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Newborn screening (NBS) is performed to identify neonates at risk for actionable, severe, early-onset disorders, many of which are genetic. The BabySeq Project randomized neonates to receive conventional NBS or NBS plus exome sequencing (ES) capable of detecting sequence variants that may also diagnose monogenic disease or indicate genetic disease risk. We therefore evaluated how ES and conventional NBS results differ in this population. We compared results of NBS (including hearing screens) and ES for 159 infants in the BabySeq Project. Infants were considered “NBS positive” if any abnormal result was found indicating disease risk and “ES positive” if ES identified a monogenic disease risk or a genetic diagnosis. Most infants (132/159, 84%) were NBS and ES negative. Only one infant was positive for the same disorder by both modalities. Nine infants were NBS positive/ES negative, though seven of these were subsequently determined to be false positives. Fifteen infants were ES positive/NBS negative, all of which represented risk of genetic conditions that are not included in NBS programs. No genetic explanation was identified for eight infants referred on the hearing screen. These differences highlight the complementarity of information that may be gleaned from NBS and ES in the newborn period.

Purpose: Genomic sequencing (GS) for newborns may enable detection of conditions for which early knowledge can improve health outcomes. One of the major challenges hindering its broader application is the time it takes to assess the clinical relevance of detected variants and the genes they impact so that disease risk is reported appropriately. Methods: To facilitate rapid interpretation of GS results in newborns, we curated a catalog of genes with putative pediatric relevance for their validity based on the ClinGen clinical validity classification framework criteria, age of onset, penetrance, and mode of inheritance through systematic evaluation of published evidence. Based on these attributes, we classified genes to guide the return of results in the BabySeq Project, a randomized, controlled trial exploring the use of newborn GS (nGS), and used our curated list for the first 15 newborns sequenced in this project. Results: Here, we present our curated list for 1,514 gene–disease associations. Overall, 954 genes met our criteria for return in nGS. This reference list eliminated manual assessment for 41% of rare variants identified in 15 newborns. Conclusion: Our list provides a resource that can assist in guiding the interpretive scope of clinical GS for newborns and potentially other populations. Genet Med advance online publication 12 January 2017

Duchenne muscular dystrophy (DMD) is not currently part of mandatory newborn screening, despite the availability of a test since 1975. In the absence of screening, a DMD diagnosis is often not established in patients until 3–6 years of age. During this time, irreversible muscle degeneration takes place, and clinicians agree that the earlier therapy is initiated, the better the long-term outcome. With recent availability of FDA-approved DMD therapies, interest has renewed for adoption by state public health programs, but such implementation is a multiyear process. To speed access to approved therapies, we implemented a unique, hospital-based program offering parents of newborns an optional, supplemental DMD newborn screen (NBS) via a two-tiered approach: utilizing a creatine kinase (CK) enzyme assay coupled with rapid targeted next-generation sequencing (tNGS) for the DMD gene (using a Whole-Exome Sequencing (WES) assay). The tNGS/WES assay integrates the ability to detect both point mutations and large deletion/duplication events. This tiered newborn screening approach allows for the opportunity to improve treatment and outcomes, avoid the diagnostic delays, and diminish healthcare disparities. To implement this screening algorithm through hospitals in a way that would ultimately be acceptable to public health laboratories, we chose an FDA-approved CK-MM immunoassay to avoid the risks of false-negative/-positive results. Because newborn CK values can be affected due to non-DMD-related causes such as birth trauma, a confirmatory repeat CK assay on a later dried blood spot (DBS) collection has been proposed. Difficulties associated with non-routine repeat DBS collection, including the tracking and recall of families, and the potential creation of parental anxiety associated with false-positive results, can be avoided with this algorithm. Whereas a DMD diagnosis is essentially ruled out by the absence of detected DMD sequence abnormalities, a subsequent CK would still be warranted to confirm resolution of the initial elevation, and thus the absence of non-DMD muscular dystrophy or other pathologies. To date, we have screened over 1500 newborns (uptake rate of ~80%) by a CK-MM assay, and reflexed DMD tNGS in 29 of those babies. We expect the experience from this screening effort will serve as a model that will allow further expansion to other hospital systems until a universal public health screening is established.

On Dec. 16, 2016, the U.S. Food and Drug Administration (FDA) released a warning regarding the potential neurotoxicity of anesthesia and sedation agents on the developing brain in children younger than 3 years and in women during their 3rd trimester of pregnancy. These concerns have relevance to the pediatric radiologist who must take into consideration how the child’s state might impact image quality. In this review the author provides background on the special concerns in the potentially highest-risk group, pre-term and term neonates, and provides guidance and rationale for the avoidance of sedation in procedural imaging of the newborn.

To investigate the impact of rapid-turnaround exome sequencing in critically ill neonates using phenotype-based subject selection criteria. Intensive care unit babies aged <6 months with hypotonia, seizures, a complex metabolic phenotype, and/or multiple congenital malformations were prospectively enrolled for rapid (<7 day) trio-based exome sequencing. Genomic variants relevant to the presenting phenotype were returned to the medical team. A genetic diagnosis was attained in 29 of 50 (58%) sequenced cases. Twenty-seven (54%) patients received a molecular diagnosis involving known disease genes; two additional cases (4%) were solved with pathogenic variants found in novel disease genes. In 24 of the solved cases, diagnosis had impact on patient management and/or family members. Management changes included shift to palliative care, medication changes, involvement of additional specialties, and the consideration of new experimental therapies. Phenotype-based patient selection is effective at identifying critically ill neonates with a high likelihood of receiving a molecular diagnosis via rapid-turnaround exome sequencing, leading to faster and more accurate diagnoses, reducing unnecessary testing and procedures, and informing medical care.

ObjectiveInternational Classification of Diseases (ICD) codes in electronic health records (EHRs) are increasingly used for health services research, in spite of unknown diagnostic accuracy. The accuracy of ICD codes to identify bronchopulmonary dysplasia (BPD) is unknown.Study designRetrospective cohort study in a single-center NICU (n = 166) to evaluate sensitivity and specificity of ICD-10 codes for the diagnosis of BPD. Analysis of large insurance claims database (n = 7887) to determine date of assignment of the code.ResultsThe sensitivity of any BPD-related ICD codes ranged from 0.82 to 0.95, while the specificity ranged from 0.25 to 0.36. In a large national insurance database, the most common date of ICD-9 or ICD-10 code assignment was the day of birth, which is inconsistent with the clinical definition.ConclusionsICD codes registered for BPD are unlikely to accurately reflect the current clinical definition and should be interpreted with caution.

Background The greatest opportunity for lifelong impact of genomic sequencing is during the newborn period. The “BabySeq Project” is a randomized trial that explores the medical, behavioral, and economic impacts of integrating genomic sequencing into the care of healthy and sick newborns. Methods Families of newborns are enrolled from Boston Children’s Hospital and Brigham and Women’s Hospital nurseries, and half are randomized to receive genomic sequencing and a report that includes monogenic disease variants, recessive carrier variants for childhood onset or actionable disorders, and pharmacogenomic variants. All families participate in a disclosure session, which includes the return of results for those in the sequencing arm. Outcomes are collected through review of medical records and surveys of parents and health care providers and include the rationale for choice of genes and variants to report; what genomic data adds to the medical management of sick and healthy babies; and the medical, behavioral, and economic impacts of integrating genomic sequencing into the care of healthy and sick newborns. Discussion The BabySeq Project will provide empirical data about the risks, benefits and costs of newborn genomic sequencing and will inform policy decisions related to universal genomic screening of newborns. Trial registration The study is registered in ClinicalTrials.gov Identifier: NCT02422511 . Registration date: 10 April 2015.

Abdominal ultrasound (AUS) is a promising adjunct to abdominal x-ray (AXR) for evaluating necrotizing enterocolitis (NEC). We developed a multivariable risk score incorporating AUS to predict surgical NEC. 83 patients were evaluated by AXR and AUS for suspected NEC. A subset had surgical NEC. Multivariate logistic regression determined predictors of surgical NEC, which were incorporated into a risk score. 14/83 patients (16.9%) had surgical NEC. 10/83 (12.0%) patients required acute intervention, while 4/83 (4.8%) patients only required delayed surgery. Four predictors of surgical NEC were identified: abdominal wall erythema (OR: 8.2, p = 0.048), portal venous gas on AXR (OR: 29.8, p = 0.014), and echogenic free fluid (OR: 17.2, p = 0.027) and bowel wall thickening (OR: 12.5, p = 0.030) on AUS. A multivariable risk score incorporating these predictors had excellent area-under-the-curve of 0.937 (95% CI: 0.879–0.994). AUS, as an adjunct to physical exam and AXR, has utility for predicting surgical NEC. [Display omitted] •This new multivariable risk score has excellent discrimination for surgical NEC.•Abdominal ultrasound has utility for predicting surgical NEC.•Abdominal wall erythema and x-ray portal venous gas are also predictors.

Genetic testing is routinely used for second-tier confirmation of newborn sequencing results to rule out false positives and to confirm diagnoses in newborns undergoing inpatient and outpatient care. We developed a targeted next-generation sequencing panel coupled with a variant processing pipeline and demonstrated utility and performance benchmarks across multiple newborn disease presentations in a retrospective clinical study. The test utilizes an in silico gene filter that focuses directly on 126 genes related to newborn screening diseases and is applied to the exome or a next-generation sequencing panel called NBDx. NBDx targets the 126 genes and additional newborn-specific disorders. It integrates DNA isolation from minimally invasive biological specimens, targeted next-generation screening, and rapid characterization of genetic variation. We report a rapid parallel processing of 8 to 20 cases within 105 hours with high coverage on our NBDx panel. Analytical sensitivity of 99.8% was observed across known mutation hotspots. Concordance calls with or without clinical summaries were 94% and 75%, respectively. Rapid, automated targeted next-generation sequencing and analysis are practical in newborns for second-tier confirmation and neonatal intensive care unit diagnoses, laying a foundation for future primary DNA-based molecular screening of additional disorders and improving existing molecular testing options for newborns. Genet Med17 5, 337–347.

PurposeWe evaluated the diagnostic utility of abdominal ultrasound (AUS), an adjunct to abdominal X-ray (AXR), for necrotizing enterocolitis (NEC) in congenital heart disease (CHD) patients.Methods86 patients with suspected NEC from 2009 to 2018 were classified as with CHD (n = 18) if they required cardiac intervention versus without CHD (n = 68). Clinical and radiological data were collected, including AXR and AUS concordance. Wilcoxon rank-sum test and Fisher’s exact test were performed.ResultsCHD patients had higher birth weights (p < 0.001) and gestational ages (p < 0.001) than non-CHD patients. CHD patients presented more frequently with hypotension (p = 0.041) and less frequently with bilious emesis (p < 0.001). Overall, CHD patients were less likely to have AUS findings of pneumatosis (33.3 vs. 72.1%; p = 0.005) and decreased mural flow (0 vs. 20.6%; p = 0.035) compared to non-CHD patients. On concordance analysis, CHD patients had 3.9-fold more discordant studies with pneumatosis on AXR but not on AUS (33.3 vs. 8.8%; p = 0.016) compared to non-CHD patients. Urgent surgery was required in 5.6% of CHD patients versus 16.2% of non-CHD patients.ConclusionCHD patients with suspected NEC represent a distinct clinical population. AUS has particular utility in assessing findings of bowel viability in the CHD NEC population, reflecting reduced rates of surgical NEC.