Rare and de novo variants in 827 congenital diaphragmatic hernia probands implicate LONP1 as candidate risk gene.

Congenital diaphragmatic hernia (CDH) is a severe congenital anomaly that is often accompanied by other anomalies. Although the role of genetics in the pathogenesis of CDH has been established, only a small number of disease-associated genes have been identified. To further investigate the genetics of CDH, we analyzed de novo coding variants in 827 proband-parent trios and confirmed an overall significant enrichment of damaging de novo variants, especially in constrained genes. We identified LONP1 (lon peptidase 1, mitochondrial) and ALYREF (Aly/REF export factor) as candidate CDH-associated genes on the basis of de novo variants at a false discovery rate below 0.05. We also performed ultra-rare variant association analyses in 748 affected individuals and 11,220 ancestry-matched population control individuals and identified LONP1 as a risk gene contributing to CDH through both de novo and ultra-rare inherited largely heterozygous variants clustered in the core of the domains and segregating with CDH in affected familial individuals. Approximately 3% of our CDH cohort who are heterozygous with ultra-rare predicted damaging variants in LONP1 have a range of clinical phenotypes, including other anomalies in some individuals and higher mortality and requirement for extracorporeal membrane oxygenation. Mice with lung epithelium-specific deletion of Lonp1 die immediately after birth, most likely because of the observed severe reduction of lung growth, a known contributor to the high mortality in humans. Our findings of both de novo and inherited rare variants in the same gene may have implications in the design and analysis for other genetic studies of congenital anomalies.

The next generation of natural history collections.

The last 50 years have witnessed rapid changes in the ways that natural history specimens are collected, preserved, analyzed, and documented. Those changes have produced unprecedented access to specimens, images, and data as well as impressive research results in organismal biology. The stage is now set for a new generation of collecting, preserving, analyzing, and integrating biological samples-a generation devoted to interdisciplinary research into complex biological interactions and processes. Next-generation collections may be essential for breakthrough research on the spread of infectious diseases, feeding Earth's growing population, adapting to climate change, and other grand research challenges. A decade-long investment in research collection infrastructure will be needed.

Twin-twin transfusion syndrome complicated by single ventricle physiology: A case report.

Clinically significant extrauterine twin-twin transfusion syndrome in conjoined twins is rare and carries a high risk of perinatal mortality. The ensuing postnatal imbalance in circulation across connecting vessels results in hypovolemia in the donor and hypervolemia in the recipient. Data on management and treatment are sparse especially in the setting of a single ventricle congenital heart defect. We present a case of a pair of omphalopagus conjoined twins, one with a single ventricle physiology (Twin B), who developed twin-twin transfusion syndrome shortly after birth. The resulting pathophysiology in the setting of a single ventricle congenital heart defect created added layers of complexity to their management and expedited surgical separation. Shunting from Twin B to Twin A-with an anatomically normal heart-resulted in mal-perfusion and rapid deterioration jeopardizing the health of both twins. In the preoperative course, steps taken to medically optimize the twins prior to surgery and the anesthetic considerations are detailed in this report.

Fetal liver and lung volume index of neonatal survival with congenital diaphragmatic hernia.

BACKGROUND: Magnetic resonance imaging (MRI) assesses pulmonary hypoplasia in fetal congenital diaphragmatic hernia (CDH). Neonatal mortality may occur with CDH. OBJECTIVE: To quantify MRI parameters associated with neonatal survival in fetuses with isolated CDH. MATERIALS AND METHODS: Fetal MRI for assessing CDH included region of interest (ROI) measurements for total lung volume (TLV), herniated liver volume, herniated other organ volume and predicted lung volume. Ratios of observed lung volume and liver up volume to predicted lung volume (observed to predicted TLV, percentage of the thorax occupied by liver) were calculated and compared to neonatal outcomes. Analyses included Wilcoxon rank sum test, multivariate logistic regression and receiver operating characteristic (ROC) curves. RESULTS: Of 61 studies, the median observed to predicted TLV was 0.25 in survivors and 0.16 in non-survivors (P=0.001) with CDH. The median percentage of the thorax occupied by liver was 0.02 in survivors and 0.22 in non-survivors (P<0.001). The association of observed to predicted TLV and percentage of the thorax occupied by liver with survival for gestational age (GA) >28 weeks was greater compared to GA ≤28 weeks. The ROC analysis demonstrated an area under the curve of 0.96 (95% confidence interval 0.91-1.00) for the combined observed to predicted TLV, percentage of the thorax occupied by liver and GA. CONCLUSION: The percentage of the thorax occupied by liver and observed to predicted TLV was predictive of neonatal survival in fetuses with CDH.

Likely damaging de novo variants in congenital diaphragmatic hernia patients are associated with worse clinical outcomes.

PURPOSE: Congenital diaphragmatic hernia (CDH) is associated with significant mortality and long-term morbidity in some but not all individuals. We hypothesize monogenic factors that cause CDH are likely to have pleiotropic effects and be associated with worse clinical outcomes. METHODS: We enrolled and prospectively followed 647 newborns with CDH and performed genomic sequencing on 462 trios to identify de novo variants. We grouped cases into those with and without likely damaging (LD) variants and systematically assessed CDH clinical outcomes between the genetic groups. RESULTS: Complex cases with additional congenital anomalies had higher mortality than isolated cases (P = 8 × 10-6). Isolated cases with LD variants had similar mortality to complex cases and much higher mortality than isolated cases without LD (P = 3 × 10-3). The trend was similar with pulmonary hypertension at 1 month. Cases with LD variants had an estimated 12-17 points lower scores on neurodevelopmental assessments at 2 years compared with cases without LD variants, and this difference is similar in isolated and complex cases. CONCLUSION: We found that the LD genetic variants are associated with higher mortality, worse pulmonary hypertension, and worse neurodevelopment outcomes compared with non-LD variants. Our results have important implications for prognosis, potential intervention and long-term follow up for children with CDH.

Impact of Additional Anomalies on Postnatal Outcomes in Congenital Lung Malformations.

BACKGROUND: Approximately 20% of fetuses diagnosed with congenital lung malformations (CLMs) are found to have additional anomalies. We aim to determine if additional anomalies have an impact on postnatal outcomes for patients with CLMs. METHODS: After institutional review board approval, we performed a retrospective review of live-born patients with CLMs from 2008 to 2018. All patients were prenatally diagnosed with CLMs. Clinical information pertaining to additional congenital anomalies and outcomes was collected from the electronic health record and analyzed. RESULTS: Of the 88 patients who had a prenatal diagnosis of CLMs, 20.5% had additional anomalies. Ten of the 18 patients (56%) were considered to have a major anomaly in addition to CLMs. Outcomes for patients electing nonoperative management of CLMs were similar between those with and without an additional anomaly. Although patients with an additional anomaly were more likely to have perinatal respiratory complications (44% versus 17%, P = 0.03), the number of preoperative clinic and emergency department visits, age at surgery, minimally invasive approach to surgical resection of CLM, estimated blood loss, length of hospital stay, intubation, duration of intubation, 30-day postoperative complications, and long term sequelae were not statistically different. This held true when stratified for major versus minor anomalies. CONCLUSIONS: Twenty percent of fetuses diagnosed with CLM in our population have additional anomalies. Newborns with additional anomalies have a higher risk of pre-excision pulmonary complications. However, the overall outcomes of all patients with CLMs are similar.

Air Guns: A Contemporary Review of Injuries at Six Pediatric Level I Trauma Centers.

BACKGROUND: Studies spanning the last three decades demonstrated the injury causing capability of air gun (AG) projectiles. Recent studies have suggested the impact and incidence of these injuries may be declining because of edcational efforts. We hypothesize that injuries in the pediatric population resulting from AGs remain a significant health concern. METHODS: A retrospective review (1/1/2007 to 12/31/2016), of AG-injured children < 19 years old, was performed across six level I Pediatric Trauma Centers, part of the ATOMAC research consortium. AG injuries were defined as injuries sustained by ball-bearing or pellet air-powered guns. Paint ball and soft foam AGs were excluded. Following institutional review board approval, patients were identified by ICD code from the trauma registry. Included were demographic data, injury severity scores, length of stay (LOS), outcome at discharge, and overall cost of admission. Descriptive statistics and parametric tests were employed. RESULTS: A total of 499 patients sustained injuries. Mean age 9.5 (±4.0) y; 81% of victims were male; all survived to hospital discharge. 30% (n = 151) required operative intervention. Hospital LOS was 2.3 (±2.2) d; with mean cost of $23,756 (±$34,441). Injury severity score mean of 3.7 (±4.6) on admission. Over 40% of the injuries to the head/thorax that were severe (AIS ≥ 3) required operative intervention (P < 0.001). CONCLUSIONS: AG injuries to the head or thorax seen at trauma centers were likely to require operative management. While no fatalities occurred, the cost was substantial. This study demonstrates pediatric injuries resulting from AG projectiles remain a significant health concern.

Does Age Affect Surgical Outcomes After Ileal Pouch-Anal Anastomosis in Children?

BACKGROUND: Younger children are referred for surgical intervention in the treatment of ulcerative colitis (UC) and familial adenomatous polyposis (FAP). Outcome data in this population after a laparoscopic restorative proctocolectomy and Ileal pouch-anal anastomosis (LRS-IPAA) are limited. We reviewed our experience to determine if younger children would have similar functional outcomes. METHODS: After institutional review board approval, a review of children with FAP and UC undergoing LRS-IPAA at a children's hospital from 2002 to 2017 occurred. The study groups were defined based on age: young group (YG; 5-12 y) and older group (OG; 13-18 y). Data points included demographics, postprocedure course, and outcomes. Statistical analysis was performed. RESULTS: Sixty-five children were identified and grouped by age: YG (n = 22, average age 9 y) and OG (n = 43, average age 15.4 y). Thirteen children in YG had UC, and nine had FAP. Twenty-eight children in OG were diagnosed with UC, and 15 with FAP. After LRS-IPAA, continence, appetite recovery, and use of antidiarrheal medications were not significantly different between groups. The incidence of pouch stricture, diagnosis of pouchitis, and complications were also not significantly different. Two children (YG), aged 11 and 12 y at the time of colectomy, were initially diagnosed with UC and then reassigned as having Crohn's disease because of persistent symptoms. One child, who underwent colectomy at 17 y for FAP, had invasive rectal cancer and died 3 y later from metastatic disease. Time of follow-up for OG is 8-61 mo (average: 37 mo). Period of follow-up for YG is 11-73 mo (average: 43 mo). CONCLUSIONS: There are no significant differences in the functional outcomes between groups after LRS-IPAA. Although numbers are small, these data suggest younger age should not be a deterrent when contemplating LRS-IPAA in the treatment of UC and FAP in the pediatric population. Younger patients with FAP may benefit from early intervention.

Role of Nerve and Muscle Biopsies in Pediatric Patients in the Era of Genetic Testing.

BACKGROUND: An operative biopsy is an important component in the diagnosis and treatment of neuromuscular disorders (NMDs). However, recent advances in molecular genetics suggest less invasive genetic testing should be the initial approach. The purpose of our study was to demonstrate the diagnostic value of muscle or nerve biopsy within the pediatric population at a pediatric academic center and offer recommendations for genetic testing in relation to biopsy to achieve the highest diagnostic yield. METHODS: Following institutional review board approval, we retrospectively reviewed the electronic medical record of 221 pediatric patients who underwent muscle and/or nerve biopsy for suspicion of NMD from January 2007 to March 2018. Demographics, family history, clinical presentations, genetic testing results, pathology results, anesthesia complications, clinical diagnoses, and clinic follow-up data were collected. Chi-square analysis was done for statistical significance. RESULTS: A total of 220 underwent muscle biopsy, and 15 underwent nerve biopsy. Not all patients received genetic testing. The average age at biopsy was 7.7 y. Biopsy revealed significant histologic abnormalities in 62.9% (139), directly leading to a specific clinical diagnosis in 33.9% (75). When genetic testing was done before biopsy, definite pathogenic variants were found in 7.6% (9). When genetic testing was done after biopsy, definite pathogenic variants were found in 45.0% (27). Genetic testing yield for pathogenic variants was higher when done after biopsy (P value < 0.00001). CONCLUSIONS: Muscle and nerve biopsies may provide significant diagnostic value. Biopsy helped to rule in or out NMD and guide genetic testing. Our data suggest NMD genetic testing yield was higher when done after biopsy.

Fetal Head and Neck Masses: MRI Prediction of Significant Morbidity.

OBJECTIVE: The purpose of this study is to determine which MRI parameters of fetal head and neck masses predict high-morbidity neonatal outcomes, including ex utero intrapartum treatment (EXIT) procedure. MATERIALS AND METHODS: This retrospective study (2004-2016) included parameters of polyhydramnios (based on largest vertical pocket), mass effect on the trachea, mass midline extension, and morphologic grade and size of masses. The morbid cohort included those requiring an EXIT procedure, difficult intubation at delivery, or lethal outcome. Predictive modeling with a multivariable logistic regression and ROC analysis was then performed. RESULTS: Of 36 fetuses, five were delivered by EXIT procedures, there was one neonatal death within 12 hours after delivery, and another neonate required multiple intubation attempts. The remaining 29 fetuses were delivered at outside institutions with no interventions or neonatal morbidity. The largest vertical pocket and mass effect on the trachea were selected as independent predictors by the logistic regression. The cross-validated ROC AUC was 0.951 (95% CI, 0.8795-1). CONCLUSION: The largest vertical pocket measurement and mass effect on the trachea were the most contributory MRI parameters that predicted significant morbidity in fetuses with masses of the face and neck, along with other significant parameters. These parameters predict significant morbid neonatal outcomes, including the need for EXIT procedures.

Prognostic significance of an antenatal magnetic resonance imaging staging system on airway outcomes of fetal craniofacial venolymphatic malformations.

BACKGROUND: The aim of the article was to determine if anatomical findings on fetal magnetic resonance imaging (MRI) of venolymphatic malformations of the face and neck (VLMFN) can be used to create a staging system predictive of airway outcomes. METHODS: We reviewed 13 fetuses evaluated for VLMFN. Stage was assigned based on anatomical findings on fetal MRI. Stage I: no evidence of polyhydramnios with free egress of amniotic fluid and clear visualization of the aryepiglottic folds and larynx. Stage II: lesions of the tongue or epiglottis but with normal aryepiglottic folds without polyhydramnios. Stage III: lesions of the tongue or larynx; nonvisualization of the aryepiglottic folds without free egress of amniotic fluid along with polyhydramnios. RESULTS: Six met stage I criteria with no airway involvement, nor any subsequent issues. Two met stage II criteria and were managed by ex-utero intrapartum therapy and intubated. One had minimal involvement of the upper airway, was extubated, and had no subsequent issues. Child two had involvement of the tongue and larynx and received a tracheostomy. Five were assigned stage III, delivered by ex-utero intrapartum therapy and intubated. Postnatal evaluation showed involvement of the upper airway by the lesion and was managed with tracheostomy. All treated by tracheostomy remain cannulated because of persistent symptomatic lesions at follow-up (relative risk 4.0; confidence interval 1.2-13.3). Median follow-up was 4 y (range 2-7 y). CONCLUSIONS: Although numbers are small, data suggest anatomical details obtained by antenatal fetal MRI appear to correlate with airway outcomes in children affected by a VLMFN. This information may be useful when counseling expectant families of affected fetuses.

A definition of gentle ventilation in congenital diaphragmatic hernia: a survey of neonatologists and pediatric surgeons.

Ventilation practices have changed significantly since the initial reports in the mid 1980 of successful use of permissive hypercapnia and spontaneous ventilation [often called gentle ventilation (GV)] in infants with congenital diaphragmatic hernia (CDH). However, there has been little standardization of these practices or of the physiologic limits that define GV. We sought to ascertain among Diaphragmatic Hernia Research and Exploration; Advancing Molecular Science (DHREAMS) centers' GV practices in the neonatal management of CDH. Pediatric surgeons and neonatologists from DHREAMS centers completed an online survey on GV practices in infants with CDH. The survey gathered data on how individuals defined GV including ventilator settings, blood gas parameters and other factors of respiratory management. A total of 87 respondents, from 12 DHREAMS centers completed the survey for an individual response rate of 53% and a 92% center response rate. Approximately 99% of the respondents defined GV as accepting higher carbon dioxide (PCO2) and 60% of the respondents also defined GV as accepting a lower pH. There was less consensus about the use of sedation and neuromuscular blocking agents in GV, both within and across the centers. Acceptable pH and PCO2 levels are broader than the goal ranges. Despite a lack of formal standardization, the results suggest that GV practice is consistently defined as the use of permissive hypercapnia with mild respiratory acidosis and less consistently with the use of sedation and neuromuscular blocking agents. GV is the reported practice of surveyed neonatologists and pediatric surgeons in the respiratory management of infants with CDH.

The Global Genome Biodiversity Network (GGBN) Data Portal.

The Global Genome Biodiversity Network (GGBN) was formed in 2011 with the principal aim of making high-quality well-documented and vouchered collections that store DNA or tissue samples of biodiversity, discoverable for research through a networked community of biodiversity repositories. This is achieved through the GGBN Data Portal (http://data.ggbn.org), which links globally distributed databases and bridges the gap between biodiversity repositories, sequence databases and research results. Advances in DNA extraction techniques combined with next-generation sequencing technologies provide new tools for genome sequencing. Many ambitious genome sequencing projects with the potential to revolutionize biodiversity research consider access to adequate samples to be a major bottleneck in their workflow. This is linked not only to accelerating biodiversity loss and demands to improve conservation efforts but also to a lack of standardized methods for providing access to genomic samples. Biodiversity biobank-holding institutions urgently need to set a standard of collaboration towards excellence in collections stewardship, information access and sharing and responsible and ethical use of such collections. GGBN meets these needs by enabling and supporting accessibility and the efficient coordinated expansion of biodiversity biobanks worldwide.

A Martian acoustic anemometer.

An acoustic anemometer for use on Mars has been developed. To understand the processes that control the interaction between surface and atmosphere on Mars, not only the mean winds, but also the turbulent boundary layer, the fluxes of momentum, heat and molecular constituents between surface and atmosphere must be measured. Terrestrially this is done with acoustic anemometers, but the low density atmosphere on Mars makes it challenging to adapt such an instrument for use on Mars. This has been achieved using capacitive transducers and pulse compression, and was successfully demonstrated on a stratospheric balloon (simulating the Martian environment) and in a dedicated Mars Wind Tunnel facility. This instrument achieves a measurement accuracy of ∼5 cm/s with an update rate of >20 Hz under Martian conditions.

Creating Virtuous Cycles for DNA Barcoding: A Case Study in Science Innovation, Entrepreneurship, and Diplomacy.

This chapter on the history of the DNA barcoding enterprise attempts to set the stage for the more scholarly contributions in this volume by addressing the following questions. How did the DNA barcoding enterprise begin? What were its goals, how did it develop, and to what degree are its goals being realized? We have taken a keen interest in the barcoding movement and its relationship to taxonomy, collections, and biodiversity informatics more broadly considered. This chapter integrates our two different perspectives on barcoding. DES was the Executive Secretary of the Consortium for the Barcode of Life from 2004 to 2017, with the mission to support the success of DNA barcoding without being directly involved in generating barcode data. RDMP viewed barcoding as an important entry into the landscape of biodiversity data, with many potential linkages to other components of that landscape. We also saw it as a critical step toward the era of international genomic research that was sure to follow. Like the Mercury Program that paved the way for lunar landings by the Apollo Program, we saw DNA barcoding as the proving grounds for the interdisciplinary and international cooperation that would be needed for success of whole-genome research.

Establishment of a multidisciplinary fetal center streamlines approach for congenital lung malformations.

PURPOSE: Fetuses with a diagnosis of congenital lung malformations (CLM) on prenatal imaging are commonly referred to a multi-disciplinary specialty team for prenatal assessment and postnatal management. The net effect of such services is broadly stated to improve the outcomes of affected newborns. However, these claims are relatively unsubstantiated. METHODS: After IRB approval, a retrospective review of children diagnosed with CLM from 2008 to 2018 and referred to a large urban children's hospital was performed. A comparison was performed between prenatally diagnosed patients having a multi-disciplinary fetal center evaluation (FC) and prenatally diagnosed patients who did not receive a referral or were seen prior to the establishment of the center (NON-FC). RESULTS: Eighty-eight live-born patients with a prenatal diagnosis of CLM were identified, with 49 in the FC group and 39 NON-FC. Thirty-four (63%) and 23 (59%) patients underwent operative resection of CLM, respectively. FC patients presented earlier at first postnatal follow-up (42 vs. 145 days, p = .03), had fewer preoperative office visits (2.1 vs. 3.4, p = .0003), received fewer preoperative chest radiographs (0.5 vs. 1.3; p = .002) and chest computed tomography (0.9 vs. 1.4; p = .001), and had fewer preoperative pneumonias (0 vs. 17.4%; p = .02) compared to their NON-FC counterparts. FC patients were also more likely to undergo resection at an earlier age (217 vs. 481 days, p = .003) and were more likely to undergo a minimally invasive resection (75% vs. 39.1%, p = .015). There were no differences in post-operative outcomes between the two groups. CONCLUSION: Children with a prenatal diagnosis of CLM appear to benefit from an organized multi-specialty team approach in several impactful parameters. Hospital systems and providers that invest in similar strategies are likely to achieve improved outcomes in the care of newborns prenatally diagnosed with a CLM.

The in-utero diagnosis of choledochal cyst: can postnatal imaging predict benefit from early surgical intervention?

BACKGROUND: Infants prenatally suspected of having a choledochal cyst (CDC) typically undergo ultrasound imaging shortly after birth. This study sought to evaluate features on the initial postnatal ultrasound (IPU) that could identify newborns at risk for early complications. METHODS: Following IRB approval, patients from four US fetal centers with prenatal suspicion for CDC and postnatal imaging from 2000 to 2017 were reviewed. Imaging and clinical courses were assessed. RESULTS: Forty-two patients had prenatal ultrasounds suspicious for CDC. Nineteen (45.2%) were excluded due to diagnostic revision (n = 9), cyst resolution (n = 5), lack of IPU measurements (n = 3), or lack of follow-up (n = 2). The 23 remaining patients were included in the study. Of these, five (21.7%) developed symptoms at a median age of 16.5 days (IQR 16-19 days), and 18 (78.3%) remained asymptomatic throughout the first year after birth. Five patients (21.7%) had cysts ≥ 4.5 cm on IPU (Symptomatic: n = 3; Asymptomatic: n = 2). Eighteen patients (78.3%) had cysts < 4.5 cm on IPU (Symptomatic: n = 2; Asymptomatic: n = 16). An IPU cyst size ≥ 4.5 cm was associated with neonatal symptom manifestation (p = 0.048), with 88.9% specificity (95% CI 65.3-98.6%) and 60% sensitivity (95% CI 14.7-94.7%). CONCLUSIONS: In newborns with prenatally diagnosed CDC, a cyst size ≥ 4.5 cm on IPU is associated with symptom development during the first month after birth and therefore early cyst excision is recommended.