosomal regions associated with birth defects. However, most genetic studies of nonsyndromic birth defects continue to rely on candidate SNPs, leaving most of the genome unexplored.34,35 Thus, there is a need to comprehensively explore the genome to identify new regions harboring genes associated with birth defects.36 In addition to SNPs, which affect only a single nucleotide base, multiple lines of evidence indicate that copy number variants (CNVs) can play an important role in the etiology of some cases of birth defects. Copy number variants are defined as DNA sequences, ranging from kilobases to megabases in length, that are present in variable copy numbers in comparison to a reference genome.37 In the past decade, molecular techniques such as array-based comparative genomic hybridization, genotyping microarrays, and high-throughput DNA sequencing have given a much richer picture of this form of genetic variation, and CNVs have increasingly been discovered to be associated with birth defects. For example, a survey38 of CNVs in 114 individuals with tetralogy of Fallot and their unaffected parents identified 11 de novo CNVs that were absent or extremely rare in more than 2000 controls, and pathogenic CNVs affecting the GATA4 and NODAL genes have been found in more than 1 study of congenital heart disease.39 Rare and/or de novo CNVs have also been implicated in microphthalmia,40 congenital diaphragmatic hernia,41 cleft lip and/or palate,42 other craniofacial defects,43 and renal defects.44

For most GWASs, replication and validation of findings is necessary to separate true relationships from chance findings (type I errors). Genetic variants identified by GWASs are theoretically in linkage disequilibrium with functional variants that may be causal. To identify causal variants, targeted resequencing of genomic regions in close proximity to selected SNPs and whole-exome sequencing are new technological advances that hold considerable promise. In contrast to SNPs, which are often simply regional markers, CNV associations with birth defects are more likely to be directly causal of the phenotype being studied—via gene dosage increase or decrease, direct gene disruption, and cis-acting effects via disruption of gene regulatory sequences.45

Genetic predispositions in conjunction with environmental influences are thought to be implicated in most birth defects. However, investigations into birth defects and interactions between functional or marker SNPs and environmental or lifestyle exposures are few in number.8 This paucity of studies may, in part, reflect the difficulty of obtaining robust genetic and environmental measures on the same samples, and the increased statistical power needed to detect gene and environment interactions. Nonetheless, there have been some indications of an interaction between functional SNPs in the methyl donor pathway and the beneficial effects of folic acid supplementation against neural tube defects and other birth defects.35

The first human genome was sequenced over a period of 10 years using classic Sanger (dideoxy terminator) sequencing, at a cost of almost $3 billion.46 “Next-generation” massively parallel sequencing has exploded into the research and clinical genetics arena since its availability in 2005, with major advantages including markedly reduced sequencing time, reduced cost per nucleotide base, and substantial increases in data output.47 With new technologies, a genome can be sequenced within days at a current cost of less than $10 000. Reviews detailing next-generation sequencing (NGS) chemistries and the practical advantages of specific platforms have been published.4850 Data storage and protection, data analysis, clinical interpretation, and ethical issues, such as whether to report incidental, potentially adverse, findings to the patient or family, remain major challenges in the incorporation of NGS into the clinical arena.51,52

For the discovery and clinical testing of genes implicated in common birth defects such as congenital heart defects (CHDs), neural tube defects, and cleft lip and palate, different NGS-based approaches may be used. One approach is to select candidate genes for targeted deep resequencing. For conditions in which multiple genes with strong evidence of disease pathogenicity exist, such as those identified through GWASs and CNV studies, a targeted resequencing approach may be warranted. Although targeted NGS gene panels are offered clinically for certain conditions, such as mitochondrial disorders,51 they are not yet offered clinically for the major types of nonsyndromic birth defects. Another approach is the investigation of the exome (all gene exons; ie, all protein-coding regions) of the genome. Although the human exome consists of only 1% to 2% of the entire genome, it is estimated that up to 85% of disease-causing mutations are harbored within it. The merits of sequencing the exome as a diagnostic tool have been delineated, and exome sequencing is starting to aid in the diagnosis and treatment of inherited conditions.48,52 Whole-genome sequencing is also available, but, to date, the sequencing cost and the difficulties associated with data warehousing, analysis, and interpretation remain prohibitive.

Next-generation sequencing technology holds promise for nonsyndromic birth defects research and genetic diagnosis because (1) it allows for the simultaneous analysis of the many candidate genes that have been identified so far and (2) the technology is capable of detecting rare genetic variation. Although GWASs have identified many loci associated with complex traits, common genetic variation accounts for only a small percentage of heritability.53 Thus, identification of rare genetic variation may yield larger effect sizes in complex diseases, including isolated birth defects.

The use of NGS for discovering causal mutations in nonsyndromic birth defects is still in its early stages. Next-generation sequencing was used recently to show that de novo mutations contribute to approximately 10% of severe CHDs.54 Strikingly, several genes encoding histone-modifying and chromatin-remodeling enzymes, such as MLL2, CHD7, KDM5-A, and KDM5-B, were found mutated in that study,54 implicating epigenetic alterations in CHD pathogenesis. Likewise, NGS approaches may become fruitful for finding mutations, such as those already known in the HNF1B and PAX2 genes, that can underlie congenital kidney malformations.55 Genome scanning methods for CNVs continue to identify lesions underlying CHDs, some predisposing to it generally, and others with lesion specificity,56 and it can be expected that additional recurrent CNVs will be detected in nonsyndromic birth defect cases using NGS.

Next-generation sequencing–targeted resequencing of candidate genes, whole-exome sequencing, and even whole-genome sequencing are being offered clinically in a growing number of laboratories. The GeneTests website57 and the National Institutes of Health genetic testing registry58 provide valuable resources for clinicians to identify clinical genetic testing laboratories. Recently, the merits, considerations, and challenges of using NGS technologies in a clinical diagnostic setting have been discussed in publications through the American College of Medical Genetics and the Association for Molecular Pathology.59,60 Although resequencing assays are clinically available for complex diseases, including cardiomyopathy,61 autism spectrum disorder,62 and intellectual disability,63 targeted assays using NGS are not yet available for nonsyndromic birth defects such as CHDs, neural tube defects, and cleft lip and palate. Whole-exome sequencing is a potential genetic testing option for these conditions, but large research studies are only now being conducted on nonsyndromic birth defects. Nonetheless, the apparent multigenic nature of nonsyndromic birth defects makes NGS experimental approaches ideal for gene discovery and further pathogenic mutation characterization. Overall, the evidence accumulated through many dedicated research studies suggests that nonsyndromic CHDs, neural tube defects, and cleft lip and palate may be caused by multiple rare, familial, genetic mutations, interacting with maternal genotype and exposures. Large population studies using NGS may delineate the genetic causes of common birth defects, may aid in determining preconception risk factors, and may help guide future therapeutic interventions.

Despite the tremendous advances in human genetics enabled by the Human Genome Project and brought to fruition with GWASs and NGS, many aspects of human embryology and biology still cannot be adequately explained by genetics alone. Normal embryogenesis requires the specification of a multitude of cell types/organs that depend on transcriptional regulation programmed by epigenetic mechanisms (namely, modifications to DNA and its associated proteins that define the distinct gene expression profiles for individual cell types at specific developmental stages). Disruption of such control mechanisms is associated with a variety of diseases with behavioral, endocrine, or neurologic manifestations and, quite strikingly, with disorders of tissue growth, which will in all likelihood include structural birth defects. As a precedent, several well-studied syndromic birth defects, including Prader-Willi syndrome, Angelman syndrome, Beckwith-Wiedemann syndrome, and Russell-Silver syndrome, are known to be caused by loss of imprinting, uniparental disomy, or deletion/mutation of epigenetically regulated genes.64

An epigenetic trait can be defined as a “stably heritable phenotype resulting from changes in a chromosome without alterations in the DNA sequence.”65(p781) Several classes of epigenetic phenomena have been identified and recently reviewed.8,66 Epigenetic patterns, essential for controlling gene expression in normal growth and development, are established by a number of mechanisms, including DNA methylation at cytosine residues in CpG dinucleotides and covalent modifications of histone proteins, as well as by less well-understood mechanisms controlling long-range chromatin architecture within the cell nucleus. DNA methylation involves the transfer of a methyl group to cytosine in a CpG dinucleotide, catalyzed by DNA methyltransferase (DNMT) enzymes that establish and maintain these patterns through cell division. Importantly, DNA methylation has been shown to be essential for normal development.66,67 DNMT1, the major maintenance methylase, has a high affinity for hemimethylated DNA,68 and it therefore acts to propagate methylation patterns in somatic cell divisions, while other enzymes, such as DNMT3A-DNMT3L, are responsible for initiating the epigenetic patterns. Importantly, there is already some evidence for an interaction of environment with epigenetics. Research on mice with a mutation in the Agouti gene has provided an excellent example of how maternal diet and epigenetics may affect fetal phenotypes.69 This model has shown that variations in maternal dietary constituents affecting the methyl donor pool, such as folic acid, can result in alterations in coat color in the offspring, as a result of differential CpG methylation.69,70 As another example, with clinical implications, a high folate diet given to Helicobacter felis–infected gastric cancer–prone mice at weaning prevented the development of gastric dysplasia and cancer.71

Many techniques, which we reviewed recently,64 have been developed to study DNA methylation. The gold standard for comprehensive analysis of the methylation status of CpG sites (ie, DNA methylation patterns) is the sodium bisulfite chemical conversion of DNA.72 This procedure deaminates nonmethylated deoxycytidine to deoxyuracil residues; during subsequent polymerase chain reaction (PCR) amplification, the latter are converted to A/T base pairs. However, if the C is methylated, the DNA sequence obtained after PCR does not change. Methylation-specific PCR or pyrosequencing using bisulfite-converted DNA provides quantitative measurements of DNA methylation levels, whereas another approach, which has now been made high throughput via NGS, involves amplification of bisulfite PCR products followed by sequencing of clones. This more thorough approach permits DNA methylation levels of a large number of contiguous CpG sites to be quantified, and the precise patterns of methylation, including clonal heterogeneity and allele specificity, to be displayed. By combining sodium bisulfite conversion and microarrays or NGS, genome-wide DNA methylation patterns can be determined essentially genome-wide. A number of initiatives have now been implemented to define human epigenetic patterns at high resolution with complete genomic coverage, with the goal of integrating epigenetics into the study of common but complex human diseases.73 These new technologies and approaches may provide keys to unraveling genetic and environmental factors that impinge on epigenomes to affect normal processes in embryological development and lead to human malformations when these processes go awry. In searching for evidence of “epigenome and environment” interactions in data sets from such studies, it will be crucial to take the cell types being sampled and the age of the individuals into account because methylation patterns are highly specific to cell type and, for some genes, can change with age.74 It will also be important to remember that the genetic makeup of an individual exerts a strong influence on his or her epigenome: specifically, multiple studies have now shown a strong influence of human haplotypes (ie, clusters of SNPs in a given chromosomal region) on the patterns of DNA methylation in that region.75

We concluded our 2002 article1 by stating that the identification of genes associated with birth defects does not lead to an immediate understanding of the relation between the gene and the birth defect with which it is associated. Identification “is only the first step in a long path to understanding the cause of the condition and ultimately to finding preventive or corrective strategies.”1(p319) As new technologies are made available, genetic epidemiologists are quick to use these new platforms to generate databases that seem to be ever increasing in size. Our increased understanding of the importance of epigenetics in the development of birth defects suggests that an approach that simultaneously investigates genome-wide genetic and epigenetic variation in participants for whom environmental exposure data have been obtained may be a major step forward. Such studies may help to establish the mechanistic link between genetic variants and environmental exposures.

Corresponding Author: Charlotte A. Hobbs, MD, PhD, Department of Pediatrics, University of Arkansas for Medical Sciences, College of Medicine, 13 Children’s Way, Mail Slot 512-40, Little Rock, AR 72202 (hobbscharlotte@uams.edu).

Accepted for Publication: October 20, 2013.

Published Online: February 10, 2014. doi:10.1001/jamapediatrics.2013.4858.

Author Contributions: Dr Hobbs had full access to all of the data in the study and takes responsibility for the integrity of the data and the accuracy of the literature reviewed.

Study concept and design: Hobbs, Chowdhury, Cleves, Shaw, Witte, Tycko.

Acquisition of data: MacLeod.

Analysis and interpretation of data: Chowdhury, Erickson, Shete, Tycko.

Drafting of the manuscript: Hobbs, Chowdhury, Cleves, Erickson, MacLeod, Shaw, Witte, Tycko.

Critical revision of the manuscript for important intellectual content: Chowdhury, Cleves, MacLeod, Shaw, Shete, Witte, Tycko.

Statistical analysis: Erickson.

Obtained funding: Chowdhury, Tycko.

Administrative, technical, and material support: Chowdhury, Cleves, MacLeod, Shaw, Witte.

Study supervision: Hobbs, Shete.

Conflict of Interest Disclosures: None reported.

Funding/Support: This research was supported by the Centers for Disease Control and Prevention (grant 5U01 DD000491), the Eunice Kennedy Shriver National Institute of Child Health and Human Development (grant R01 HD039054 to Dr Hobbs and grant P01 HD035897 to Dr Tycko), and the Arkansas Biosciences Institute.

Role of the Sponsor: The funding agencies had no role in the design and conduct of the study; collection, management, analysis, or interpretation of the data; preparation, review, or approval of the manuscript; and decision to submit the manuscript for publication.

Disclaimer: The views expressed herein are solely those of the authors and do not reflect the official views or positions of the Centers for Disease Control and Prevention or the Eunice Kennedy Shriver National Institute of Child Health and Human Development.

Additional Contributions: We gratefully acknowledge Zuzana Gubrij, MA, and Ashley Block, MA, from the Department of Pediatrics, University of Arkansas for Medical Sciences, College of Medicine, and Phaedra Yount, MA, and John Gregan, MA, from the Arkansas Children's Hospital Research Institute, in Little Rock, for their support with the design, copy editing, and formatting of the article. They were not compensated from a funding sponsor.

Hobbs  CA, Cleves  MA, Simmons  CJ.  Genetic epidemiology and congenital malformations: from the chromosome to the crib [published correction appears in Arch Pediatr Adolesc Med. 2002;156(10):1051]. Arch Pediatr Adolesc Med. 2002;156(4):315-320.
PubMed   |  Link to Article
Christianson  A, Howson  CP, Modell  B. March of Dimes Global Report on Birth Defects: The Hidden Toll of Dying and Disabled children. White Plains, NY: March of Dimes Foundation; 2006.
Autism and Developmental Disabilities Monitoring Network Surveillance Year 2008 Principal Investigators; Centers for Disease Control and Prevention.  Prevalence of autism spectrum disorders—Autism and Developmental Disabilities Monitoring Network, 14 sites, United States, 2008. MMWR Surveill Summ. 2012;61(3):1-19.
PubMed
Department of Health and Human Services; Centers for Disease Control and Prevention; National Cancer Institute. 1999–2005 United States Cancer Statistics (USCS): Incidence and Mortality Web-Based Report. Atlanta, GA: Centers for Disease Control and Prevention; 2009.
Liese  AD, D’Agostino  RB  Jr, Hamman  RF,  et al; SEARCH for Diabetes in Youth Study Group.  The burden of diabetes mellitus among US youth: prevalence estimates from the SEARCH for Diabetes in Youth Study. Pediatrics. 2006;118(4):1510-1518.
PubMed   |  Link to Article
Parker  SE, Mai  CT, Canfield  MA,  et al; National Birth Defects Prevention Network.  Updated National Birth Prevalence estimates for selected birth defects in the United States, 2004-2006. Birth Defects Res A Clin Mol Teratol. 2010;88(12):1008-1016.
PubMed   |  Link to Article
Hobbs  CA, Cleves  MA, Melnyk  S, Zhao  W, James  SJ.  Congenital heart defects and abnormal maternal biomarkers of methionine and homocysteine metabolism. Am J Clin Nutr. 2005;81(1):147-153.
PubMed
Friedman  JM.  Using genomics for birth defects epidemiology: can epigenetics cut the GxE Gordian knot? Birth Defects Res A Clin Mol Teratol. 2011;91(12):986-989.
PubMed   |  Link to Article
Waddington  CH. Organisers and Genes. Cambridge, England: Cambridge University Press; 1940.
Srivastava  D.  Genetic regulation of cardiogenesis and congenital heart disease. Annu Rev Pathol. 2006;1:199-213.
PubMed   |  Link to Article
Itikala  PR, Watkins  ML, Mulinare  J, Moore  CA, Liu  Y.  Maternal multivitamin use and orofacial clefts in offspring. Teratology. 2001;63(2):79-86.
PubMed   |  Link to Article
van Beynum  IM, den Heijer  M, Blom  HJ, Kapusta  L.  The MTHFR 677C->T polymorphism and the risk of congenital heart defects: a literature review and meta-analysis. QJM. 2007;100(12):743-753.
PubMed   |  Link to Article
Botto  LD, Mulinare  J, Erickson  JD.  Occurrence of congenital heart defects in relation to maternal multivitamin use. Am J Epidemiol. 2000;151(9):878-884.
PubMed   |  Link to Article
Shaw  GM, Lu  W, Zhu  H,  et al.  118 SNPs of folate-related genes and risks of spina bifida and conotruncal heart defects. BMC Med Genet. 2009;10:49.
PubMed   |  Link to Article
Pan  Y, Zhang  W, Ma  J,  et al.  Infants’ MTHFR polymorphisms and nonsyndromic orofacial clefts susceptibility: a meta-analysis based on 17 case-control studies. Am J Med Genet A. 2012;158A(9):2162-2169.
PubMed   |  Link to Article
Yin  M, Dong  L, Zheng  J, Zhang  H, Liu  J, Xu  Z.  Meta analysis of the association between MTHFR C677T polymorphism and the risk of congenital heart defects. Ann Hum Genet. 2012;76(1):9-16.
PubMed   |  Link to Article
Hinds  DA, Stuve  LL, Nilsen  GB,  et al.  Whole-genome patterns of common DNA variation in three human populations. Science. 2005;307(5712):1072-1079.
PubMed   |  Link to Article
Kruglyak  L, Nickerson  DA.  Variation is the spice of life. Nat Genet. 2001;27(3):234-236.
PubMed   |  Link to Article
International HapMap Consortium.  The International HapMap Project. Nature. 2003;426(6968):789-796.
PubMed   |  Link to Article
Couzin  J.  Genomics: consensus emerges on HapMap strategy. Science. 2004;304(5671):671-673.
PubMed   |  Link to Article
Leslie  EJ, Murray  JC.  Evaluating rare coding variants as contributing causes to non-syndromic cleft lip and palate. Clin Genet. 2013;84(5):496-500.
PubMed   |  Link to Article
Greene  ND, Stanier  P, Copp  AJ.  Genetics of human neural tube defects. Hum Mol Genet. 2009;18(R2):R113-R129.
PubMed   |  Link to Article
Gelb  B, Brueckner  M, Chung  W,  et al; Pediatric Cardiac Genomics Consortium.  The Congenital Heart Disease Genetic Network Study: rationale, design, and early results. Circ Res. 2013;112(4):698-706.
PubMed   |  Link to Article
Dixon  MJ, Marazita  ML, Beaty  TH, Murray  JC.  Cleft lip and palate: understanding genetic and environmental influences. Nat Rev Genet. 2011;12(3):167-178.
PubMed   |  Link to Article
Rana  MS, Christoffels  VM, Moorman  AF.  A molecular and genetic outline of cardiac morphogenesis. Acta Physiol (Oxf). 2013;207(4):588-615.
PubMed   |  Link to Article
Tan  WH, Gilmore  EC, Baris  HN. Human developmental genetics. In: Rimoin  DL, Pyeritz  RE, Korf  BR, eds. Emery and Rimoin’s Principles and Practice of Medical Genetics.6th ed. Philadelphia, PA: Elsevier Science; 2013.
Genome-wide association studies. National Human Genome Research Institute website. http://www.genome.gov/20019523. Accessed June 17, 2013.
Hunter  DJ, Chanock  SJ.  Genome-wide association studies and “the art of the soluble”. J Natl Cancer Inst. 2010;102(12):836-837.
PubMed   |  Link to Article
van der Zanden  LF, van Rooij  IA, Feitz  WF,  et al.  Common variants in DGKK are strongly associated with risk of hypospadias. Nat Genet. 2011;43(1):48-50.
PubMed   |  Link to Article
Mangold  E, Ludwig  KU, Birnbaum  S,  et al.  Genome-wide association study identifies two susceptibility loci for nonsyndromic cleft lip with or without cleft palate. Nat Genet. 2010;42(1):24-26.
PubMed   |  Link to Article
Birnbaum  S, Ludwig  KU, Reutter  H,  et al.  Key susceptibility locus for nonsyndromic cleft lip with or without cleft palate on chromosome 8q24. Nat Genet. 2009;41(4):473-477.
PubMed   |  Link to Article
Beaty  TH, Murray  JC, Marazita  ML,  et al.  A genome-wide association study of cleft lip with and without cleft palate identifies risk variants near MAFB and ABCA4 [published correction appears in Nat Genet. 2010;42(8):727]. Nat Genet. 2010;42(6):525-529.
PubMed   |  Link to Article
Grant  SF, Wang  K, Zhang  H,  et al.  A genome-wide association study identifies a locus for nonsyndromic cleft lip with or without cleft palate on 8q24. J Pediatr. 2009;155(6):909-913.
PubMed   |  Link to Article
Hobbs  CA, Cleves  MA, Keith  C, Ghaffar  S, James  SJ.  NKX2.5 and congenital heart defects: a population-based study. Am J Med Genet A. 2005;134A(2):223-225.
PubMed   |  Link to Article
Hobbs  CA, James  SJ, Parsian  A,  et al.  Congenital heart defects and genetic variants in the methylenetetrahydroflate reductase gene. J Med Genet. 2006;43(2):162-166.
PubMed   |  Link to Article
Olshan  AF, Hobbs  CA, Shaw  GM.  Discovery of genetic susceptibility factors for human birth defects: an opportunity for a National Agenda. Am J Med Genet A. 2011;155A(8):1794-1797.
PubMed   |  Link to Article
Redon  R, Ishikawa  S, Fitch  KR,  et al.  Global variation in copy number in the human genome. Nature. 2006;444(7118):444-454.
PubMed   |  Link to Article
Greenway  SC, Pereira  AC, Lin  JC,  et al.  De novo copy number variants identify new genes and loci in isolated sporadic tetralogy of Fallot. Nat Genet. 2009;41(8):931-935.
PubMed   |  Link to Article
Warburton  D, Ronemus  M, Kline  J,  et al.  The contribution of de novo and rare inherited copy number changes to congenital heart disease in an unselected sample of children with conotruncal defects or hypoplastic left heart disease. Hum Genet. 2014;133(1):11-27.
PubMed   |  Link to Article
Bardakjian  TM, Kwok  S, Slavotinek  AM, Schneider  AS.  Clinical report of microphthalmia and optic nerve coloboma associated with a de novo microdeletion of chromosome 16p11.2. Am J Med Genet A. 2010;152A(12):3120-3123.
PubMed   |  Link to Article
Srisupundit  K, Brady  PD, Devriendt  K,  et al.  Targeted array comparative genomic hybridisation (array CGH) identifies genomic imbalances associated with isolated congenital diaphragmatic hernia (CDH). Prenat Diagn. 2010;30(12-13):1198-1206.
PubMed   |  Link to Article
Shi  M, Mostowska  A, Jugessur  A,  et al.  Identification of microdeletions in candidate genes for cleft lip and/or palate. Birth Defects Res A Clin Mol Teratol. 2009;85(1):42-51.
PubMed   |  Link to Article
Mefford  HC, Shafer  N, Antonacci  F,  et al.  Copy number variation analysis in single-suture craniosynostosis: multiple rare variants including RUNX2 duplication in two cousins with metopic craniosynostosis. Am J Med Genet A. 2010;152A(9):2203-2210.
PubMed   |  Link to Article
Weber  S, Landwehr  C, Renkert  M,  et al.  Mapping candidate regions and genes for congenital anomalies of the kidneys and urinary tract (CAKUT) by array-based comparative genomic hybridization. Nephrol Dial Transplant. 2011;26(1):136-143.
PubMed   |  Link to Article
Zhang  F, Gu  W, Hurles  ME, Lupski  JR.  Copy number variation in human health, disease, and evolution. Annu Rev Genomics Hum Genet. 2009;10:451-481.
PubMed   |  Link to Article
International Human Genome Sequencing Consortium.  Finishing the euchromatic sequence of the human genome. Nature. 2004;431(7011):931-945.
PubMed   |  Link to Article
Metzker  ML.  Sequencing technologies—the next generation. Nat Rev Genet. 2010;11(1):31-46.
PubMed   |  Link to Article
Korf  BR, Rehm  HL.  New approaches to molecular diagnosis. JAMA. 2013;309(14):1511-1521.
PubMed   |  Link to Article
Liu  L, Li  Y, Li  S,  et al.  Comparison of next-generation sequencing systems. J Biomed Biotechnol. 2012;2012:251364.
PubMed
Loman  NJ, Misra  RV, Dallman  TJ,  et al.  Performance comparison of benchtop high-throughput sequencing platforms. Nat Biotechnol. 2012;30(5):434-439.
PubMed   |  Link to Article
Vasta  V, Merritt  JL  II, Saneto  RP, Hahn  SH.  Next-generation sequencing for mitochondrial diseases: a wide diagnostic spectrum. Pediatr Int. 2012;54(5):585-601.
PubMed   |  Link to Article
Bamshad  MJ, Ng  SB, Bigham  AW,  et al.  Exome sequencing as a tool for Mendelian disease gene discovery. Nat Rev Genet. 2011;12(11):745-755.
PubMed   |  Link to Article
Manolio  TA, Collins  FS, Cox  NJ,  et al.  Finding the missing heritability of complex diseases. Nature. 2009;461(7265):747-753.
PubMed   |  Link to Article
Zaidi  S, Choi  M, Wakimoto  H,  et al.  De novo mutations in histone-modifying genes in congenital heart disease. Nature. 2013;498(7453):220-223.
PubMed   |  Link to Article
Thomas  R, Sanna-Cherchi  S, Warady  BA, Furth  SL, Kaskel  FJ, Gharavi  AG.  HNF1B and PAX2 mutations are a common cause of renal hypodysplasia in the CKiD cohort. Pediatr Nephrol. 2011;26(6):897-903.
PubMed   |  Link to Article
Gelb  BD.  Recent advances in understanding the genetics of congenital heart defects [published online August 29, 2013]. Curr Opin Pediatr. doi:10.1097/MOP.0b013e3283648826.
PubMed
GeneTests. Bio-Reference Laboratories website. http://www.genetests.org. Accessed May 14, 2013.
Rubinstein  WS, Maglott  DR, Lee  JM,  et al.  The NIH genetic testing registry: a new, centralized database of genetic tests to enable access to comprehensive information and improve transparency. Nucleic Acids Res. 2013;41(Database issue):D925-D935.
PubMed   |  Link to Article
Green RC, Berg JS, Grody WW, et al. American College of Medicine Genetics and Genomics: ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing. https://www.acmg.net/docs/ACMG_Releases_Highly-Anticipated_Recommendations_on_Incidental_Findings_in_Clinical_Exome_and_Genome_Sequencing.pdf. Accessed January 10, 2014.
Schrijver  I, Aziz  N, Farkas  DH,  et al.  Opportunities and challenges associated with clinical diagnostic genome sequencing: a report of the Association for Molecular Pathology. J Mol Diagn. 2012;14(6):525-540.
PubMed   |  Link to Article
Norton  N, Li  D, Hershberger  RE.  Next-generation sequencing to identify genetic causes of cardiomyopathies. Curr Opin Cardiol. 2012;27(3):214-220.
PubMed   |  Link to Article
Iossifov  I, Ronemus  M, Levy  D,  et al.  De novo gene disruptions in children on the autistic spectrum. Neuron. 2012;74(2):285-299.
PubMed   |  Link to Article
de Ligt  J, Willemsen  MH, van Bon  BW,  et al.  Diagnostic exome sequencing in persons with severe intellectual disability. N Engl J Med. 2012;367(20):1921-1929.
PubMed   |  Link to Article
Weksberg  R, Butcher  DT, Grafodatskaya  D, Choufani  S, Tycko  B. Epigenetics. In: Rimoin  DL, Pyeritz  RE, Korf  BR, eds. Emery and Rimoin's Principles and Practice of Medical Genetics.6th ed. Philadelphia, PA: Elsevier Sciences; 2013.
Berger  SL, Kouzarides  T, Shiekhattar  R, Shilatifard  A.  An operational definition of epigenetics. Genes Dev. 2009;23(7):781-783.
PubMed   |  Link to Article
Li  E, Bestor  TH, Jaenisch  R.  Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell. 1992;69(6):915-926.
PubMed   |  Link to Article
Okano  M, Bell  DW, Haber  DA, Li  E.  DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell. 1999;99(3):247-257.
PubMed   |  Link to Article
Pradhan  S, Bacolla  A, Wells  RD, Roberts  RJ.  Recombinant human DNA (cytosine-5) methyltransferase: I, expression, purification, and comparison of de novo and maintenance methylation. J Biol Chem. 1999;274(46):33002-33010.
PubMed   |  Link to Article
Wolff  GL, Kodell  RL, Moore  SR, Cooney  CA.  Maternal epigenetics and methyl supplements affect agouti gene expression in Avy/a mice. FASEB J. 1998;12(11):949-957.
PubMed
Cooney  CA, Dave  AA, Wolff  GL.  Maternal methyl supplements in mice affect epigenetic variation and DNA methylation of offspring. J Nutr. 2002;132(8 suppl):2393S-2400S.
PubMed
Gonda  TA, Kim  YI, Salas  MC,  et al.  Folic acid increases global DNA methylation and reduces inflammation to prevent Helicobacter-associated gastric cancer in mice. Gastroenterology.2012;142(4):824-833.e7.
PubMed   |  Link to Article
Frommer  M, McDonald  LE, Millar  DS,  et al.  A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc Natl Acad Sci U S A. 1992;89(5):1827-1831.
PubMed   |  Link to Article
Rakyan  VK, Down  TA, Balding  DJ, Beck  S.  Epigenome-wide association studies for common human diseases. Nat Rev Genet. 2011;12(8):529-541.
PubMed   |  Link to Article
Maegawa  S, Hinkal  G, Kim  HS,  et al.  Widespread and tissue specific age-related DNA methylation changes in mice. Genome Res. 2010;20(3):332-340.
PubMed   |  Link to Article
Tycko  B.  Allele-specific DNA methylation: beyond imprinting. Hum Mol Genet. 2010;19(R2):R210-R220.
PubMed   |  Link to Article

Figures

Tables

References

Hobbs  CA, Cleves  MA, Simmons  CJ.  Genetic epidemiology and congenital malformations: from the chromosome to the crib [published correction appears in Arch Pediatr Adolesc Med. 2002;156(10):1051]. Arch Pediatr Adolesc Med. 2002;156(4):315-320.
PubMed   |  Link to Article
Christianson  A, Howson  CP, Modell  B. March of Dimes Global Report on Birth Defects: The Hidden Toll of Dying and Disabled children. White Plains, NY: March of Dimes Foundation; 2006.
Autism and Developmental Disabilities Monitoring Network Surveillance Year 2008 Principal Investigators; Centers for Disease Control and Prevention.  Prevalence of autism spectrum disorders—Autism and Developmental Disabilities Monitoring Network, 14 sites, United States, 2008. MMWR Surveill Summ. 2012;61(3):1-19.
PubMed
Department of Health and Human Services; Centers for Disease Control and Prevention; National Cancer Institute. 1999–2005 United States Cancer Statistics (USCS): Incidence and Mortality Web-Based Report. Atlanta, GA: Centers for Disease Control and Prevention; 2009.
Liese  AD, D’Agostino  RB  Jr, Hamman  RF,  et al; SEARCH for Diabetes in Youth Study Group.  The burden of diabetes mellitus among US youth: prevalence estimates from the SEARCH for Diabetes in Youth Study. Pediatrics. 2006;118(4):1510-1518.
PubMed   |  Link to Article
Parker  SE, Mai  CT, Canfield  MA,  et al; National Birth Defects Prevention Network.  Updated National Birth Prevalence estimates for selected birth defects in the United States, 2004-2006. Birth Defects Res A Clin Mol Teratol. 2010;88(12):1008-1016.
PubMed   |  Link to Article
Hobbs  CA, Cleves  MA, Melnyk  S, Zhao  W, James  SJ.  Congenital heart defects and abnormal maternal biomarkers of methionine and homocysteine metabolism. Am J Clin Nutr. 2005;81(1):147-153.
PubMed
Friedman  JM.  Using genomics for birth defects epidemiology: can epigenetics cut the GxE Gordian knot? Birth Defects Res A Clin Mol Teratol. 2011;91(12):986-989.
PubMed   |  Link to Article
Waddington  CH. Organisers and Genes. Cambridge, England: Cambridge University Press; 1940.
Srivastava  D.  Genetic regulation of cardiogenesis and congenital heart disease. Annu Rev Pathol. 2006;1:199-213.
PubMed   |  Link to Article
Itikala  PR, Watkins  ML, Mulinare  J, Moore  CA, Liu  Y.  Maternal multivitamin use and orofacial clefts in offspring. Teratology. 2001;63(2):79-86.
PubMed   |  Link to Article
van Beynum  IM, den Heijer  M, Blom  HJ, Kapusta  L.  The MTHFR 677C->T polymorphism and the risk of congenital heart defects: a literature review and meta-analysis. QJM. 2007;100(12):743-753.
PubMed   |  Link to Article
Botto  LD, Mulinare  J, Erickson  JD.  Occurrence of congenital heart defects in relation to maternal multivitamin use. Am J Epidemiol. 2000;151(9):878-884.
PubMed   |  Link to Article
Shaw  GM, Lu  W, Zhu  H,  et al.  118 SNPs of folate-related genes and risks of spina bifida and conotruncal heart defects. BMC Med Genet. 2009;10:49.
PubMed   |  Link to Article
Pan  Y, Zhang  W, Ma  J,  et al.  Infants’ MTHFR polymorphisms and nonsyndromic orofacial clefts susceptibility: a meta-analysis based on 17 case-control studies. Am J Med Genet A. 2012;158A(9):2162-2169.
PubMed   |  Link to Article
Yin  M, Dong  L, Zheng  J, Zhang  H, Liu  J, Xu  Z.  Meta analysis of the association between MTHFR C677T polymorphism and the risk of congenital heart defects. Ann Hum Genet. 2012;76(1):9-16.
PubMed   |  Link to Article
Hinds  DA, Stuve  LL, Nilsen  GB,  et al.  Whole-genome patterns of common DNA variation in three human populations. Science. 2005;307(5712):1072-1079.
PubMed   |  Link to Article
Kruglyak  L, Nickerson  DA.  Variation is the spice of life. Nat Genet. 2001;27(3):234-236.
PubMed   |  Link to Article
International HapMap Consortium.  The International HapMap Project. Nature. 2003;426(6968):789-796.
PubMed   |  Link to Article
Couzin  J.  Genomics: consensus emerges on HapMap strategy. Science. 2004;304(5671):671-673.
PubMed   |  Link to Article
Leslie  EJ, Murray  JC.  Evaluating rare coding variants as contributing causes to non-syndromic cleft lip and palate. Clin Genet. 2013;84(5):496-500.
PubMed   |  Link to Article
Greene  ND, Stanier  P, Copp  AJ.  Genetics of human neural tube defects. Hum Mol Genet. 2009;18(R2):R113-R129.
PubMed   |  Link to Article
Gelb  B, Brueckner  M, Chung  W,  et al; Pediatric Cardiac Genomics Consortium.  The Congenital Heart Disease Genetic Network Study: rationale, design, and early results. Circ Res. 2013;112(4):698-706.
PubMed   |  Link to Article
Dixon  MJ, Marazita  ML, Beaty  TH, Murray  JC.  Cleft lip and palate: understanding genetic and environmental influences. Nat Rev Genet. 2011;12(3):167-178.
PubMed   |  Link to Article
Rana  MS, Christoffels  VM, Moorman  AF.  A molecular and genetic outline of cardiac morphogenesis. Acta Physiol (Oxf). 2013;207(4):588-615.
PubMed   |  Link to Article
Tan  WH, Gilmore  EC, Baris  HN. Human developmental genetics. In: Rimoin  DL, Pyeritz  RE, Korf  BR, eds. Emery and Rimoin’s Principles and Practice of Medical Genetics.6th ed. Philadelphia, PA: Elsevier Science; 2013.
Genome-wide association studies. National Human Genome Research Institute website. http://www.genome.gov/20019523. Accessed June 17, 2013.
Hunter  DJ, Chanock  SJ.  Genome-wide association studies and “the art of the soluble”. J Natl Cancer Inst. 2010;102(12):836-837.
PubMed   |  Link to Article
van der Zanden  LF, van Rooij  IA, Feitz  WF,  et al.  Common variants in DGKK are strongly associated with risk of hypospadias. Nat Genet. 2011;43(1):48-50.
PubMed   |  Link to Article
Mangold  E, Ludwig  KU, Birnbaum  S,  et al.  Genome-wide association study identifies two susceptibility loci for nonsyndromic cleft lip with or without cleft palate. Nat Genet. 2010;42(1):24-26.
PubMed   |  Link to Article
Birnbaum  S, Ludwig  KU, Reutter  H,  et al.  Key susceptibility locus for nonsyndromic cleft lip with or without cleft palate on chromosome 8q24. Nat Genet. 2009;41(4):473-477.
PubMed   |  Link to Article
Beaty  TH, Murray  JC, Marazita  ML,  et al.  A genome-wide association study of cleft lip with and without cleft palate identifies risk variants near MAFB and ABCA4 [published correction appears in Nat Genet. 2010;42(8):727]. Nat Genet. 2010;42(6):525-529.
PubMed   |  Link to Article
Grant  SF, Wang  K, Zhang  H,  et al.  A genome-wide association study identifies a locus for nonsyndromic cleft lip with or without cleft palate on 8q24. J Pediatr. 2009;155(6):909-913.
PubMed   |  Link to Article
Hobbs  CA, Cleves  MA, Keith  C, Ghaffar  S, James  SJ.  NKX2.5 and congenital heart defects: a population-based study. Am J Med Genet A. 2005;134A(2):223-225.
PubMed   |  Link to Article
Hobbs  CA, James  SJ, Parsian  A,  et al.  Congenital heart defects and genetic variants in the methylenetetrahydroflate reductase gene. J Med Genet. 2006;43(2):162-166.
PubMed   |  Link to Article
Olshan  AF, Hobbs  CA, Shaw  GM.  Discovery of genetic susceptibility factors for human birth defects: an opportunity for a National Agenda. Am J Med Genet A. 2011;155A(8):1794-1797.
PubMed   |  Link to Article
Redon  R, Ishikawa  S, Fitch  KR,  et al.  Global variation in copy number in the human genome. Nature. 2006;444(7118):444-454.
PubMed   |  Link to Article
Greenway  SC, Pereira  AC, Lin  JC,  et al.  De novo copy number variants identify new genes and loci in isolated sporadic tetralogy of Fallot. Nat Genet. 2009;41(8):931-935.
PubMed   |  Link to Article
Warburton  D, Ronemus  M, Kline  J,  et al.  The contribution of de novo and rare inherited copy number changes to congenital heart disease in an unselected sample of children with conotruncal defects or hypoplastic left heart disease. Hum Genet. 2014;133(1):11-27.
PubMed   |  Link to Article
Bardakjian  TM, Kwok  S, Slavotinek  AM, Schneider  AS.  Clinical report of microphthalmia and optic nerve coloboma associated with a de novo microdeletion of chromosome 16p11.2. Am J Med Genet A. 2010;152A(12):3120-3123.
PubMed   |  Link to Article
Srisupundit  K, Brady  PD, Devriendt  K,  et al.  Targeted array comparative genomic hybridisation (array CGH) identifies genomic imbalances associated with isolated congenital diaphragmatic hernia (CDH). Prenat Diagn. 2010;30(12-13):1198-1206.
PubMed   |  Link to Article
Shi  M, Mostowska  A, Jugessur  A,  et al.  Identification of microdeletions in candidate genes for cleft lip and/or palate. Birth Defects Res A Clin Mol Teratol. 2009;85(1):42-51.
PubMed   |  Link to Article
Mefford  HC, Shafer  N, Antonacci  F,  et al.  Copy number variation analysis in single-suture craniosynostosis: multiple rare variants including RUNX2 duplication in two cousins with metopic craniosynostosis. Am J Med Genet A. 2010;152A(9):2203-2210.
PubMed   |  Link to Article
Weber  S, Landwehr  C, Renkert  M,  et al.  Mapping candidate regions and genes for congenital anomalies of the kidneys and urinary tract (CAKUT) by array-based comparative genomic hybridization. Nephrol Dial Transplant. 2011;26(1):136-143.
PubMed   |  Link to Article
Zhang  F, Gu  W, Hurles  ME, Lupski  JR.  Copy number variation in human health, disease, and evolution. Annu Rev Genomics Hum Genet. 2009;10:451-481.
PubMed   |  Link to Article
International Human Genome Sequencing Consortium.  Finishing the euchromatic sequence of the human genome. Nature. 2004;431(7011):931-945.
PubMed   |  Link to Article
Metzker  ML.  Sequencing technologies—the next generation. Nat Rev Genet. 2010;11(1):31-46.
PubMed   |  Link to Article
Korf  BR, Rehm  HL.  New approaches to molecular diagnosis. JAMA. 2013;309(14):1511-1521.
PubMed   |  Link to Article
Liu  L, Li  Y, Li  S,  et al.  Comparison of next-generation sequencing systems. J Biomed Biotechnol. 2012;2012:251364.
PubMed
Loman  NJ, Misra  RV, Dallman  TJ,  et al.  Performance comparison of benchtop high-throughput sequencing platforms. Nat Biotechnol. 2012;30(5):434-439.
PubMed   |  Link to Article
Vasta  V, Merritt  JL  II, Saneto  RP, Hahn  SH.  Next-generation sequencing for mitochondrial diseases: a wide diagnostic spectrum. Pediatr Int. 2012;54(5):585-601.
PubMed   |  Link to Article
Bamshad  MJ, Ng  SB, Bigham  AW,  et al.  Exome sequencing as a tool for Mendelian disease gene discovery. Nat Rev Genet. 2011;12(11):745-755.
PubMed   |  Link to Article
Manolio  TA, Collins  FS, Cox  NJ,  et al.  Finding the missing heritability of complex diseases. Nature. 2009;461(7265):747-753.
PubMed   |  Link to Article
Zaidi  S, Choi  M, Wakimoto  H,  et al.  De novo mutations in histone-modifying genes in congenital heart disease. Nature. 2013;498(7453):220-223.
PubMed   |  Link to Article
Thomas  R, Sanna-Cherchi  S, Warady  BA, Furth  SL, Kaskel  FJ, Gharavi  AG.  HNF1B and PAX2 mutations are a common cause of renal hypodysplasia in the CKiD cohort. Pediatr Nephrol. 2011;26(6):897-903.
PubMed   |  Link to Article
Gelb  BD.  Recent advances in understanding the genetics of congenital heart defects [published online August 29, 2013]. Curr Opin Pediatr. doi:10.1097/MOP.0b013e3283648826.
PubMed
GeneTests. Bio-Reference Laboratories website. http://www.genetests.org. Accessed May 14, 2013.
Rubinstein  WS, Maglott  DR, Lee  JM,  et al.  The NIH genetic testing registry: a new, centralized database of genetic tests to enable access to comprehensive information and improve transparency. Nucleic Acids Res. 2013;41(Database issue):D925-D935.
PubMed   |  Link to Article
Green RC, Berg JS, Grody WW, et al. American College of Medicine Genetics and Genomics: ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing. https://www.acmg.net/docs/ACMG_Releases_Highly-Anticipated_Recommendations_on_Incidental_Findings_in_Clinical_Exome_and_Genome_Sequencing.pdf. Accessed January 10, 2014.
Schrijver  I, Aziz  N, Farkas  DH,  et al.  Opportunities and challenges associated with clinical diagnostic genome sequencing: a report of the Association for Molecular Pathology. J Mol Diagn. 2012;14(6):525-540.
PubMed   |  Link to Article
Norton  N, Li  D, Hershberger  RE.  Next-generation sequencing to identify genetic causes of cardiomyopathies. Curr Opin Cardiol. 2012;27(3):214-220.
PubMed   |  Link to Article
Iossifov  I, Ronemus  M, Levy  D,  et al.  De novo gene disruptions in children on the autistic spectrum. Neuron. 2012;74(2):285-299.
PubMed   |  Link to Article
de Ligt  J, Willemsen  MH, van Bon  BW,  et al.  Diagnostic exome sequencing in persons with severe intellectual disability. N Engl J Med. 2012;367(20):1921-1929.
PubMed   |  Link to Article
Weksberg  R, Butcher  DT, Grafodatskaya  D, Choufani  S, Tycko  B. Epigenetics. In: Rimoin  DL, Pyeritz  RE, Korf  BR, eds. Emery and Rimoin's Principles and Practice of Medical Genetics.6th ed. Philadelphia, PA: Elsevier Sciences; 2013.
Berger  SL, Kouzarides  T, Shiekhattar  R, Shilatifard  A.  An operational definition of epigenetics. Genes Dev. 2009;23(7):781-783.
PubMed   |  Link to Article
Li  E, Bestor  TH, Jaenisch  R.  Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell. 1992;69(6):915-926.
PubMed   |  Link to Article
Okano  M, Bell  DW, Haber  DA, Li  E.  DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell. 1999;99(3):247-257.
PubMed   |  Link to Article
Pradhan  S, Bacolla  A, Wells  RD, Roberts  RJ.  Recombinant human DNA (cytosine-5) methyltransferase: I, expression, purification, and comparison of de novo and maintenance methylation. J Biol Chem. 1999;274(46):33002-33010.
PubMed   |  Link to Article
Wolff  GL, Kodell  RL, Moore  SR, Cooney  CA.  Maternal epigenetics and methyl supplements affect agouti gene expression in Avy/a mice. FASEB J. 1998;12(11):949-957.
PubMed
Cooney  CA, Dave  AA, Wolff  GL.  Maternal methyl supplements in mice affect epigenetic variation and DNA methylation of offspring. J Nutr. 2002;132(8 suppl):2393S-2400S.
PubMed
Gonda  TA, Kim  YI, Salas  MC,  et al.  Folic acid increases global DNA methylation and reduces inflammation to prevent Helicobacter-associated gastric cancer in mice. Gastroenterology.2012;142(4):824-833.e7.
PubMed   |  Link to Article
Frommer  M, McDonald  LE, Millar  DS,  et al.  A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc Natl Acad Sci U S A. 1992;89(5):1827-1831.
PubMed   |  Link to Article
Rakyan  VK, Down  TA, Balding  DJ, Beck  S.  Epigenome-wide association studies for common human diseases. Nat Rev Genet. 2011;12(8):529-541.
PubMed   |  Link to Article
Maegawa  S, Hinkal  G, Kim  HS,  et al.  Widespread and tissue specific age-related DNA methylation changes in mice. Genome Res. 2010;20(3):332-340.
PubMed   |  Link to Article
Tycko  B.  Allele-specific DNA methylation: beyond imprinting. Hum Mol Genet. 2010;19(R2):R210-R220.
PubMed   |  Link to Article

Correspondence

CME
Also Meets CME requirements for:
Browse CME for all U.S. States
Accreditation Information
The American Medical Association is accredited by the Accreditation Council for Continuing Medical Education to provide continuing medical education for physicians. The AMA designates this journal-based CME activity for a maximum of 1 AMA PRA Category 1 CreditTM per course. Physicians should claim only the credit commensurate with the extent of their participation in the activity. Physicians who complete the CME course and score at least 80% correct on the quiz are eligible for AMA PRA Category 1 CreditTM.
Note: You must get at least of the answers correct to pass this quiz.
Please click the checkbox indicating that you have read the full article in order to submit your answers.
Your answers have been saved for later.
You have not filled in all the answers to complete this quiz
The following questions were not answered:
Sorry, you have unsuccessfully completed this CME quiz with a score of
The following questions were not answered correctly:
Commitment to Change (optional):
Indicate what change(s) you will implement in your practice, if any, based on this CME course.
Your quiz results:
The filled radio buttons indicate your responses. The preferred responses are highlighted
For CME Course: A Proposed Model for Initial Assessment and Management of Acute Heart Failure Syndromes
Indicate what changes(s) you will implement in your practice, if any, based on this CME course.
Submit a Comment

Multimedia

Some tools below are only available to our subscribers or users with an online account.

991 Views
1 Citations

Related Content

Customize your page view by dragging & repositioning the boxes below.

Articles Related By Topic
Related Collections
PubMed Articles
×