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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.

IMPORTANCE: Newborn genomic sequencing (nGS) may provide health benefits throughout the life span, but there are concerns that it could also have an unfavorable (ie, negative) psychosocial effect on families. OBJECTIVE: To assess the psychosocial effect of nGS on families from the BabySeq Project, a randomized clinical trial evaluating the effect of nGS on the clinical care of newborns from well-baby nurseries and intensive care units. DESIGN, SETTING, AND PARTICIPANTS: In this randomized clinical trial conducted from May 14, 2015, to May 21, 2019, at well-baby nurseries and intensive care units at 3 Boston, Massachusetts, area hospitals, 519 parents of 325 infants completed surveys at enrollment, immediately after disclosure of nGS results, and 3 and 10 months after results disclosure. Statistical analysis was performed on a per-protocol basis from January 16, 2019, to December 1, 2019. INTERVENTION: Newborns were randomized to receive either standard newborn screening and a family history report (control group) or the same plus an nGS report of childhood-onset conditions and highly actionable adult-onset conditions (nGS group). MAIN OUTCOMES AND MEASURES: Mean responses were compared between groups and, within the nGS group, between parents of children who received a monogenic disease risk finding and those who did not in 3 domains of psychosocial impact: parent-child relationship (Mother-to-Infant Bonding Scale), parents’ relationship (Kansas Marital Satisfaction Scale), and parents’ psychological distress (Edinburgh Postnatal Depression Scale anxiety subscale). RESULTS: A total of 519 parents (275 women [53.0%]; mean [SD] age, 35.1 [4.5] years) were included in this study. Although mean scores differed for some outcomes at singular time points, generalized estimating equations models did not show meaningful differences in parent-child relationship (between-group difference in adjusted mean [SE] Mother-to-Infant Bonding Scale scores: postdisclosure, 0.04 [0.15]; 3 months, –0.18 [0.18]; 10 months, –0.07 [0.20]; joint P = .57) or parents’ psychological distress (between-group ratio of adjusted mean [SE] Edinburgh Postnatal Depression Scale anxiety subscale scores: postdisclosure, 1.04 [0.08]; 3 months, 1.07 [0.11]; joint P = .80) response patterns between study groups over time for any measures analyzed in these 2 domains. Response patterns on one parents’ relationship measure differed between groups over time (between-group difference in adjusted mean [SE] Kansas Marital Satisfaction Scale scores: postdisclosure, –0.19 [0.07]; 3 months, –0.04 [0.07]; and 10 months, –0.01 [0.08]; joint P = .02), but the effect decreased over time and no difference was observed on the conflict measure responses over time. We found no evidence of persistent negative psychosocial effect in any domain. CONCLUSIONS AND RELEVANCE: In this randomized clinical trial of nGS, there was no persistent negative psychosocial effect on families among those who received nGS nor among those who received a monogenic disease risk finding for their infant. TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT02422511

Objective: International 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 design: Retrospective 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. Results: The 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. Conclusions: ICD codes registered for BPD are unlikely to accurately reflect the current clinical definition and should be interpreted with caution.

Purpose: To investigate the impact of rapid-turnaround exome sequencing in critically ill neonates using phenotype-based subject selection criteria. Methods: 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. Results: 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. Conclusion: 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.

To investigate the impact of rapid-turnaround exome sequencing in critically ill neonates using phenotype-based subject selection criteria.

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

Most professional guidelines recommend against genetic screening for adult-onset only (AO) conditions until adulthood, yet others argue that there may be benefit to disclosing such results. We explored parents’ decision-making on this issue in the BabySeq Project, a clinical trial of newborn genomic sequencing.

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.

Purpose: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.Methods: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.Results: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.Conclusion: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 Med 17 5, 337–347.

Improvements in obstetric sonography US have led to an increased prenatal detection of clubfoot, but studies have not been able to correlate sonographic severity to clinical deformity at birth. The purpose of this study was to decrease the false positive FP rate for prenatally identified clubfeet, and to predict clinical severity using a new prenatal sonographic classification system.

Purpose: To study the follow-up of genetic counseling performed in families with a newborn detected with one cystic fibrosis (CF) mutation in a statewide newborn screening pilot program.Methods: Newborns in Massachusetts with an elevated trypsinogen level on newborn screen who are found to have one mutation for CF on a selected mutation assay undergo sweat testing for CF, and their families receive genetic counseling. The genetic counseling focuses on carrier risk for the parents of the newborn and offers carrier testing. We studied the yield of genetic counseling and the resulting genetic testing performed on the families of infants found to be CF carriers who underwent sweat testing in a single institution.Results: Of 102 newborns evaluated with a single CF mutation, 2 (twins) had sweat test results consistent with CF. A total of 101 families were counseled, and 95 were offered DNA-based CF carrier testing. Eighty-two percent of all parents chose to have CF carrier testing, and in five couples, both members were carriers. One of these couples (whose newborn was only a carrier) had an older child who was unexpectedly found to have CF.Conclusions: Sweat testing of newborns at increased risk for CF in conjunction with genetic counseling for their parents allows identification of infants with CF, finds couples at high risk for having a child with CF, identifies previously undiagnosed siblings with CF, and allows for potential identification of CF carriers in the extended family.

To study the follow-up of genetic counseling performed in families with a newborn detected with one cystic fibrosis (CF) mutation in a statewide newborn screening pilot program.

ABSTRACTWhether allelic variants of the cystic fibrosis (CF) transmembrane conductance regulator (CFTR) independently contribute to pulmonary outcome in CF patients has not been resolved. We used both cross-sectional and mixed-model longitudinal analyses of data from CF patients that were at least 12 years old to determine the influence on pulmonary function (percent predicted forced expiratory volume [FEV1]) of the CFTR gene genotype, gender, mucoidPseudomonas aeruginosa(MPA) infection status, presence of total opsonic antibody to MPA, and, separately, the opsonic antibody activity specific to the mucoid exopolysaccharide (MEP) surface antigen. Two different factors were independently associated with the lack of MPA infection: a high level of MEP-specific opsonic activity (MSOA), implicating an immunologically based mechanism of resistance to infection, and a lack of any type of opsonic antibody to MPA, indicative of no significant exposure or infection. This latter phenotype was found in a subset of CF patients who carried at least one uncommon CFTR gene allele suggestive of a genetic basis for resistance to infection in this group of older CF patients. For CF patients in whom both CFTR gene alleles were identified by screening for the 12 most common variants (75% of alleles), cross-sectional analysis showed that MPA infection was best correlated with lower percent predicted FEV1, while genotype (two versus one ΔF508 CFTR gene allele) and a low level of MSOA were associated with increased risk of infection. A mixed-model analysis of longitudinal spirometric measurements that considered multiple risk factors to derive regression equations was used to determine which clinical parameters had the greatest effect on the annual rate of decline in percent predicted FEV1. This analysis showed that the CFTR gene genotype only modestly modified the constant (yintercept) of the derived equations, while gender and MPA infection status had the largest effects on annual rates of decline in percent predicted FEV1. These results indicate that the CFTR genotype is usually not a primary determinant of pulmonary function in most CF patients, but gender and MPA infection status are. Infection status is potentially influenced by both immunologic (a high level of MSOA) and genetic factors, such as carriage of a CFTR gene allele that leads to a diagnosis of CF but still confers resistance to infection that is comparable to that of the wild-type CFTR gene.

Heterozygosity for a mutant dysfunctional C1 inhibitor protein, a member of the serine proteinase inhibitor (serpin) superfamily, results in type II hereditary angioneurotic oedema. We identified a “hinge” region mutation in C1 inhibitor with a Val to Glu replacement at P14 Val–432. Recombinant C1 inhibitors P10 Ala→Thr and P14 Val→Glu did not form stable complexes with fluid phase C1s or kallikrein. The P14 Val→Glu mutant, however, was cleaved to a 96K form by C1s, while the P10 Ala→Thr mutant was not. The recombinant P10 mutant also did not complex with C1s, kallikrein or β–factor XIIa–Sepharose. The two mutations, therefore, result in dysfunction by different mechanisms: in one (P14 Val→Glu), the inhibitor is converted to a substrate, while in the other (P10 Ala→Thr), interaction with target protease is blocked.