Description of the methodology used in an ongoing pediatric care interventional study of children born with cleft lip and palate in South America [NCT00097149]

Rare variant modifier analysis identifies variants in SEC24D associated with orofacial cleft subtypes

As one of the most common structural birth defects, orofacial clefts (OFCs) have been studied for decades, and recent studies have demonstrated that there are genetic differences between the different phenotypic presentations of OFCs. However, the contribution of rare genetic variation genome-wide to different subtypes of OFCs has been understudied, with most studies focusing on common genetic variation or rare variation within targeted regions of the genome. Therefore, we used whole-genome sequencing data from the Gabriella Miller Kids First Pediatric Research Program to conduct a gene-based burden analysis to test for genetic modifiers of cleft lip (CL) vs cleft lip and palate (CLP). We found that there was a significantly increased burden of rare variants in SEC24D in CL cases compared to CLP cases (p = 6.86 [Formula: see text] 10-7). Of the 15 variants within SEC24D, 53.3% were synonymous, but overlapped a known craniofacial enhancer. We then tested whether these variants could alter predicted transcription factor binding sites (TFBS), and found that the rare alleles destroyed binding sites for 9 transcription factors (TFs), including Pax1 (p = 0.0009), and created binding sites for 23 TFs, including Pax6 (p = 6.12 [Formula: see text] 10-5) and Pax9 (p = 0.0001), which are known to be involved in normal craniofacial development, suggesting a potential mechanism by which these synonymous variants could have a functional impact. Overall, this study indicates that rare genetic variation may contribute to the phenotypic heterogeneity of OFCs and suggests that regulatory variation may also contribute and warrant further investigation in future studies of genetic variants controlling risk to OFC.

Rare genetic variants in SEC24D modify orofacial cleft phenotypes

As one of the most common structural birth defects, orofacial clefts (OFCs) have been studied for decades, and recent studies have demonstrated that there are genetic differences between the different phenotypic presentations of OFCs. However, the contribution of rare genetic variation genome-wide to different subtypes of OFCs has been understudied, with most studies focusing on common genetic variation or rare variation within targeted regions of the genome. Therefore, we used whole-genome sequencing data from the Gabriella Miller Kids First Pediatric Research Program to conduct a gene-based burden analysis to test for genetic modifiers of cleft lip (CL) vs cleft lip and palate (CLP). We found that there was a significantly increased burden of rare variants in SEC24D in CL cases compared to CLP cases (p=6.86×10-7). Of the 15 variants within SEC24D, 53.3% were synonymous, but overlapped a known craniofacial enhancer. We then tested whether these variants could alter predicted transcription factor binding sites (TFBS), and found that the rare alleles destroyed binding sites for 9 transcription factors (TFs), including Pax1 (p=0.0009), and created binding sites for 23 TFs, including Pax6 (p=6.12×10-5) and Pax9 (p= 0.0001), which are known to be involved in normal craniofacial development, suggesting a potential mechanism by which these synonymous variants could have a functional impact. Overall, this study demonstrates that rare genetic variation contributes to the phenotypic heterogeneity of OFCs and suggests that regulatory variation may also contribute and warrant further investigation in future studies of genetic variants controlling risk to OFC.

Gene×environment associations in orofacial clefting

This chapter reviews the evidence of gene×environment interactions (G×E) in the etiology of orofacial cleft birth defects (OFCs), specifically cleft lip (CL), cleft palate (CP), and cleft lip with or without cleft palate (CL/P). We summarize the current state of our understanding of the genetic architecture of nonsyndromic OFCs and the evidence that maternal exposures during pregnancy influence risk of OFCs. Further, we present possible candidate gene pathways for these exposures including metabolism of folates, metabolism of retinoids, retinoic acid receptor signaling, aryl hydrocarbon receptor signaling, glucocorticoid receptor signaling, and biotransformation and transport. We review genes in these pathways with prior evidence of association with OFCs, genes with evidence from prior candidate gene G×E studies, and genes identified from genome-wide searches specifically for identifying G×E. Finally, we suggest future directions for G×E research in OFCs.

FAT4 identified as a potential modifier of orofacial cleft laterality

Orofacial clefts (OFCs) are common (1 in 700 births) congenital malformations that include a cleft lip (CL) and cleft lip and palate (CLP). These OFC subtypes are also heterogeneous themselves, with the CL occurring on the left, right, or both sides of the upper lip. Unilateral CL and CLP have a 2:1 bias towards left-sided clefts, suggesting a nonrandom process. Here, we performed a study of left- and right-sided clefts within the CL and CLP subtypes to better understand the genetic factors controlling cleft laterality. We conducted genome-wide modifier analyses by comparing cases that had right unilateral CL (RCL; N = 130), left unilateral CL (LCL; N = 216), right unilateral CLP (RCLP; N = 416), or left unilateral CLP (LCLP; N = 638), and identified a candidate region on 4q28, 400 kb downstream from FAT4, that approached genome-wide significance for LCL versus RCL (p = 8.4 × 10^-8 ). Consistent with its potential involvement as a genetic modifier of CL, we found that Fat4 exhibits a specific domain of expression in the mesenchyme of the medial nasal processes that form the median upper lip. Overall, these results suggest that the epidemiological similarities in left- to right-sided clefts in CL and CLP are not reflected in the genetic association results.

Oral Health-Related Quality of Life of Children Born With Orofacial Clefts in Ethiopia and Their Parents

OBJECTIVE

To assess the oral health-related quality of life (OH-RQoL) using a translated standardized measure in an understudied population of Ethiopian children born with orofacial clefts (OFCs) and their parents.

METHODS

Using a descriptive study design, we assessed the OH-RQoL of 41 patients with OFCs between the ages of 8 and 17 years and their parents. Participants received multidisciplinary cleft care from 2008 to 2016. They completed an Amharic translation of the Child Oral Health Impact Profile (COHIP).

RESULTS

There was strong internal reliability with the translated COHIP for parents and patients. Parents' COHIP scores ranged from 67 to 186, and patients' scores were 78 to 190. The mean for patients and parents was 155, indicating good OH-RQoL.

CONCLUSION

The Amharic translation of the COHIP appears appropriate for use with families in Ethiopia. Both parents and patients reported OH-RQoL at similar levels as other international populations.

Long-term effects of oral clefts on health care utilization: a sibling comparison

Oral clefts are among the most common birth defects affecting thousands of newborns each year, but little is known about their potential long-term consequences. In this paper, we explore the impact of oral clefts on health care utilization over most of the lifespan. To account for time-invariant unobservable parental characteristics, we compare affected individuals with their own unaffected siblings. The analysis is based on unique data comprising the entire cohort of individuals born with oral clefts in Denmark tracked until adulthood in administrative register data. We find that children with oral clefts use more health services than their unaffected siblings. Additional results show that the effects are driven primarily by congenital malformation-related hospitalizations and intake of anti-infectives. Although the absolute differences in most health care utilization diminish over time, affected individuals have slightly higher utilization of some health care services in adulthood (particularly for diseases of the nervous and respiratory system). These results have important implications for affected individuals, their families, and their health professionals.

Genetics of cleft lip and cleft palate

Orofacial clefts are common birth defects and can occur as isolated, nonsyndromic events or as part of Mendelian syndromes. There is substantial phenotypic diversity in individuals with these birth defects and their family members: from subclinical phenotypes to associated syndromic features that is mirrored by the many genes that contribute to the etiology of these disorders. Identification of these genes and loci has been the result of decades of research using multiple genetic approaches. Significant progress has been made recently due to advances in sequencing and genotyping technologies, primarily through the use of whole exome sequencing and genome-wide association studies. Future progress will hinge on identifying functional variants, investigation of pathway and other interactions, and inclusion of phenotypic and ethnic diversity in studies.

Application of neurodevelopmental screening to a sample of South American infants: the Bayley Infant Neurodevelopmental Screener (BINS)

OBJECTIVE

To evaluate the utility of the Bayley Infant Neurodevelopmental Screener (BINS), standardized in the US, for South American infants, 3-24 months of age.

METHODS

Thirty-five physicians administered the BINS to 2471 South American infants recruited during routine well-child visits, 578 (23%) from Brazil and 1893 (77%) from six other South American countries. The BINS was translated into Spanish and Portuguese and participating physicians were trained to administer the BINS. Physician inter-rater agreement with training tapes was 84.4%; test-retest reliability for age item sets ranged from 0.80 to 0.93 (Pearson's r). Infants were classified into being at low, moderate, or high risk for developmental delay or neurological impairment based on their total BINS score. The sample was stratified by infant's age, sex and language (Spanish and Portuguese). The BINS scores were compared to the scores of the US infant sample used to standardize the BINS.

RESULTS

Female infants performed higher than male at 16-20 months and 21-24 months; male infant scores were more variable at 5-6 months. Scores on only two items were significantly different between Spanish and Portuguese speaking participants. South American scores were typically significantly higher than the US sample, and a lower proportion of infants were classified as being at high risk in the South American sample than in the US standardization sample.

CONCLUSION

Overall, the results of this study indicate that the BINS is feasible and appropriate for neurodevelopmental screening in South America. Further studies are needed to confirm the BINS utility in South America, including its use with a clinical sample.

The effects of oral clefts on hospital use throughout the lifespan

Background

Oral clefts are one of the most common birth defects worldwide. They require multiple healthcare interventions and add significant burden on the health and quality of life of affected individuals. However, not much is known about the long term effects of oral clefts on health and healthcare use of affected individuals. In this study, we evaluate the effects of oral clefts on hospital use throughout the lifespan.

Methods

We estimate two-part regression models for hospital admission and length of stay for several age groups up to 68 years of age. The study employs unique secondary population-based data from several administrative inpatient, civil registration, demographic and labor market databases for 7,670 individuals born with oral clefts between 1936 and 2002 in Denmark, and 220,113 individuals without oral clefts from a 5% random sample of the total birth population from 1936 to 2002.

Results

Oral clefts significantly increase hospital use for most ages below 60 years by up to 233% for children ages 0-10 years and 16% for middle age adults. The more severe cleft forms (cleft lip with palate) have significantly larger effects on hospitalizations than less severe forms.

Conclusions

The results suggest that individuals with oral clefts have higher hospitalization risks than the general population throughout most of the lifespan.

The Impact of Household Investments on Early Child Neurodevelopment and on Racial and Socioeconomic Developmental Gaps - Evidence from South America

This paper assesses the effects of household investments through child educating activities on child neurodevelopment between the ages of 3 and 24 months, and evaluates whether investments explain racial and socioeconomic developmental gaps in South America. Quantile regression is used to evaluate the heterogeneity in investment effects by unobserved developmental endowments. The study finds large positive investment effects on early child neurodevelopment, with generally larger effects among children with low developmental endowments (children at the left margin of the development distribution). Investments explain part of the observed racial gaps and the whole socioeconomic developmental gap. Investments may compensate for low endowments and policy interventions to increase investments may reduce early development gaps and result in high social and economic returns.

The effect of systematic pediatric care on neonatal mortality and hospitalizations of infants born with oral clefts

Background

Cleft lip and/or palate (CL/P) increase mortality and morbidity risks for affected infants especially in less developed countries. This study aimed at assessing the effects of systematic pediatric care on neonatal mortality and hospitalizations of infants with cleft lip and/or palate (CL/P) in South America.

Methods

The intervention group included live-born infants with isolated or associated CL/P in 47 hospitals between 2003 and 2005. The control group included live-born infants with CL/P between 2001 and 2002 in the same hospitals. The intervention group received systematic pediatric care between the 7^th and 28^th day of life. The primary outcomes were mortality between the 7^th and 28^th day of life and hospitalization days in this period among survivors adjusted for relevant baseline covariates.

Results

There were no significant mortality differences between the intervention and control groups. However, surviving infants with associated CL/P in the intervention group had fewer hospitalization days by about six days compared to the associated control group.

Conclusions

Early systematic pediatric care may significantly reduce neonatal hospitalizations of infants with CL/P and additional birth defects in South America. Given the large healthcare and financial burden of CL/P on affected families and the relatively low cost of systematic pediatric care, improving access to such care may be a cost-effective public policy intervention.

Trial Registration

ClinicalTrials.gov: NCT00097149

Elevated infant mortality rates among oral cleft and isolated oral cleft cases: a meta-analysis of studies from 1943 to 2010

Objective : To review available published literature in order to obtain a more comprehensive assessment of the association between infant mortality and oral clefts, overall and isolated. Design : A wide-ranging search of published studies relating infant mortality rates to oral clefts and congenital malformations was conducted, yielding applicable data sets. Settings of the included studies varied to a limited extent, although all were conducted within high-income countries with superior health indicators. These results were tabulated and meta-analyzed. Random effects odds ratios comparing each data set with its respective population have been used to account for differing settings and specific infant mortality rates. Results : Nine articles with relatable data were included in these meta-analyses. The calculated odds ratio of infant mortality associated with oral cleft cases, including those with associated malformations, was substantial: 9.466 (95% confidence interval, 6.153 to 14.560). Excluding oral cleft cases with associated malformations, the odds ratio, although lower, was still significant: 2.073 (95% confidence interval, 1.390 to 3.092). Conclusions : Compared with the overall population, infants with oral clefts have nine times the odds of dying within the first year of life. Furthermore, even without additional malformations, infants with oral clefts are still twice as likely to die before 1 year of age. Current research points to a substantially higher relative risk of infant mortality among oral cleft cases in developing countries. Additional research is essential to determine the sources of these raised infant mortality rates and possible interventions to decrease them.

Associated anomalies among infants with oral clefts at birth and during a 1-year follow-up

Reports of birth defects rates may focus on defects observed in the newborn period or include defects diagnosed at older ages. However, little information is available on the rates of additional anomalies detected after birth or on the ages at which such anomalies are diagnosed. The aims of this work were to describe the initial diagnoses of oral clefts, isolated or associated with other defects, in newborn infants ascertained in hospitals of the ECLAMC network, and diagnostic changes that occurred due to detection of additional defects during a 1-year follow-up period. Seven hundred ten liveborn infants with cleft lip only (CLO), cleft lip with cleft palate (CLP), or cleft palate (CP) were ascertained between 2003 and 2005. Prevalence estimates of isolated and associated (ASO) clefts, diagnoses in infants with associated clefts, and the percentage of isolated clefts that were reclassified as associated were established. Birth prevalence estimates (per 1,000) were as follows: Total: 1.7; CLP: 0.94 (ASO = 23.5%); CP: 0.46 (ASO = 42.3%); CLO: 0.28 (ASO = 7.6%). Initial diagnoses in infants with associated clefts included 38 infants with chromosomal abnormalities, 33 with non-chromosomal syndromes, 16 with malformation sequences, and 98 with multiple anomalies of unknown etiology. Seven percent of newborns initially classified as isolated were later reclassified as associated. Ten infants without associated defects or clinically suspected syndromes were diagnosed as syndromic only through laboratory findings or family history, illustrating the difference between the terms associated versus isolated, which refers to presence or absence of associated anomalies, and syndromic versus non-syndromic, which refers to etiology.

The Impact of Maternal Smoking during Pregnancy on Early Child Neurodevelopment

Early child neurodevelopment has major impacts on future human capital and health. However, not much is known about the impacts of prenatal risk factors on child neurodevelopment. This study evaluates the effects of maternal smoking during pregnancy on child neurodevelopment between 3 and 24 months of age and interactions with socioeconomic status (SES). Data from a unique sample of children from South America are employed. Smoking has large adverse effects on neurodevelopment, with larger effects in the low SES sample. The study results highlight the importance of early interventions beginning before and during pregnancy for enhancing child development and future human capital attainment.

The association between interferon regulatory factor 6 (IRF6) and nonsyndromic cleft lip with or without cleft palate in a Honduran population

OBJECTIVES/HYPOTHESIS

Interferon regulatory factor 6 (IRF6), the gene that causes van der Woude syndrome (VWS), is a candidate gene for nonsyndromic cleft lip with or without cleft palate (NSCLP) because a number of studies have supported an association between NSCLP and single nucleotide polymorphisms (SNPs) in IRF6 in several populations. This project investigated the contribution of IRF6 to NSCLP in the Honduran population, a previously unstudied group with a high prevalence of NSCLP.

STUDY DESIGN

Family-based joint linkage and association study.

METHODS

A set of five SNPs in and around IRF6 previously reported to be associated with NSCLP were tested for association with NSCLP in 276 affected and unaffected Honduran individuals from 59 families with at least two members affected by clefting and at least one member with confirmed NSCLP.

RESULTS

We observed support of linkage for three SNPs-rs1856161, rs2235371, and rs2235377-under a dominant model (log of odds [LODs] = 1.97, 1.56, 1.73, respectively). Subsequent single-point, haplotype, and joint linkage and association analyses continued to support the association with NSCLP (P < or = .05) at these three SNPs. When analysis was restricted to NSCLP cases, excluding cleft palate only cases, support for association strengthened.

CONCLUSIONS

This is the first study to demonstrate that three candidate SNPs within IRF6 are significantly associated with NSCLP in the Honduran population, providing the first genetic clue to NSCLP observed in the Honduran population and confirming findings from populations in other parts of the world. Further studies are needed to identify the putative variant(s).

The impact of orofacial clefts on quality of life and healthcare use and costs

Orofacial clefts are common birth defects that may impose a large burden on the health, quality of life, and socioeconomic well-being of affected individuals and families. They also result in significant healthcare use and costs. Understanding the impact of orofacial clefts on these outcomes is important for identifying unmet needs and developing public policies to reduce the burden of orofacial clefts at the individual, family and societal levels. This paper reviews and summarizes the main findings of recent studies that have evaluated the impact of orofacial clefts on these outcomes, with a focus on quality of life, socioeconomic outcomes, long-term health, and healthcare use and costs. Several studies identify an increased burden of orofacial clefts on these outcomes, but some of the findings are inconsistent. A summary of the primary limitations of the studies in this area is presented, along with recommendations and directions for future research.

Pregnancy outcome after levonorgestrel-only emergency contraception failure: a prospective cohort study

BACKGROUND

Levonorgestrel (LNG), as a dedicated emergency contraception (EC) product, has been available over-the-counter in China for 10 years. Until now, only a small number of deliveries after LNG-EC failure have been documented.

METHODS

This study was a prospective comparative cohort study. A group of 332 pregnant women who had used LNG-EC during the conception cycle was recruited, and matched to a group of 332 pregnant women without the exposure to LNG. Congenital malformations, perinatal complications and delivery circumstances were investigated in this study.

RESULTS

There were 31 pregnant women in the study group and 28 in the comparison group miscarried within 14 weeks of gestation. In the study and comparison groups, four malformations were found in each group. In the study group, both birthweight (3416 versus 3345 g, P = 0.040) and the sex ratio of birth (boys/girls, 1.14 versus 0.90, P = 0.153) were higher than in the comparison group. There were no statistically significant differences in the incidence of miscarriage or malformation or in the neonatal outcome between the two groups.

CONCLUSIONS

There was no association between the use of LNG-EC pills and the risk of major congenital malformations, pregnancy complications or any other adverse pregnancy outcomes in our study.