[Gastroschisis and omphalocele: Incidence and outcome].

INTRODUCTION: Gastroschisis and omphalocele are the most common congenital abdominal wall defects. The main purpose of this study was to investigate the incidence, other associated anomalies and the course of these diseases in Iceland. MATERIAL AND METHODS: The study was retrospective. The population was all newborns who were admitted to the NICU of Children's Hospital Iceland due to gastroschisis or omphalocele in 1991-2020. Furthermore, all fetuses diagnosed prenatally or post mortem where the pregnancy ended in spontaneous or induced abortion, were included. RESULTS: During the study period, 54 infants were born with gastroschisis and five with omphalocele. The incidence of gastroschisis was 4.11 and omphalocele 0,38/10,000 births. There was no significant change in the incidence of the diseases during the study period. In addition, five fetuses were diagnosed with gastroschisis and 31 with omphalocele where the pregnancy was terminated. In addition to gastroschisis in the live born infants and fetuses the most common associated anomalies were in the gastrointestinal or urinary tract but in infants and fetuses with omphalocele anomalies of the cardiac, central nervous or skeletal systems were the most common. Sixteen fetuses diagnosed with omphalocele had trisomy 18. Mothers aged 16-20 were more likely to give birth to an infant with gastroschisis than older mothers (p< 0.001). Primary closure was successful in 86% of the infants. Those reached full feedings significantly earlier and were discharged earlier. Overall survival rate was 95%. Three children were still receiving parenteral nutrition at discharge due to short bowel syndrome. CONCLUSIONS: The incidence of gastroschisis in Iceland is in accordance with studies in other countries but but the incidence of omphalocele is lower, which can be partly explained by spontaneous or induced abortions. Other anomalies associated with omphalocele are more severe than those associated with gastroschisis. Primary closure was associated with more benign course. Children with gastroschisis may need prolonged parenteral nutrition due to shortening of their intestines.

Altered Transcript Levels of MMP13 and VIT Genes in the Muscle and Connective Tissue of Pigs with Umbilical Hernia.

Umbilical hernia (UH) and inguinal hernia (IH) are among the most common defects in pigs, affecting their welfare and resulting in economic losses. In this study, we aimed to verify the association of previously reported differences in transcript levels of the ACAN, COL6A5, MMP13, and VIT genes with the occurrence of UH and IH. We examined mRNA levels in muscle and connective tissue from 68 animals-34 affected by UH and 34 controls. In a second cohort, we examined inguinal channel samples from 46 pigs (in four groups). We determined DNA methylation levels in muscle tissue for the UH and control animals. The transcript level of MMP13 changed in the UH cases, being upregulated and downregulated in muscle and connective tissue, respectively, and the VIT gene also showed an increased muscular mRNA level. The transcript of the ACAN gene significantly decreased in old pigs with IH. We further observed an increased DNA methylation level for one CpG site within the MMP13 gene in UH individuals. We conclude that these alterations in gene mRNA levels in the UH animals depend on the tissue and can sometimes be a consequence of, not a cause of, the affected phenotype.

Searching for new signals for susceptibility to umbilical hernia through genome-wide association analysis in three pig breeds.

Umbilical hernia (UH) is a prevalent congenital disorder in pigs, resulting in considerable economic losses and severe animal welfare issues. In the present study, we conducted a genome-wide association study (GWAS) using the GeneSeek 50K Chip in 2777 pigs (Duroc, n = 1267; Landrace, n = 696; and Yorkshire, n = 814) to explore the candidate genes underlying the risk of umbilical hernia in pigs. After quality control analyses, 2748 animals and 48 524 single nucleotide polymorphisms (SNPs) were retained for subsequent GWAS analysis using the FarmCPU model. The heritability of umbilical hernias was estimated to 0.51 ± 0.04, indicating a reasonable basis for investigating genetic markers associated with this disorder. We identified 54 SNPs and 517 candidate genes that showed significant associations with susceptibility to umbilical hernia across the combined population of the three pig breeds. Gene enrichment analyses highlighted several crucial pathways for platelet degranulation, inflammatory mediator regulation of TRP channels and ion transport. These findings provide further insights into the underlying genetic architecture of umbilical hernias in pigs.

Ultrasonographic characteristics, genetic features, and maternal and fetal outcomes in fetuses with omphalocele in China: a single tertiary center study.

BACKGROUND: Patients with omphalocele, a midline abdominal wall defect at the umbilical cord base, have a low survival rate. However, the long-term outcomes of fetuses with prenatally diagnosed omphalocele have scarcely been studied. Therefore, we investigated the ultrasonographic features, genetic characteristics, and maternal and fetal outcomes of fetuses with omphalocele and provided a reference for the perinatal management of such cases. METHODS: A total of 120 pregnant females with fetal omphalocele were diagnosed using prenatal ultrasonography at the Fujian Provincial Maternity and Child Health Hospital from January 2015 to March 2022. Amniotic fluid or cord blood samples were drawn at different gestational weeks for routine karyotype analysis, chromosomal microarray analysis (CMA) detection, and whole exome sequencing (WES). The maternal and fetal outcomes were followed up. RESULTS: Among the 120 fetuses, 27 were diagnosed with isolated omphalocele and 93 with nonisolated omphalocele using prenatal ultrasonography. Cardiac anomalies were the most observed cause in 17 fetuses. Routine karyotyping and CMA were performed on 35 patients, and chromosomal abnormalities were observed in five patients, trisomy 18 in three, trisomy 13 in one, and chromosome 8-11 translocation in one patient; all were non-isolated omphalocele cases. Six nonisolated cases had normal CMA results and conventional karyotype tests, and further WES examination revealed one pathogenic variant and two suspected pathogenic variants. Of the 120 fetuses, 112 were successfully followed up. Eighty of the 112 patients requested pregnancy termination. Seven of the cases died in utero. A 72% 1-year survival rate was observed from the successful 25 live births. CONCLUSION: The prognosis of fetuses with nonisolated omphalocele varies greatly, and individualized analysis should be performed to determine fetal retention carefully. Routine karyotyping with CMA testing should be provided for fetuses with omphalocele. WES is an option if karyotype and CMA tests are normal. If the fetal karyotype is normal and no associated abnormalities are observed, fetuses with omphalocele could have a high survival rate, and most will have a good prognosis.

A confirmed association between DNA variants in CAPN9, OSM, and ITGAM candidate genes and the risk of umbilical hernia in pigs.

Umbilical hernia (UH) is one of the most prevalent defects of swine, affecting their welfare and causing considerable economic loss. The molecular mechanisms behind UH in pigs remain poorly understood. The aim of this study was to verify the association between UH and previously reported DNA variants in the CAPN9, OSM, ITGAM, and NUGGC genes. A case/control study design was applied in two different crossbred cohorts of commercial fatteners containing 412 and 171 pigs, respectively. SNPs within CAPN9, OSM, and ITGAM were analyzed using Sanger sequencing, and 10 SNPs in CAPN9, five in OSM, and two in ITGAM were identified. A structural variant in the NUGGC gene was studied by droplet-digital PCR, and an elevated copy number was detected in only a single individual. Significant differences in allele frequencies for four SNPs in CAPN9 were detected. The haplotype analysis showed the effect on the risk of UH for two genes. The CAGGA haplotype within OSM and AT haplotype in ITGAM reduced the relative risk of UH by 52% and 45%, respectively, confirming that variants in those genes are associated with the risk of UH in pigs. Moreover, the interaction between the CAPN9 haplotype and the sex of animals had also significant impact on UH risk.

Pregnancy outcomes and prenatal traditional karyotype analysis with fetal omphalocele.

BACKGROUND: Omphalocele is associated with many aneuploidies, deletions and congenital anomalies. This study evaluates pregnancies diagnosed with omphalocele and its relevance to concomitant genetic disorders. METHODS: The data of patients with the intrauterine diagnosis of omphalocele who had invasive diagnostic testing performed between January 2017 and January 2020 were evaluated retrospectively. The traditional karyotype analysis was performed to prenatal diagnosis for all fetuses. During the study period, all patients were scanned via ultrasonography by an experienced perinatologist, prenatally. RESULTS: We evaluated 22 cases of omphalocele whose genetic testing results were available. The mean maternal age was 25 (18-41) years. The median gestational week at diagnosis was 13 (11-22). Invasive genetic testing revealed aneuploidy in 7 patients (31.8%), 2 with trisomy 13 (9.1%), and 5 with trisomy 18 (22.8%). There were 5 fetuses (22.7%) that had extracorporeal liver: 1 had trisomy 18 (20%), 1 had trisomy 13 (20%), and the other 3 fetuses had a normal karyotype (60%). Further, 14 (63.6%) pregnancies were terminated: 4 had trisomy 18 (28.6%), 1 had trisomy 13 (7.1%), and 9 of the terminated pregnancies (64.3%) had additional congenital anomalies. There were 4 infants who died (50%) born from 8 patients who decided to continue with their pregnancy. The omphalocele sac of 1 infant spontaneously regressed in the ensuing weeks of pregnancy who is now 1 year old. CONCLUSIONS: The chromosomal abnormalities presented in up to 31.8% of cases diagnosed with omphalocele. Moreover, for cases with normal genetic testing results, the propensity for additional structural defects was high and the prognosis remains poor. Counseling parents to consider their option of terminating the pregnancy is appropriate.

Turner syndrome-omphalocele association: Incidence, karyotype, phenotype and fetal outcome.

OBJECTIVE: Omphalocele is known to be associated with genetic anomalies like trisomy 13, 18 and Beckwith-Wiedemann syndrome, but not with Turner syndrome (TS). Our aim was to assess the incidence of omphalocele in fetuses with TS, the phenotype of this association with other anomalies, their karyotype, and the fetal outcomes. METHOD: Retrospective multicenter study of fetuses with confirmed diagnosis of TS. Data were extracted from a detailed questionnaire sent to specialists in prenatal ultrasound. RESULTS: 680 fetuses with TS were included in this analysis. Incidence of small omphalocele in fetuses diagnosed ≥12 weeks was 3.1%. Including fetuses diagnosed before 12 weeks, it was 5.1%. 97.1% (34/35) of the affected fetuses had one or more associated anomalies including increased nuchal translucency (≥3 mm) and/or cystic hygroma (94.3%), hydrops/skin edema (71.1%), and cardiac anomalies (40%). The karyotype was 45,X in all fetuses. Fetal outcomes were poor with only 1 fetus born alive. CONCLUSION: TS with 45,X karyotype but not with X chromosome variants is associated with small omphalocele. Most of these fetuses have associated anomalies and a poor prognosis. Our data suggest an association of TS with omphalocele, which is evident from the first trimester.

Fetal Omphalocele: Review of Predictive Factors Important for Antenatal Counseling?

Importance: Congenital omphalocele is among the most common antenatally diagnosed anomalies. As additional abnormalities are found in majority of cases, antenatal investigations target the search for additional structural anomalies and genetic disorders, including aneuploidy. Antenatal management focuses on the assessment of fetal well-being. Unfortunately, antenatal prediction of postnatal and long-term outcomes represents 2 less well-documented but crucial facets of this pathology. A large part of the prognosis relies on aspects that are difficult to predict such as quality of life, neurological development, and autonomy, which cause significant anxiety in expectant parents. Objective: This article offers a comprehensive review of antenatal management of omphalocele with a specific focus on predictive factors and long-term outcomes. Evidence Acquisition, Results: We conducted an extensive literature review targeting management of fetal omphalocele. We had a specific interest in factors predictive of fetal and neonatal outcome as well as long-term consequences of omphalocele. Fetuses with large defects and those containing the liver are at higher risk of having a complicated postnatal course. Neonates may experience pulmonary hypoplasia, pulmonary hypertension, and gastroesophageal reflux. In selected cases, motor and cognitive delay may be present, but the overall life-long prognosis and quality of life is good. Conclusions and Relevance: A multidisciplinary approach should be encouraged after the diagnosis of fetal omphalocele. In addition to clinical team experience, antenatal counseling should be based on objective and gestational age-dependent criteria and should include long-term outcomes.

Bovine omphalocele: errors in embryonic development, veterinarian importance, and the way forward.

Omphalocele is an embryonic developmental error presented as a neonatal visceral umbilical herniation. Epidemiological and embryological studies are reviewed that revise our understanding of midgut development and defects in cattle. Google Scholar and PubMed were searched for omphalocele, exomphalos, calves, calf, cattle, epidemiology, genetics, disease presentation, and omphalocele treatments of bovine neonates. Omphalocele contains small intestine and sometimes liver and/or pyloric abomasum. This condition may arise from inadequately expanded abdominal cavity, herniated midgut entrapment, or inappropriate umbilical ring growth. Full-term neonates are otherwise healthy but comorbidities may be present. Limited epidemiological evidence suggests neonates, commonly female, of dairy dams have much higher omphalocele prevalence than humans but with fewer co-morbidities. Genetic or environmental influences may present at low incidences, especially with co-defects, while also epigenetics operate in metabolically challenged dairy cattle. Calf survival after surgical repair was commonly good if damage to eviscerated tissue was minimal and surgery prompt. Inadequate follow-ups prevented assessment of their commercial value. We also revised understanding of embryonic midgut development. There is little useful epidemiological information on bovine omphaloceles. To address this, we suggest: (i) Observations on omphaloceles should report herd and dam histories, abdominal disposition of contents, and comorbidities. (ii) Cases of surgical restitution must report full histories and thoroughly explore post-surgical follow-ups to assess animal commercial viability. There is a need for very large-scale multi-centre prospective observational studies on cattle health and productivity that should include omphaloceles.

Application of quantitative fluorescent polymerase chain reaction analysis for the rapid confirmation of trisomy 13 of maternal origin in a pregnancy with fetal holoprosencephaly, cyclopia, polydactyly, omphalocele and cell culture failure.

OBJECTIVE: We present the application of quantitative fluorescent polymerase chain reaction (QF-PCR) for the rapid confirmation of trisomy 13 of maternal origin in a pregnancy with fetal holoprosencephaly (HPE), cyclopia, polydactyly, omphalocele and cell culture failure. CASE REPORT: A 21-year-old, gravida 2, para 0, woman was referred for termination of the pregnancy at 17 weeks of gestation because of the abnormal ultrasound finding of alobar HPE. The pregnancy was subsequently terminated, and a 118-g malformed male fetus was delivered with cyclopia, bilateral postaxial polydactyly of the hands and ruptured omphalocele. Postmortem cell culture of the placental tissue and umbilical cord was not successful. The parental karyotypes were normal. QF-PCR analysis using the polymorphic DNA markers of D13S1810, D13S790 and D13S251 on the DNA extracted from placenta, umbilical cord and parental bloods showed trisomy 13 of maternal origin. CONCLUSION: Perinatal diagnosis of concomitant HPE, polydactyly and omphalocele should raise a suspicion of fetal trisomy 13. QF-PCR analysis is useful for rapid confirmation of trisomy 13 and the parental origin especially under the circumstance of cell culture failure, and the information acquired is very useful for genetic counseling of the parents.

A joint analysis using exome and transcriptome data identifiescandidate polymorphisms and genes involved with umbilical hernia in pigs.

BACKGROUND: Umbilical Hernia (UH) is characterized by the passage of part of the intestine through the umbilical canal forming the herniary sac. There are several potential causes that can lead to the umbilical hernia such as bacterial infections, management conditions and genetic factors. Since the genetic components involved with UH are poorly understood, this study aimed to identify polymorphisms and genes associated with the manifestation of umbilical hernia in pigs using exome and transcriptome sequencing in a case and control design. RESULTS: In the exome sequencing, 119 variants located in 58 genes were identified differing between normal and UH-affected pigs, and in the umbilical ring transcriptome, 46 variants were identified, located in 27 genes. Comparing the two methodologies, we obtained 34 concordant variants between the exome and transcriptome analyses, which were located in 17 genes, distributed in 64 biological processes (BP). Among the BP involved with UH it is possible to highlight cell adhesion, cell junction regulation, embryonic morphogenesis, ion transport, muscle contraction, within others. CONCLUSIONS: We have generated the first exome sequencing related to normal and umbilical hernia-affected pigs, which allowed us to identify several variants possibly involved with this disorder. Many of those variants present in the DNA were confirmed with the RNA-Seq results. The combination of both exome and transcriptome sequencing approaches allowed us to better understand the complex molecular mechanisms underlying UH in pigs and possibly in other mammals, including humans. Some variants found in genes and other regulatory regions are highlighted as strong candidates to the development of UH in pigs and should be further investigated.

Prenatal genetic diagnosis of omphalocele by karyotyping, chromosomal microarray analysis and exome sequencing.

OBJECTIVES: The aim of this study is to share our experience in the prenatal diagnosis of omphalocele by karyotyping, chromosomal microarray analysis (CMA) and whole exome sequencing (WES). METHODS: In this retrospective study, 81 cases of omphalocele were identified from 2015 to 2020. Associated anomalies and prenatal diagnosis based on karyotyping, CMA and WES were analysed. RESULTS: Fifty-eight (71.6%) of the 81 foetuses had other ultrasound anomalies. Giant omphalocele was present in 11 cases (13.6%) and small omphalocele was present in 70 cases (86.4%). Chromosomal abnormalities were found in 24 foetuses (29.6%, 24/81), the most common of which were trisomy 18 (58.8%, 11/24) and trisomy 13 (29.2%, 7/24). Compared to isolated omphalocele, non-isolated omphalocele was accompanied by an increased prevalence of chromosomal abnormalities (4.3% (1/23) vs. 39.7% (23/58), χ2 = 8.226, p = .004). All chromosomal abnormalities were found in small omphalocele. Aside from aneuploidy, CMA showed one pathogenic copy number variants (CNVs) for a detection rate of 1.2%, one variants of unknown significance (VOUS) and one instance of loss of heterozygosity (LOH). WES was performed on 3 non-isolated cases, and one was found to have pathogenic variants. CONCLUSIONS: The most common genetic cause of omphalocele is aneuploidy and the prevalence of chromosomal abnormalities is increased with non-isolated and small omphalocele. CMA and WES can be useful for providing further genetic information to assist in prenatal counselling and pregnancy management.

Association of myostatin deficiency with collagen related disease-umbilical hernia and tippy toe standing in pigs.

Herein, we investigate the high incidence of umbilical hernia and tippy-toe standing and their underlying changes in gene expression and proliferation in myostatin knockout (MSTN-/-) pigs. Thirty-six male MSTN-/- pigs were generated by somatic cell nuclear transfer (SCNT). These pigs presented a considerably high incidence of tippy-toe standing and umbilical hernia (69.4% and 61.1%, respectively). The tendon to body weight ratio was significantly lower than wild-type pigs (0.202 ± 0.017 vs 0.250 ± 0.004, respectively). The crimp length of the MSTN-/- tendon was significantly longer than that of wild-type pigs. The expression of MSTN and the activin type IIB (ACVR2B) was detected in the tendon and linea alba of MSTN-/- pigs. MSTN treatment significantly increased the phosphorylation of Smad2/3 in both tendon and linea alba fibroblasts. Type I collagen (Col1A) and Scleraxis (Scx) expression levels in the tendon and linea alba of MSTN-/- pigs were significantly lower than those in wild-type in vivo, whereas and cyclin-dependent kinase inhibitor 1 (p21) expression levels were higher. Treatment of tendon and linea alba fibroblasts with recombinant MSTN increased Col1A and Scx and decreased p21 expression in vivo. Moreover, there was a significant increase in fibroblast proliferation after treatment. The results indicated that MSTN regulates collagen expression and proliferation in tendon and linea alba fibroblasts; thus, MSTN deficiency causes collagen-related pathological features in MSTN-/- pigs. Hence, MSTN could be used as a therapeutic target for treating UH and tendon abnormalities.

Co-occurring non-omphalocele and non-gastroschisis anomalies among cases with congenital omphalocele and gastroschisis.

The pathogenesis of omphalocele and gastroschisis is not obvious. Their etiology is disputed. The prevalence and the types of anomalies co-occurring with omphalocele and gastroschisis are variable in the different series published. The aim of this study was to estimate the frequency and the types of co-occurring anomalies in cases with gastroschisis and omphalocele. This study was performed in a well-described population of 387,067 consecutive births between 1979 and 2007. Hundred-one cases with omphalocele were registered (2.61 per 10,000), 75 (74.3%) had co-occurring anomalies comprising chromosomal anomalies (28 cases, 27.7%, including 18 trisomy 18), non-chromosomal syndromes (16 cases, 15.8%, including 3 cases with Beckwith-Wiedemann syndrome, 2 cases with the OEIS sequence, and one case with the Pentalogy of Cantrell complex), and 31 cases, 30.7% with MCA (multiple congenital anomalies). The most common MCA were musculoskeletal (23.5%), urogenital (20.4%), cardiovascular (15.1%), and central nervous (9.1%). Seventy-one cases of gastroschisis were ascertained (1.83 per 10,000). However, the prevalence increased during the study period. The frequency was highest in the mothers 15-19 years old. Sixteen out of the 71 cases with gastroschisis, (22.5%) had co-occurring anomalies including 11 cases of MCA and 5 cases with syndromes. To conclude, the frequency and the types of anomalies co-occurring with omphalocele and gastroschisis are peculiar. Therefore, cases with gastroschisis and omphalocele need to be screened for co-occurring anomalies.

Can cell-free DNA testing be used in pregnancies with isolated fetal omphalocele? Preliminary evidence from cytogenetic results of prenatal cases.

Objective: To evaluate whether cell-free DNA (cfDNA) testing could replace an invasive procedure in pregnancies with isolated fetal omphalocele.Study design: This was a retrospective study of all pregnancies with sonographically detected fetal omphalocele at three tertiary referral centers between 2012 and 2016. Invasive diagnostic testing was performed for genetic investigations using conventional karyotyping or chromosomal microarray. cfDNA testing was assumed to be offered to patients with isolated fetal omphalocele for screening for common aneuploidies.Results: Invasive genetic testing was performed in a total of 107 pregnancies with a fetal omphalocele. Abnormal karyotype was found in 66% (31/47) of nonisolated omphalocele cases and in 1.7% (1/60) of isolated omphalocele cases. No pathogenic copy number variations (CNVs) were detected in 59 cases with isolated omphalocele and normal karyotype. If cfDNA screening was used in cases with isolated omphalocele, the affected fetus with trisomy 18 would be detected, and no rare chromosomal aberrations or submicroscopic pathogenic CNVs would be missed.Conclusions: cfDNA testing could be recommended for prenatal genetic evaluation in pregnancies with isolated fetal omphalocele after thorough pretest counseling.Key Message: A very low percentage of aneuploidies and rare chromosomal/subchromosomal abnormalities are found in prenatal cases of isolated omphalocele. It seems that for pregnancies with isolated omphalocele, cfDNA testing represents an alternative for patients who choose to continue the pregnancies and are reluctant to undertake invasive diagnostic testing.

Reproduction traits of heterozygous myostatin knockout sows crossbred with homozygous myostatin knockout boars.

Few studies exist on homozygous myostatin gene mutant (MSTN-/- ) pigs, especially on their reproductive ability. We have previously shown that semen quality of homozygous MSTN-/- boars is comparable to that of wild type (WT). However, no data exist on the reproductive ability of heterozygous MSTN gene mutant (MSTN+/ - ) sows. The present study highlights showed that the heterozygous MSTN+/ - sows have delayed pubertal age than WT sows (255.80 ± 6.79 versus 191.10 ± 3.42, respectively). The number of services per pregnancy of heterozygous MSTN+/ - sows is significantly higher than that of WT sows (3.33 ± 0.43 versus 1.60 ± 0.25, respectively). Moreover, although heterozygous MSTN+/ - sows have natural reproduction ability, their litter size was significantly lower than that of WT sows (7.75 ± 0.44 versus 14.25 ± 0.60, respectively). Offsprings generated from heterozygous MSTN+/ - sow and homozygous MSTN-/- boar were genotyped with the PCR and sequencing method to detect myostatin mutation and to identify whether the piglets are homozygous MSTN-/- or heterozygous MSTN+/ - . The proportion of homozygous MSTN-/- piglets was significantly lower than that of heterozygous MSTN+/ - piglets (2.50 ± 0.35 versus 5.25 ± 0.60, respectively). Furthermore, none of the sows presented dystocia, and the phenotype of heterozygous MSTN+/ - piglets was normal. However, 10% homozygous MSTN-/- piglets died of dyspnoea within 2 hr after birth, 60% of homozygous MSTN-/- piglets showed large tongues, and 50% had umbilical hernias. In summary, this study for the first time reports the reproduction traits of heterozygous MSTN+/ - sows crossbred with homozygous MSTN-/- boars. This study will pave the way in a new direction for the breeding and development of super lean meat varieties in the future.

Birth defects that co-occur with non-syndromic gastroschisis and omphalocele.

Gastroschisis and omphalocele are the two most common abdominal wall birth defects, and epidemiologic characteristics and frequency of occurrence as part of a syndromic condition suggest distinct etiologies between the two defects. We assessed complex patterns of defect co-occurrence with these defects separately using the Texas Birth Defects Registry. We used co-occurring defect analysis (CODA) to compute adjusted observed-to-expected (O/E) ratios for all observed birth defect patterns. There were 2,998 non-syndromic (i.e., no documented syndrome diagnosis identified) cases with gastroschisis and 789 (26%) of these had additional co-occurring defects. There were 720 non-syndromic cases with omphalocele, and 404 (56%) had additional co-occurring defects. Among the top 30 adjusted O/E ratios for gastroschisis, most of the co-occurring defects were related to the gastrointestinal system, though cardiovascular and kidney anomalies were also present. Several of the top 30 combinations co-occurring with omphalocele appeared suggestive of OEIS (omphalocele, exstrophy of cloaca, imperforate anus, spinal defects) complex. After the exclusion of additional cases with features suggestive of OEIS in a post-hoc sensitivity analysis, the top combinations involving defects associated with OEIS (e.g., spina bifida) were no longer present. The remaining top combinations involving omphalocele included cardiovascular, gastrointestinal, and urogenital defects. In summary, we identified complex patterns of defects that co-occurred more frequently than expected with gastroschisis and omphalocele using a novel software platform. Better understanding differences in the patterns between gastroschisis and omphalocele could lead to additional etiologic insights.

Transcriptome analysis identifies genes involved with the development of umbilical hernias in pigs.

Umbilical hernia (UH) is one of the most frequent defects affecting pig production, however, it also affects humans and other mammals. UH is characterized as an abnormal protrusion of the abdominal contents to the umbilical region, causing pain, discomfort and reduced performance in pigs. Some genomic regions associated to UH have already been identified, however, no study involving RNA sequencing was performed when umbilical tissue is considered. Therefore, here, we have sequenced the umbilical ring transcriptome of five normal and five UH-affected pigs to uncover genes and pathways involved with UH development. A total of 13,216 transcripts were expressed in the umbilical ring tissue. From those, 230 genes were differentially expressed (DE) between normal and UH-affected pigs (FDR <0.05), being 145 downregulated and 85 upregulated in the affected compared to the normal pigs. A total of 68 significant biological processes were identified and the most relevant were extracellular matrix, immune system, anatomical development, cell adhesion, membrane components, receptor activation, calcium binding and immune synapse. The results pointed out ACAN, MMPs, COLs, EPYC, VIT, CCBE1 and LGALS3 as strong candidates to trigger umbilical hernias in pigs since they act in the extracellular matrix remodeling and in the production, integrity and resistance of the collagen. We have generated the first transcriptome of the pig umbilical ring tissue, which allowed the identification of genes that had not yet been related to umbilical hernias in pigs. Nevertheless, further studies are needed to identify the causal mutations, SNPs and CNVs in these genes to improve our understanding of the mechanisms of gene regulation.