Innovative approach to identify multigenomic and environmental interactions associated with birth defects in family-based hybrid designs.

Genes, including those with transgenerational effects, work in concert with behavioral, environmental, and social factors via complex biological networks to determine human health. Understanding complex relationships between causal factors underlying human health is an essential step towards deciphering biological mechanisms. We propose a new analytical framework to investigate the interactions between maternal and offspring genetic variants or their surrogate single nucleotide polymorphisms (SNPs) and environmental factors using family-based hybrid study design. The proposed approach can analyze diverse genetic and environmental factors and accommodate samples from a variety of family units, including case/control-parental triads, and case/control-parental dyads, while minimizing potential bias introduced by population admixture. Comprehensive simulations demonstrated that our innovative approach outperformed the log-linear approach, the best available method for case-control family data. The proposed approach had greater statistical power and was capable to unbiasedly estimate the maternal and child genetic effects and the effects of environmental factors, while controlling the Type I error rate against population stratification. Using our newly developed approach, we analyzed the associations between maternal and fetal SNPs and obstructive and conotruncal heart defects, with adjustment for demographic and lifestyle factors and dietary supplements. Fourteen and 11 fetal SNPs were associated with obstructive and conotruncal heart defects, respectively. Twenty-seven and 17 maternal SNPs were associated with obstructive and conotruncal heart defects, respectively. In addition, maternal body mass index was a significant risk factor for obstructive defects. The proposed approach is a powerful tool for interrogating the etiological mechanism underlying complex traits.

Generalized multifactor dimensionality reduction approaches to identification of genetic interactions underlying ordinal traits.

The manifestation of complex traits is influenced by gene-gene and gene-environment interactions, and the identification of multifactor interactions is an important but challenging undertaking for genetic studies. Many complex phenotypes such as disease severity are measured on an ordinal scale with more than two categories. A proportional odds model can improve statistical power for these outcomes, when compared to a logit model either collapsing the categories into two mutually exclusive groups or limiting the analysis to pairs of categories. In this study, we propose a proportional odds model-based generalized multifactor dimensionality reduction (GMDR) method for detection of interactions underlying polytomous ordinal phenotypes. Computer simulations demonstrated that this new GMDR method has a higher power and more accurate predictive ability than the GMDR methods based on a logit model and a multinomial logit model. We applied this new method to the genetic analysis of low-density lipoprotein (LDL) cholesterol, a causal risk factor for coronary artery disease, in the Multi-Ethnic Study of Atherosclerosis, and identified a significant joint action of the CELSR2, SERPINA12, HPGD, and APOB genes. This finding provides new information to advance the limited knowledge about genetic regulation and gene interactions in metabolic pathways of LDL cholesterol. In conclusion, the proportional odds model-based GMDR is a useful tool that can boost statistical power and prediction accuracy in studying multifactor interactions underlying ordinal traits.

Early and late C-peptide responses during oral glucose tolerance testing are oppositely predictive of type 1 diabetes in autoantibody-positive individuals.

We examined whether the timing of the C-peptide response during an oral glucose tolerance test (OGTT) in relatives of patients with type 1 diabetes (T1D) is predictive of disease onset. We examined baseline 2-h OGTTs from 670 relatives participating in the Diabetes Prevention Trial-Type 1 (age: 13.8 ± 9.6 years; body mass index z-score: 0.3 ± 1.1; 56% male) using univariate regression models. T1D risk increased with lower early C-peptide responses (30-0 min) (χ2 = 28.8, P < 0.001), and higher late C-peptide responses (120-60 min) (χ2 = 23.3, P < 0.001). When both responses were included in a proportional hazards model, they remained independently and oppositely associated with T1D, with a stronger overall association for the combined model than either response alone (χ2 = 41.1; P < 0.001). Using receiver operating characteristic curve analysis, the combined early and late C-peptide response was more accurately predictive of T1D than area under the curve C-peptide (P = 0.005). Our findings demonstrate that lower early and higher late C-peptide responses serve as indicators of increased T1D risk.

Estimated fetal weight and severe neonatal outcomes in preterm prelabor rupture of membranes.

Objectives Our aim was to study the association of clinical variables obtainable before delivery for severe neonatal outcomes (SNO) and develop a clinical tool to calculate the prediction probability of SNO in preterm prelabor rupture of membranes (PPROM). Methods This was a prospective study from October 2015 to May 2018. We included singleton pregnancies with PPROM and an estimated fetal weight (EFW) two weeks before delivery. We excluded those with fetal anomalies or fetal death. We examined the association between SNO and variables obtainable before delivery such as gestational age (GA) at PPROM, EFW, gender, race, body mass index, chorioamnioitis. SNO was defined as having at least one of the following: respiratory distress syndrome, intraventricular hemorrhage, necrotizing enterocolitis, neonatal sepsis, or neonatal death. The most parsimonious logistic regression models was constructed using the best subset selection model approach, and receiver operator curves were utilized to evaluate the prognostic accuracy of these clinical variables for SNO. Results We included 106 pregnancies, 42 had SNO (39.6%). The EFW (area under the receiver operating characteristic curve [AUC]=0.88) and GA at PPROM (AUC=0.83) were significant predictors of SNO. The addition of any of the other variables did not improve the predictive probability of EFW for the prediction of SNO. Conclusions The EFW had the strongest association with SNO in in our study among variables obtainable before delivery. Other variables had no significant effect on the prediction probability of the EFW. Our findings should be validated in larger studies.

Associations of HbA1c with the timing of C-peptide responses during the oral glucose tolerance test at the diagnosis of type 1 diabetes.

BACKGROUND: In new onset type 1 diabetes (T1D), overall C-peptide measures such as area under the curve (AUC) C-peptide and peak C-peptide are useful for estimating the extent of ß-cell dysfunction, and for assessing responses to intervention therapy. However, measures of the timing of C-peptide responsiveness could have additional value. OBJECTIVES: We assessed the contribution of the timing of C-peptide responsiveness during oral glucose tolerance tests (OGTTs) to hemoglobin A1c (HbA1c) variation at T1D diagnosis. METHODS: We analyzed data from 85 individuals <18 years with OGTTs and HbA1c measurements at diagnosis. Overall [AUC and peak C-peptide] and timing measures [30-0 minute C-peptide (early); 60 to 120 minute C-peptide sum-30 minutes (late); 120/30 C-peptide; time to peak C-peptide] were utilized. RESULTS: At diagnosis, the mean (±SD) age was 11.2 ± 3.3 years, body mass index (BMI)-z was 0.4 ± 1.1, 51.0% were male. The average HbA1c was 43.54 ± 8.46 mmol/mol (6.1 ± 0.8%). HbA1c correlated inversely with the AUC C-peptide (P < 0.001), peak C-peptide (P < 0.001), early and late C-peptide responses (P < 0.001 each), and 120/30 C-peptide (P < 0.001). Those with a peak C-peptide occurring at ≤60 minutes had higher HbA1c values than those with peaks later (P = 0.003). HbA1c variance was better explained with timing measures added to regression models (R2 = 11.6% with AUC C-peptide alone; R2 = 20.0% with 120/30 C-peptide added; R2 = 13.7% with peak C-peptide alone, R2 = 20.4% with timing of the peak added). Similar associations were seen between the 2-hour glucose and the C-peptide measures. CONCLUSIONS: These findings show that the addition of timing measures of C-peptide responsiveness better explains HbA1c variation at diagnosis than standard measures alone.

Impact of Radiation and Transcorporeal Artificial Sphincter Placement in Patients with Prior Urethral Cuff Erosion: Results from a Retrospective Multicenter Analysis.

PURPOSE: Many providers elect to use a transcorporeal approach for artificial urinary sphincter placement in an attempt to minimize risks, given the increased risk of complications in revision cases. We present outcomes in a multicenter retrospective analysis of artificial urinary sphincter cuff reimplantation in patients with prior cuff erosion with special consideration given to the transcorporeal approach. MATERIALS AND METHODS: We compiled a multi-institutional database of patients who underwent artificial urinary sphincter reimplantation after prior urethral erosion. Of the 34 identified patients 24 underwent transcorporeal cuff replacement. Patients with transcorporeal cuff replacement were further analyzed with specific stratification for radiation therapy. RESULTS: The rate of subsequent complications after eroded cuff reimplantation was 32.4% (11 of 34 patients). The most frequent complication was recurrent erosion, which developed in 9 of the 34 patients (26.4%). Repeat artificial urinary sphincter complications developed more frequently in patients with history of radiation compared to nonirradiated patients (8 of 16 or 50% vs 3 of 18 or 16.7%). However, this difference was not statistically significant (p = 0.066). The transcorporeal technique was applied in 24 of 33 patients (70.5%) and relative to the nontranscorporeal group there was no difference in the complication rate (p = 0.438). On subgroup analysis of the transcorporeal group there was a higher rate of repeat complications in irradiated patients (p = 0.006). CONCLUSIONS: These data suggest that transcorporeal cuff reimplantation may not decrease the incidence of repeat complications after prior cuff erosion. However, radiation therapy is associated with a worse outcome even when transcorporeal cuff placement is performed.

Prior Radiation Therapy Decreases Time to Idiopathic Erosion of Artificial Urinary Sphincter: A Multi-Institutional Analysis.

PURPOSE: Substantial controversy and conflicting data exist regarding the survival of the artificial urinary sphincter in patients with prior radiation therapy. We present data from a multi-institutional analysis examining the effect of prior radiation for prostate cancer on device survival. MATERIALS AND METHODS: A database was compiled of patients with artificial urinary sphincter cuff erosion, which included demographic and comorbid patient characteristics, functional analyses and interventions. We identified 80 patients with iatrogenic or idiopathic artificial urinary sphincter erosion. Idiopathic erosion cases were further analyzed to determine factors influencing device survival with specific stratification for radiation therapy. RESULTS: A total of 56 patients were identified with idiopathic artificial urinary sphincter erosion. Of those men 33 (58.9%) had not undergone radiation treatment while 23 (41.1%) had a history of brachytherapy or external beam radiotherapy. In patients without radiation erosion-free median device survival was 3.15 years (95% CI 1.95-5.80), in contrast to the median device survival of only 1.00 year (95% CI 0.36-3.00) in irradiated patients. The erosion-free survival experience of patients with vs without radiation differed significantly (Wilcoxon-Breslow test for equality of survivor functions p = 0.03). CONCLUSIONS: Radiation therapy in patients with known idiopathic cuff erosion in this contemporary analysis correlated with significantly increased time to erosion. Mean time to idiopathic cuff erosion was accelerated by approximately 2 years in irradiated cases. To our knowledge these data represent the first demonstration of substantial outcome differences associated with radiation in patients with an artificial urinary sphincter who present specifically with cuff erosion.

Human Breast-Milk Feeding Enhances the Humoral and Cell-Mediated Immune Response in Neonatal Piglets.

Background: The benefits of breastfeeding infants are well characterized, including those on the immune system. However, determining the mechanism by which human breast milk (HBM) elicits effects on immune response requires investigation in an appropriate animal model. Objective: The primary aim of this study was to develop a novel porcine model and to determine the differential effects of feeding HBM and a commercial milk formula (MF) on immune response and gastrointestinal microbial colonization in a controlled environment. Methods: Male piglets were fed HBM (n = 26) or MF (n = 26) from day 2 through day 21. Piglets were vaccinated (n = 9/diet group) with cholera toxin and cholera toxin subunit B (CTB) and tetanus toxoid at 21 d or were fed placebo (n = 6/diet group) and then weaned to a standard solid diet at the age of 21 d. Humoral and cell-mediated immune responses were assessed from blood on days 35 and 48. Immune response was further examined from tissues, including mesenteric lymph nodes (MLNs), Peyer's patches (PPs), and spleen. The colonization of gut microbiota was characterized from feces on days 16 and 49. Results: Serum antibody titers in piglets fed HBM were 4-fold higher (P < 0.05) to CTB and 3-fold higher (P < 0.05) to tetanus toxoid compared with piglets fed MF on day 48. Compared with MF, the numbers of immunoglobulin A antibody-producing cells to CTB were 13-fold higher (P < 0.05) in MLNs and 11-fold higher (P < 0.05) in PPs in the HBM diet group on day 51. In addition, significantly increased T cell proliferation was observed in the HBM group relative to the MF group. Furthermore, microbial diversity in the HBM group was lower (P < 0.05) than in the MF group. Conclusions: This porcine model appears to be valid for studying the effects of early postnatal diet on immune responses and the gastrointestinal microbiome. Our results lay the groundwork for future studies defining the role of infant diet on microbiota and immune function.

Infant Formula Feeding Increases Hepatic Cholesterol 7α Hydroxylase (CYP7A1) Expression and Fecal Bile Acid Loss in Neonatal Piglets.

Background: During the postnatal feeding period, formula-fed infants have higher cholesterol synthesis rates and lower circulating cholesterol concentrations than their breastfed counterparts. Although this disparity has been attributed to the uniformly low dietary cholesterol content of typical infant formulas, little is known of the underlying mechanisms associated with this altered cholesterol metabolism phenotype. Objective: We aimed to determine the molecular etiology of diet-associated changes in early-life cholesterol metabolism with the use of a postnatal piglet feeding model. Methods: Two-day-old male and female White-Dutch Landrace piglets were fed either sow milk (Sow group) or dairy-based (Milk group; Similac Advance powder) or soy-based (Soy group; Emfamil Prosobee Lipil powder) infant formulas until day 21. In addition to measuring serum cholesterol concentrations, hepatic and intestinal genes involved in enterohepatic circulation of cholesterol and bile acids were analyzed by real-time reverse-transcriptase polymerase chain reaction and Western blot. Bile acid concentrations were measured by liquid chromatography-mass spectrometry in serum, liver, and feces. Results: Compared with the Sow group, hepatic cholesterol 7α hydroxylase (CYP7A1) protein expression was 3-fold higher in the Milk group (P < 0.05) and expression was 10-fold higher in the Soy group compared with the Milk group (P < 0.05). Likewise, fecal bile acid concentrations were 3-fold higher in the Soy group compared with the Milk group (P < 0.05). Intestinal mRNA expression of fibroblast factor 19 (Fgf19) was reduced in the Milk and Soy groups, corresponding to 54% and 67% decreases compared with the Sow group. In the Soy group, small heterodimer protein (SHP) protein expression was 30% lower compared with the Sow group (P < 0.05). Conclusions: These results indicate that formula feeding leads to increased CYP7A1 protein expression and fecal bile acid loss in neonatal piglets, and this outcome is linked to reduced efficacy in inhibiting CYP7A1 expression through FGF19 and SHP transcriptional repression mechanisms.

Testing Allele Transmission of an SNP Set Using a Family-Based Generalized Genetic Random Field Method.

Family-based association studies are commonly used in genetic research because they can be robust to population stratification (PS). Recent advances in high-throughput genotyping technologies have produced a massive amount of genomic data in family-based studies. However, current family-based association tests are mainly focused on evaluating individual variants one at a time. In this article, we introduce a family-based generalized genetic random field (FB-GGRF) method to test the joint association between a set of autosomal SNPs (i.e., single-nucleotide polymorphisms) and disease phenotypes. The proposed method is a natural extension of a recently developed GGRF method for population-based case-control studies. It models offspring genotypes conditional on parental genotypes, and, thus, is robust to PS. Through simulations, we presented that under various disease scenarios the FB-GGRF has improved power over a commonly used family-based sequence kernel association test (FB-SKAT). Further, similar to GGRF, the proposed FB-GGRF method is asymptotically well-behaved, and does not require empirical adjustment of the type I error rates. We illustrate the proposed method using a study of congenital heart defects with family trios from the National Birth Defects Prevention Study (NBDPS).

A Behavioral Intervention to Reduce Excessive Gestational Weight Gain.

Objectives Excessive gestational weight gain (GWG) is a key modifiable risk factor for negative maternal and child health. We examined the efficacy of a behavioral intervention in preventing excessive GWG. Methods 230 pregnant women (87.4 % Caucasian, mean age = 29.2 years; second parity) participated in the longitudinal Glowing study (clinicaltrial.gov #NCT01131117), which included six intervention sessions focused on GWG. To determine the efficacy of the intervention in comparison to usual care, participants were compared to a matched contemporary cohort group from the Arkansas Pregnancy Risk Assessment Monitoring Survey (PRAMS). Results Participants attended 98 % of intervention sessions. Mean GWG for the Glowing participants was 12.7 ± 2.7 kg for normal weight women, 12.4 ± 4.9 kg for overweight women, and 9.0 ± 4.2 kg for class 1 obese women. Mean GWG was significantly lower for normal weight and class 1 obese Glowing participants compared to the PRAMS respondents. Similarly, among those who gained excessively, normal weight and class 1 obese Glowing participants had a significantly smaller mean weight gain above the guidelines in comparison to PRAMS participants. There was no significant difference in the overall proportion of the Glowing participants and the proportion of matched PRAMS respondents who gained in excess of the Institute of Medicine GWG guidelines. Conclusions for Practice This behavioral intervention was well-accepted and attenuated GWG among normal weight and class 1 obese women, compared to matched participants. Nevertheless, a more intensive intervention may be necessary to help women achieve GWG within the Institute of Medicine's guidelines.

Uterine responses to feeding soy protein isolate and treatment with 17ß-estradiol differ in ovariectomized female rats.

There are concerns regarding reproductive toxicity from consumption of soy foods, including an increased risk of endometriosis and endometrial cancer, as a result of phytoestrogen consumption. In this study, female rats were fed AIN-93G diets made with casein (CAS) or soy protein isolate (SPI) from postnatal day (PND) 30, ovariectomized on PND 50 and infused with 5 µg/kg/d 17ß-estradiol (E2) or vehicle. E2 increased uterine wet weight (P<0.05). RNAseq analysis revealed that E2 significantly altered expression of 1991 uterine genes (P<0.05). SPI feeding had no effect on uterine weight and altered expression of far fewer genes than E2 at 152 genes (P<0.05). Overlap between E2 and SPI genes was limited to 67 genes. Functional annotation analysis indicated significant differences in uterine biological processes affected by E2 and SPI and little evidence for recruitment of estrogen receptor (ER)α to the promoters of ER-responsive genes after SPI feeding. The major E2 up-regulated uterine pathways were carcinogenesis and extracellular matrix organization, whereas SPI feeding up-regulated uterine peroxisome proliferator activated receptor (PPAR) signaling and fatty acid metabolism. The combination of E2 and SPI resulted in significant regulation of 504 fewer genes relative to E2 alone. The ability of E2 to induce uterine proliferation in response to the carcinogen dimethybenz(a)anthracene (DMBA) as measured by expression of PCNA and Ki67 mRNA was suppressed by feeding SPI (P<0.05). These data suggest that SPI is a selective estrogen receptor modulator (SERM) interacting with a small sub-set of E2-regulated genes and is anti-estrogenic in the presence of endogenous estrogens.

Diets Containing Shiitake Mushroom Reduce Serum Lipids and Serum Lipophilic Antioxidant Capacity in Rats.

BACKGROUND: We previously reported that dietary intake of shiitake mushroom (SM; Lentinus edodes) decreased serum concentrations of polar lipids in male rats. OBJECTIVE: This study evaluated the dietary effects of SM on serum cholesterol-related and serum antioxidant indexes in rats of both sexes. METHODS: Sprague-Dawley rats [38 dams and their offspring (20 males and 20 females/diet)] were fed diets containing 0 (control), 1%, 4%, or 10% (wt:wt) SM powder from gestation day 4 through to postnatal day (PND) 126. Biochemical indexes were monitored during the midgrowth phase (PNDs 50-66). RESULTS: The food consumption by offspring fed the control diet and diets supplemented with SM was not different when measured on PND 65. However, the 4% and 10% SM diets resulted in male rats with 7% lower body weights than those of the other 2 groups on PND 66. SM consumption dose-dependently decreased the concentrations of lipidemia-related factors in sera, irrespective of sex. At PND 50, serum concentrations of total cholesterol, HDL cholesterol, and non-HDL cholesterol in SM-fed male and female rats were generally lower (3-27%) than those in the corresponding control groups. Consumption of the 10% SM diet resulted in significantly decreased (55%) serum triglyceride concentrations relative to the control groups for both sexes. The 10% SM diet elicited a 62% reduction of serum leptin concentrations in females but not in males, and this same diet increased serum insulin (137%) and decreased serum glucose (15%) in males compared with controls. Serum lipophilic antioxidant capacity in males and females fed SM diets was generally lower (31-86%) than that in the control groups. CONCLUSION: SM decreased the concentrations of lipidemia-related factors in rat sera irrespective of sex. The SM-elicited reduction of lipophilic antioxidant capacity irrespective of sex may reflect a lower pro-oxidative state and, hence, improved metabolic profile.

Formula diet alters small intestine morphology, microbial abundance and reduces VE-cadherin and IL-10 expression in neonatal porcine model.

BACKGROUND: Breastfeeding is associated with a variety of positive health outcomes in children and is recommended exclusively for the first 6 months of life; however, 50-70 % of infants in the US are formula-fed. To test the hypothesis that immune system development and function in neonates and infants are significantly influenced by diet, 2-day old piglets were fed soy or milk formula (n = 6/group/gender) until day 21 and compared to a sow-fed group (n = 6/gender). METHODS: Histomorphometric analyses of ileum, jejunum and Peyer's patches were carried out, to determine the inflammation status, mRNA and protein expression of pro-inflammatory, anti-inflammatory and growth-related chemokines and cytokines. RESULTS: In formula-fed animals, increases in ileum and jejunum villus height and crypt depth were observed in comparison to sow-fed animals (jejunum, p < 0.01 villus height, p < 0.04 crypt depth; ileum p < 0.001 villus height, p < 0.002 crypt depth). In formula-fed the lymphoid follicle size (p < 0.01) and germinal centers (p < 0.01) with in the Peyer's patch were significantly decreased in comparison to sow-fed, indicating less immune education. In ileum, formula diet induced significant up-regulation of AMCFII, IL-8, IL-15, VEGFA, LIF, FASL, CXCL11, CCL4, CCL25 and down-regulation of IL-6, IL-9, IL-10, IL-27, IFNA4, CSF3, LOC100152038, and LOC100736831 at the transcript level. We have confirmed some of the mRNA data by measuring protein, and significant down-regulation of anti-inflammatory molecule IL-10 in comparison to sow-fed piglets was observed. To further determine the membrane protein expression in the ileum, VE-cadherin, occludin, and claudin-3, Western blot analyses were conducted. Sow fed piglets showed significantly more VE-Cadherin, which associated with levels of calcium, and putrescine measured. It is possible that differences in GI tract and immune development are related to shifts in the microbiome; notably, there were 5-fold higher amounts of Lactobacillaceae spp and 3 fold higher Clostridia spp in the sow fed group in comparison to milk formula-fed piglets, whereas in milk formula-fed pigs Enterobacteriaceae spp was 5-fold higher. CONCLUSION: In conclusion, formula diet alters GI morphology, microbial abundance, intestinal barrier protein VE-cadherin and anti-inflammatory molecule IL-10 expression. Further characterization of formula effects could lead to modification of infant formula to improve immune function, reduce inflammation and prevent conditions such as allergies and infections.

Are early first trimester weights valid proxies for preconception weight?

BACKGROUND: An accurate estimate of preconception weight is necessary for providing a gestational weight gain range based on the Institute of Medicine's guidelines; however, an accurate and proximal preconception weight is not available for most women. We examined the validity of first trimester weights for estimating preconception body mass index category. METHODS: Under identical measurement conditions, preconception weight and two first trimester weights (i.e., 4-10 and 12 weeks gestation) were obtained (n = 43). RESULTS: The 4-10 week and the 12 week weight correctly classified 95 and 91% women, respectively. Mean weight changes were relatively small overall (M = 0.74 ± 1.99 kg at 4-10 weeks and M = 1.02 ± 2.46 at 12 weeks). There was a significant difference in mean weight gain by body mass index category at 4-10 weeks (-0.09 ± 1.86 kg for normal weight participants vs. 1.61 + 1.76 kg for overweight/obese participants, p = 0.01), but not at 12 weeks (0.53 ± 2.29 kg for normal weight participants vs. 1.54 ± 2.58 kg for overweight/obese participants). CONCLUSIONS: Assigning gestational weight gain guidelines based on an early first trimester weight resulted in 5-9% of women being misclassified depending on the gestational week the weight was obtained. Thus, most women are correctly classified based on a first trimester weight, particularly an early first trimester weight, although it is possible that modeling strategies could be developed to further improve estimates of preconception body mass index category. TRIAL REGISTRATION: Clinicaltrials.gov # NCT01131117 , registered May 25, 2010.

Detecting maternal-fetal genotype interactions associated with conotruncal heart defects: a haplotype-based analysis with penalized logistic regression.

Nonsyndromic congenital heart defects (CHDs) develop during embryogenesis as a result of a complex interplay between environmental exposures, genetics, and epigenetic causes. Genetic factors associated with CHDs may be attributed to either independent effects of maternal or fetal genes, or the intergenerational interactions between maternal and fetal genes. Detecting gene-by-gene interactions underlying complex diseases is a major challenge in genetic research. Detecting maternal-fetal genotype (MFG) interactions and differentiating them from the maternal/fetal main effects has presented additional statistical challenges due to correlations between maternal and fetal genomes. Traditionally, genetic variants are tested separately for maternal/fetal main effects and MFG interactions on a single-locus basis. We conducted a haplotype-based analysis with a penalized logistic regression framework to dissect the genetic effect associated with the development of nonsyndromic conotruncal heart defects (CTD). Our method allows simultaneous model selection and effect estimation, providing a unified framework to differentiate maternal/fetal main effect from the MFG interaction effect. In addition, the method is able to test multiple highly linked SNPs simultaneously with a configuration of haplotypes, which reduces the data dimensionality and the burden of multiple testing. By analyzing a dataset from the National Birth Defects Prevention Study (NBDPS), we identified seven genes (GSTA1, SOD2, MTRR, AHCYL2, GCLC, GSTM3, and RFC1) associated with the development of CTDs. Our findings suggest that MFG interactions between haplotypes in three of seven genes, GCLC, GSTM3, and RFC1, are associated with nonsyndromic conotruncal heart defects.

Compared with feeding infants breast milk or cow-milk formula, soy formula feeding does not affect subsequent reproductive organ size at 5 years of age.

BACKGROUND: Literature reports suggest that phytochemicals, such as isoflavones found in soybeans, impair reproductive function in animals and raise the possibility that consuming soy infant formula could alter hormonally sensitive organ development in children. OBJECTIVE: This study compared reproductive organs volumes and structural characteristics in children at age 5 y who were enrolled in the Beginnings study long-term cohort. METHODS: Breast bud, uterus, ovaries, prostate, and testes volumes and characteristics were assessed by ultrasonography in 101 children (50 boys and 51 girls) aged 5 y who were breastfed (n = 35) or fed cow-milk formula (n = 32) or soy formula (n = 34) as infants. Analyses were adjusted for race, gestational age, and birth weight. RESULTS: Among girls, no significant differences were found in breast bud, ovarian, or uterine volumes; counts of ovaries with cysts; ovarian cysts numbers; ovarian cyst size; and uterine shape between the diet groups. Among boys, no significant differences were found in breast bud, testes, or prostate volumes or structural characteristics between the diet groups. CONCLUSIONS: In this cohort, no early infant feeding effects were found on reproductive organs volumes and structural characteristics in children age 5 y. The follow-up of these children through puberty is planned and should help delineate potential early infant feeding effect on reproductive function later in life.

Brain gray and white matter differences in healthy normal weight and obese children.

PURPOSE: To compare brain gray and white matter development in healthy normal weight and obese children. METHODS: Twenty-four healthy 8- to 10-year-old children whose body mass index was either <75(th) percentile (normal weight) or >95(th) percentile (obese) completed an MRI examination which included T1-weighted three-dimensional structural imaging and diffusion tensor imaging (DTI). Voxel-based morphometry was used to compare the regional gray and white matter between the normal weight and obese children, and tract-based spatial statistics was used to compare the water diffusion parameters in the white matter between groups. RESULTS: Compared with normal weight children, obese children had significant (P < 0.05, family wise error corrected) regional gray matter reduction in the right middle temporal gyrus, left and right thalami, left superior parietal gyrus, left pre/postcentral gyri, and left cerebellum. Obese children also had higher white matter (P < 0.05, corrected) in multiple regions in the brain and higher DTI measured fractional anisotropy (FA) values (P < 0.05, corrected) in part of the left brain association and projection fibers. There was no difference in mean diffusivity at P < 0.05, corrected. DTI eigenvalues suggested that the FA differences were likely from decreased radial diffusivity (P < 0.1, corrected) and there was no change in axial diffusivity (corrected P > 0.35 for all voxels). CONCLUSION: Our results indicated that obese but otherwise healthy children have different regional gray and white matter development in the brain and differences in white matter microstructures compared with healthy normal weight children.

Obstructive heart defects associated with candidate genes, maternal obesity, and folic acid supplementation.

Right-sided and left-sided obstructive heart defects (OHDs) are subtypes of congenital heart defects, in which the heart valves, arteries, or veins are abnormally narrow or blocked. Previous studies have suggested that the development of OHDs involved a complex interplay between genetic variants and maternal factors. Using the data from 569 OHD case families and 1,644 control families enrolled in the National Birth Defects Prevention Study (NBDPS) between 1997 and 2008, we conducted an analysis to investigate the genetic effects of 877 single nucleotide polymorphisms (SNPs) in 60 candidate genes for association with the risk of OHDs, and their interactions with maternal use of folic acid supplements, and pre-pregnancy obesity. Applying log-linear models based on the hybrid design, we identified a SNP in methylenetetrahydrofolate reductase (MTHFR) gene (C677T polymorphism) with a main genetic effect on the occurrence of OHDs. In addition, multiple SNPs in betaine-homocysteine methyltransferase (BHMT and BHMT2) were also identified to be associated with the occurrence of OHDs through significant main infant genetic effects and interaction effects with maternal use of folic acid supplements. We also identified multiple SNPs in glutamate-cysteine ligase, catalytic subunit (GCLC) and DNA (cytosine-5-)-methyltransferase 3 beta (DNMT3B) that were associated with elevated risk of OHDs among obese women. Our findings suggested that the risk of OHDs was closely related to a combined effect of variations in genes in the folate, homocysteine, or glutathione/transsulfuration pathways, maternal use of folic acid supplements and pre-pregnancy obesity.

Genetic variation affects congenital heart defect susceptibility in offspring exposed to maternal tobacco use.

BACKGROUND: Congenital heart defects (CHDs) are among the most prevalent and serious birth defects, occurring in 8 to 10 of every 1000 live births in the United States. Epidemiologic studies have reported an association between CHDs and maternal smoking, but it remains unknown how genes impact the susceptibility of offspring to CHDs in the presence of maternal tobacco use. METHODS: Using data from 403 case- and 219 control-parental triads enrolled in the National Birth Defects Prevention Study between 1998 and 2008, we investigated the association between CHDs and maternal and infant genetic variants involved in the tobacco metabolism and DNA repair pathways among mothers who smoked prenatally. RESULTS: The maternal genotypes of single nucleotide polymorphisms in the excision repair cross-complementation group 1 (ERCC1), poly (ADP-ribose) polymerase 2 (PARP2), and ERCC5 genes were identified to be significantly associated with the occurrence of CHDs in the presence of maternal tobacco use. Our analysis also revealed a moderate association between the infant genotypes of polymorphisms in the O-sialoglycoprotein endopeptidase (OSGEP) gene and increased risk of CHDs among mothers who smoked. CONCLUSION: Our study provides evidence that maternal and infant polymorphisms within the ERCC1, PARP2, ERCC5, and OSGEP genes are associated with CHD risk in the presence of maternal tobacco use. These results may provide insight into the susceptibility of having a pregnancy affected by CHDs among women who smoke.