Use of a targeted, combinatorial next-generation sequencing approach for the study of bicuspid aortic valve

BACKGROUND: Bicuspid aortic valve (BAV) is the most common type of congenital heart disease with a population prevalence of 1-2%. While BAV is known to be highly heritable, mutations in single genes (such as GATA5 and NOTCH1) have been reported in few human BAV cases. Traditional gene sequencing methods are time and labor intensive, while next-generation high throughput sequencing remains costly for large patient cohorts and requires extensive bioinformatics processing. Here we describe an approach to targeted multi-gene sequencing with combinatorial pooling of samples from BAV patients. METHODS: We studied a previously described cohort of 78 unrelated subjects with echocardiogram-identified BAV. Subjects were identified as having isolated BAV or BAV associated with coarctation of aorta (BAV-CoA). BAV cusp fusion morphology was defined as right-left cusp fusion, right non-coronary cusp fusion, or left non-coronary cusp fusion. Samples were combined into 19 pools using a uniquely overlapping combinatorial design; a given mutation could be attributed to a single individual on the basis of which pools contained the mutation. A custom gene capture of 97 candidate genes was sequenced on the Illumina HiSeq 2000. Multistep bioinformatics processing was performed for base calling, variant identification, and in-silico analysis of putative disease-causing variants. RESULTS: Targeted capture identified 42 rare, non-synonymous, exonic variants involving 35 of the 97 candidate genes. Among these variants, in-silico analysis classified 33 of these variants as putative disease-causing changes. Sanger sequencing confirmed thirty-one of these variants, found among 16 individuals. There were no significant differences in variant burden among BAV fusion phenotypes or isolated BAV versus BAV-CoA. Pathway analysis suggests a role for the WNT signaling pathway in human BAV. CONCLUSION: We successfully developed a pooling and targeted capture strategy that enabled rapid and cost effective next generation sequencing of target genes in a large patient cohort. This approach identified a large number of putative disease-causing variants in a cohort of patients with BAV, including variants in 26 genes not previously associated with human BAV. The data suggest that BAV heritability is complex and polygenic. Our pooling approach saved over $39,350 compared to an unpooled, targeted capture sequencing strategy

Improving the identification of acute kidney injury in the neonatal ICU: three centers’ experiences

OBJECTIVE: To describe three different standardized approaches to improving neonatal acute kidney injury (AKI) identification and the impact on AKI identification, incidence, and nephrology consultation and referral. STUDY DESIGN: A retrospective cohort study in three academic NICUs. We compared AKI identification, AKI incidence, nephrology consultation, and nephrology follow-up before and after implantation of local protocols to standardize neonatal AKI identification. RESULT: Neonatal AKI identification improved in all three NICUs following protocol implementation (26-85%, P < 0.0001). Each center also saw increases in nephrology consultation (15-83%, P < 0.0001) and nephrology follow-up (7-73%, P < 0.0001). AKI incidence decreased significantly (21-12%, P < 0.0001). CONCLUSION: Multiple strategies can be successfully operationalized to improve neonatal AKI identification. While different in approach, each strategy resulted in increased AKI identification and nephrology involvement. This study emphasizes the importance of local standardized approaches to AKI to improve AKI identification and nephrology involvement in the NICU

Part 6: Essentials of Neonatal–Perinatal Medicine fellowship: program administration

A successful Neonatal-Perinatal Medicine fellowship (NPM-F) program requires presence and insight of national and institutional supervisory organizations as well as effective program-specific leaders: program director (PD), associate program director (APD), program coordinator (PC), and core faculty. It is becoming more common for PDs and APDs to have advanced training in medical education and conduct medical education research. While NPM-F program leaders benefit from a strong national NPM educator community, they face challenges of increased regulatory burden and unclear national guidelines with variable local interpretation for protected time. National and local organizations can support program leaders and promote their academic success while reducing burnout and turnover by providing leadership training, academic mentoring, and adequate protected time for research and program-specific tasks

Endothelial Notch1 Is Required for Proper Development of the Semilunar Valves and Cardiac Outflow Tract

Background-Congenital heart disease is the most common type of birth defect, affecting approximate to 2% of the population. Malformations involving the cardiac outflow tract and semilunar valves account for >50% of these cases predominantly because of a bicuspid aortic valve, which has an estimated prevalence of 1% in the population. We previously reported that mutations in NOTCH1 were a cause of bicuspid aortic valve in nonsyndromic autosomal-dominant human pedigrees. Subsequently, we described a highly penetrant mouse model of aortic valve disease, consisting of a bicuspid aortic valve with thickened cusps and associated stenosis and regurgitation, in Notch1-haploinsufficient adult mice backcrossed into a Nos3-null background. Methods and Results-Here, we described the congenital cardiac abnormalities in Notch1(+/-); Nos3(-/-) embryos that led to approximate to 65% lethality by postnatal day 10. Although expected Mendelian ratios of Notch1(+/-); Nos3(-/-) embryos were found at embryonic day 18.5, histological examination revealed thickened, malformed semilunar valve leaflets accompanied by additional anomalies of the cardiac outflow tract including ventricular septal defects and overriding aorta. The aortic valve leaflets of Notch1(+/-); Nos3(-/-) embryos at embryonic day 15.5 were significantly thicker than controls, consistent with a defect in remodeling of the semilunar valve cushions. In addition, we generated mice haploinsufficient for Notch1 specifically in endothelial and endothelial-derived cells in a Nos3-null background and found that Notch1(fl/+); Tie2-Cre(+/-); Nos3(-/-) mice recapitulate the congenital cardiac phenotype of Notch1(+/-); Nos3(-/-) embryos. Conclusions-Our data demonstrate the role of endothelial Notch1 in the proper development of the semilunar valves and cardiac outflow tract

Addressing bias and knowledge gaps regarding race and ethnicity in neonatology manuscript review

A recent shift in public attention to racism, racial disparities, and health equity have resulted in an abundance of calls for relevant papers and publications in academic journals. Peer-review for such articles may be susceptible to bias, as subject matter expertise in the evaluation of social constructs, like race, is variable. From the perspective of researchers focused on neonatal health equity, we share our positive and negative experiences in peer-review, provide relevant publicly available data regarding addressing bias in peer-review from 12 neonatology-focused journals, and give recommendations to address bias and knowledge gaps in the peer review process of health equity research

The impact of fluid balance on outcomes in critically ill near-term/term neonates: a report from the AWAKEN study group

BACKGROUND: In sick neonates admitted to the NICU, improper fluid balance can lead to fluid overload. We report the impact of fluid balance in the first postnatal week on outcomes in critically ill near-term/term neonates. METHODS: This analysis includes infants ≥36 weeks gestational age from the Assessment of Worldwide Acute Kidney injury Epidemiology in Neonates (AWAKEN) study (N = 645). Fluid balance: percent weight change from birthweight. PRIMARY OUTCOME: mechanical ventilation (MV) on postnatal day 7. RESULTS: The median peak fluid balance was 1.0% (IQR: -0.5, 4.6) and occurred on postnatal day 3 (IQR: 1, 5). Nine percent required MV at postnatal day 7. Multivariable models showed the peak fluid balance (aOR 1.12, 95%CI 1.08-1.17), lowest fluid balance in 1st postnatal week (aOR 1.14, 95%CI 1.07-1.22), fluid balance on postnatal day 7 (aOR 1.12, 95%CI 1.07-1.17), and negative fluid balance at postnatal day 7 (aOR 0.3, 95%CI 0.16-0.67) were independently associated with MV on postnatal day 7. CONCLUSIONS: We describe the impact of fluid balance in critically ill near-term/term neonates over the first postnatal week. Higher peak fluid balance during the first postnatal week and higher fluid balance on postnatal day 7 were independently associated with MV at postnatal day 7

The impact of fluid balance on outcomes in premature neonates: a report from the AWAKEN study group

BACKGROUND: We evaluated the epidemiology of fluid balance (FB) over the first postnatal week and its impact on outcomes in a multi-center cohort of premature neonates from the AWAKEN study. METHODS: Retrospective analysis of infants \u3c36 weeks\u27 gestational age from the AWAKEN study (N = 1007). FB was defined by percentage of change from birth weight. OUTCOME: Mechanical ventilation (MV) at postnatal day 7. RESULTS: One hundred and forty-nine (14.8%) were on MV at postnatal day 7. The median peak FB was 0% (IQR: -2.9, 2) and occurred on postnatal day 2 (IQR: 1,5). Multivariable models showed that the peak FB (aOR 1.14, 95% CI 1.10-1.19), lowest FB in first postnatal week (aOR 1.12, 95% CI 1.07-1.16), and FB on postnatal day 7 (aOR 1.10, 95% CI 1.06-1.13) were independently associated with MV on postnatal day 7. In a similar analysis, a negative FB at postnatal day 7 protected against the need for MV at postnatal day 7 (aOR 0.21, 95% CI 0.12-0.35). CONCLUSIONS: Positive peak FB during the first postnatal week and more positive FB on postnatal day 7 were independently associated with MV at postnatal day 7. Those with a negative FB at postnatal day 7 were less likely to require MV

The impact of fluid balance on outcomes in critically ill near-term/term neonates: a report from the AWAKEN study group.

BACKGROUND: In sick neonates admitted to the NICU, improper fluid balance can lead to fluid overload. We report the impact of fluid balance in the first postnatal week on outcomes in critically ill near-term/term neonates. METHODS: This analysis includes infants ≥36 weeks gestational age from the Assessment of Worldwide Acute Kidney injury Epidemiology in Neonates (AWAKEN) study (N = 645). Fluid balance: percent weight change from birthweight. PRIMARY OUTCOME: mechanical ventilation (MV) on postnatal day 7. RESULTS: The median peak fluid balance was 1.0% (IQR: -0.5, 4.6) and occurred on postnatal day 3 (IQR: 1, 5). Nine percent required MV at postnatal day 7. Multivariable models showed the peak fluid balance (aOR 1.12, 95%CI 1.08-1.17), lowest fluid balance in 1st postnatal week (aOR 1.14, 95%CI 1.07-1.22), fluid balance on postnatal day 7 (aOR 1.12, 95%CI 1.07-1.17), and negative fluid balance at postnatal day 7 (aOR 0.3, 95%CI 0.16-0.67) were independently associated with MV on postnatal day 7. CONCLUSIONS: We describe the impact of fluid balance in critically ill near-term/term neonates over the first postnatal week. Higher peak fluid balance during the first postnatal week and higher fluid balance on postnatal day 7 were independently associated with MV at postnatal day 7