Benchmarking outcomes in the Neonatal Intensive Care Unit: Cytogenetic and molecular diagnostic rates in a retrospective cohort

Role of next generation sequencing in diagnosis and management of critically ill children with suspected monogenic disorder

Next generation sequencing based diagnosis has emerged as a promising tool for evaluating critically ill neonates and children. However, there is limited data on its utility in developing countries. We assessed its diagnostic rate and clinical impact on management of pediatric patients with a suspected genetic disorder requiring critical care. The study was conducted at a single tertiary hospital in Northern India. We analyzed 70 children with an illness requiring intensive care and obtained a precise molecular diagnosis in 32 of 70 probands (45.3%) using diverse sequencing techniques such as clinical exome, whole exome, and whole genome. A significant change in clinical outcome was observed in 13 of 32 (40.6%) diagnosed probands with a change in medication in 11 subjects and redirection to palliative care in two subjects. Additional benefits included specific dietary management (three cases), avoidance of a major procedure (one case) and better reproductive counseling. Dramatic therapeutic responses were observed in three cases with SCN1A, SCN2A and KCNQ2-related epileptic encephalopathy. A delayed turn-around for sequencing results was perceived as a major limiting factor in the study, as rapid and ultra-rapid sequencing was not available. Achieving a precise molecular diagnosis has great utility in managing critically ill patients with suspected genetic disorders in developing countries.

Genetic counselling considerations with genetic/genomic testing in Neonatal and Pediatric Intensive Care Units: A scoping review

Genetic and genomic technologies can effectively diagnose numerous genetic disorders. Patients benefit when genetic counselling accompanies genetic testing and international guidelines recommend pre- and post-test genetic counselling with genome-wide sequencing. However, there is a gap in knowledge regarding the unique genetic counselling considerations with different types of genetic testing in the Neonatal Intensive Care Unit (NICU) and the Pediatric Intensive Care Unit (PICU). This scoping review was conducted to identify the gaps in care with respect to genetic counselling for infants/pediatric patients undergoing genetic and genomic testing in NICUs and PICUs and understand areas in need of improvement in order to optimize clinical care for patients, caregivers, and healthcare providers. Five databases (MEDLINE [Ovid], Embase [Ovid], PsycINFO [Ebsco], CENTRAL [Ovid], and CINHAL [Ebsco]) and grey literature were searched. A total of 170 studies were included and used for data extraction and analysis. This scoping review includes descriptive analysis, followed by a narrative account of the extracted data. Results were divided into three groups: pre-test, post-test, and comprehensive (both pre- and post-test) genetic counselling considerations based on indication for testing. More studies were conducted in the NICU than the PICU. Comprehensive genetic counselling was discussed in only 31% of all the included studies demonstrating the need for both pre-test and post-test genetic counselling for different clinical indications in addition to the need to account for different cultural aspects based on ethnicity and geographic factors.

Postnatal genetic testing on cord blood for prenatally identified high-probability cases

OBJECTIVE

To evaluate the utility of postnatal genetic testing on umbilical cord blood (CB) for prenatally identified high-probability fetuses.

METHOD

CB for genetic testing was offered to individuals who met one of the following criteria: (i) fetal anomaly, (ii) positive non-invasive prenatal screening by cfDNA or biochemical analysis, or (iii) family history. Individuals with diagnostic testing, but not microarray, were also included when recommended by society guidelines. CB was collected at Brigham and Women's and Emerson Hospitals between 2016 and 2021.

RESULTS

448 individuals consented for cord blood testing (370 (82.6%) for fetal anomalies, 51 (11.4%) for high-probability cfDNA, and 27 (6.0%) for family history) and a total of 393 (87.7%) samples were analyzed. Genetic testing yielded a diagnosis in 92 (23.4%) neonates by karyotype (n = 37), chromosomal microarray (CMA) (n = 32), and other molecular analysis (n = 23). Testing averaged 10.3 days (range 1-118 days). 68 (73.9%) diagnoses potentially impacted neonatal management. MCC could not be definitively excluded in only 1.4% (6/418) of samples.

CONCLUSION

Prenatal identification of high-probability fetuses and genetic testing on CB facilitates timely genetic diagnoses and neonatal management. Testing provides reassurance and reduces a postnatal diagnostic odyssey for high-probability neonates.

The incorporation of next-generation sequencing into pediatric care

Genetic condition is one of the major etiologies causing morbidity and mortality in infants and children. More and more etiologies can be solved using next-generation sequencing (NGS) as it develops. Currently, whole-exome sequencing (WES) and whole-genome sequencing (WGS) have been highly integrated into clinical practice. The average diagnostic yield of WES/WGS in pediatric patients with genetic condition was around 40% (range: 21%-80%), with acceptable turnaround time and cost. The higher diagnostic yield categories are deafness, ophthalmic, neurological, skeletal conditions, and inborn error of metabolism. Positive results provide benefit with those for actionable diseases, next pregnancy planning, and family members. For those in critical condition, with the emergence of sequencing technology and bioinformatics analysis tools, provisional diagnosis can be made as short as 13.5 h using ultrarapid WGS. We believe this powerful tool has changed pediatric daily practice.

Genetics in the NICU: Nurses' Perceived Knowledge and Desired Education

Background Many infants admitted to the neonatal intensive care unit (NICU) have genetic conditions. Previous research has shown that gaps exist in the genetics knowledge of nurses and that they lack comfort applying genetics information to clinical practice. Studies assessing the knowledge or comfort of NICU nurses with genetics have not previously been completed. Method A total of 122 NICU nurses completed a survey assessing perceived knowledge of genetics, comfort with clinical scenarios involving genetics, and desired genetics education. Results Perceived knowledge and overall comfort were correlated with highest degree received, how prepared a nurse felt by the genetics education received in their training, and having a close relationship with someone with a genetic condition. Almost all respondents (96%, n = 117) desired additional genetics education. Conclusion Gaps exist in the genetics knowledge of neonatal nurses in our cohort, and their overall comfort working with clinical scenarios involving genetics was low. There is significant interest in additional genetics education. [J Contin Educ Nurs. 2023;54(1):16-24.].

Evaluating use of changing technologies for rapid next-generation sequencing in pediatrics

BACKGROUND

Rapid next-generation sequencing (NGS) offers the potential to shorten the diagnostic process and improve the care of acutely ill children. The goal of this study was to report our findings, including benefits and limitations, of a targeted NGS panel and rapid genome sequencing (rGS) in neonatal and pediatric acute clinical care settings.

METHODS

Retrospective analysis of patient characteristics, diagnostic yields, turnaround time, and changes in management for infants and children receiving either RapSeq, a targeted NGS panel for 4500+ genes, or rGS, at the University of Utah Hospital and Primary Children's Hospital, from 2015 to 2020.

RESULTS

Over a 5-year period, 142 probands underwent rapid NGS: 66 received RapSeq and 76 rGS. Overall diagnostic yield was 39%. In the majority of diagnostic cases, there were one or more changes in clinical care management. Of note, 7% of diagnoses identified by rGS would not have been identified by RapSeq.

CONCLUSIONS

Our results indicate that rapid NGS impacts acute pediatric care in real-life clinical settings. Although affected by patient selection criteria, diagnostic yields were similar to those from clinical trial settings. Future studies are needed to determine relative advantages, including cost, turnaround time, and benefits for patients, of each approach in specific clinical circumstances.

IMPACT

The use of comprehensive Mendelian gene panels and genome sequencing in the clinical setting allows for early diagnosis of patients in neonatal, pediatric, and cardiac intensive care units and impactful change in management. Diagnoses led to significant changes in management for several patients in lower acuity inpatient units supporting further exploration of the utility of rapid sequencing in these settings. This study reviews the limitations of comparing sequencing platforms in the clinical setting and the variables that should be considered in evaluating diagnostic rates across studies.

Perspectives of United States neonatologists on genetic testing practices

PURPOSE

Genetic disorders often present in the neonatal intensive care unit (NICU), and detecting or confirming these diagnoses has been shown to impact care. However, the availability and use of genetic testing, particularly exome or genome sequencing, among NICUs varies widely. We therefore sought to investigate practice patterns related to genetic testing in NICUs around the country to identify and quantify potential discrepancies.

METHODS

We designed a survey that was distributed to neonatologists via email. The survey contained questions related to test availability and desirability, the process of test ordering in NICU, and general comfort with ordering and interpreting genetic testing. Demographic data related to the survey participants and characteristics of their NICU were also obtained.

RESULTS

In total, 162 neonatologists completed the survey, representing 40 states and 112 distinct NICUs. Although nearly all (93.2%) neonatologists attributed a high level of importance to identifying a genetic diagnosis for their patients, genetic consultations were only available at 78% of NICUs and exome or genome sequencing was not available on a regular basis (69% of NICUs).

CONCLUSION

Although, among US neonatologists surveyed, most feel that genetic tests are indicated for their patients, these are not always clinically available. Further research into implementation barriers is warranted.

Rapid genomic testing for critically ill children: time to become standard of care?

Rapid genomic testing in critically ill neonatal and paediatric patients has transformed the paradigm of rare disease diagnosis, delivering results in real time to inform patient management. More than 20 studies totalling over 1500 patients from diverse healthcare settings worldwide have now been published, forming a compelling evidence base for healthcare system implementation. We review the reported diagnostic and clinical outcomes, as well as broader evaluations of family and professional experiences, cost effectiveness, implementation challenges and bioethical issues arising from rapid testing. As rapid genomic testing transitions from the research to the healthcare setting to become a 'standard of care' test, there is a need to develop effective service delivery models to support scalability at both the laboratory and clinical level and promote equity of access, prompt test initiation, integrated multidisciplinary input and holistic family support. Harnessing the high level of professional engagement with rapid genomic testing programmes will continue to drive innovation and adoption, while close integration with emerging precision medicine approaches will be necessary to deliver on the promise of reduced infant and child mortality.

Congenital anomalies and genetic disorders in neonates and infants: a single-center observational cohort study

Neonates with genetic disorders or congenital anomalies (CA) contribute considerably to morbidity and mortality in neonatal intensive care units (NICUs). The objective of this study is to study the prevalence of genetic disorders in an academic level IV NICU. We retrospective collected and analyzed both clinical and genetic data of all 1444 infants admitted to the NICU of the Radboudumc (October 2013 to October 2015). Data were collected until infants reached at least 2 years of age. A total of 13% (194/1444) of the patients were genetically tested, and 32% (461/1444) had a CA. A total of 37% (72/194) had a laboratory-confirmed genetic diagnosis. In 53%, the diagnosis was made post-neonatally (median age = 209 days) using assays including exome sequencing. Exactly 63% (291/461) of the patients with CA, however, never received genetic testing, despite being clinically similar those who did.Conclusions: Genetic disorders were suspected in 13% of the cohort, but only confirmed in 5%. Most received their genetic diagnosis in the post-neonatal period. Extrapolation of the diagnostic yield suggests that up to 6% of our cohort may have remained genetically undiagnosed. Our data show the need to improve genetic care in the NICU for more inclusive, earlier, and faster genetic diagnosis to enable tailored management. What is Known: • Genetic disorders are suspected in many neonates but only genetically confirmed in a minority. • The presence of a genetic disorder can be easily missed and will often lead to a diagnostic odyssey requiring extensive evaluations, both clinically and genetically. What is New: • Different aspects of the clinical features and uptake of genetic test in a NICU cohort. • The need to improve genetic care in the NICU for more inclusive, earlier, and faster genetic diagnosis to enable tailored management.

Preferences and values for rapid genomic testing in critically ill infants and children: a discrete choice experiment

Healthcare systems are increasingly considering widespread implementation of rapid genomic testing of critically ill children, but evidence on the value of the benefits generated is lacking. This information is key for an optimal implementation into healthcare systems. A discrete choice experiment survey was designed to elicit preferences and values for rapid genomic testing in critically ill children. The survey was administered to members of the Australian public and families with lived experience of rapid genomic testing. A Bayesian D-efficient explicit partial profiles design was used, and data were analysed using a panel error component mixed logit model. Preference heterogeneity was explored using a latent class model and fractional logistic regressions. The public (n = 522) and families with lived experiences (n = 25) demonstrated strong preferences for higher diagnostic yield and clinical utility, faster result turnaround times, and lower cost. Society on average would be willing to pay an additional AU$9510 (US$6657) for rapid (2 weeks results turnaround time) and AU$11,000 (US$7700) for ultra-rapid genomic testing (2 days turnaround time) relative to standard diagnostic care. Corresponding estimates among those with lived experiences were AU$10,225 (US$7158) and AU$11,500 (US$8050), respectively. Our work provides further evidence that rapid genomic testing for critically ill children with rare conditions generates substantial utility. The findings can be used to inform cost-benefit analyses as part of broader healthcare system implementation.

Rapid genome-wide sequencing in a neonatal intensive care unit: A retrospective qualitative exploration of parental experiences

Genome-wide sequencing (GWS) is increasingly being used in neonatal intensive care units. While studies have explored its clinical utility, little is known about parental experiences with this testing post-return of results. We conducted a qualitative study, using an interpretive description framework and thematic analysis, to gain further insight into parents' perceptions of the value and utility of GWS for their infant. We sought to explore whether parents' perceptions differ if their child received a diagnosis or not, and whether their child is living or deceased. Semi-structured, telephone interviews were conducted with parents of infants who had rapid exome sequencing while in the neonatal intensive care unit at BC Women's Hospital in Vancouver, Canada. Interviews addressed perceived benefits and harms of GWS and included an evaluation of decisional regret. Parents of 27 probands were approached and 14 (52%; 13 mothers and 1 father) participated in interviews. On average, 26 months had elapsed from the time of results to the interview. Six themes were identified. Firstly, parents had a positive regard for GWS. The results of GWS helped provide context for their child's admission to the NICU, and all parents experienced relief following receiving the results. A diagnosis by GWS enabled parents to picture the future, form connections with other parents, and coordinate their child's care. Lastly, some parents experienced discomfort with the concept of a genetic diagnosis, and interestingly felt lack of a genomic diagnosis indicated a reduced severity of their infant's condition. Decisional regret post-results was found to be low. Our results highlight how parents cope with the results of GWS and suggest that a genetic counselor can have an important role in helping families understand and adjust to these results in the neonatal intensive care unit.

Ultra-rapid emergency genomic diagnosis of Donahue syndrome in a preterm infant within 17 hours

Genetic diseases are a major cause of neonatal morbidity and mortality. The clinical differential diagnosis in severely ill neonates, especially in premature infants, is challenging. Next generation sequencing (NGS) diagnostics is a valuable tool, but the turnaround time is often too long to provide a diagnosis in the time needed for clinical guidance in newborn intensive care units (NICU). To minimize turnaround time, we developed an ultra-rapid whole genome sequencing pipeline and tested it in clinical practice. Our pilot case, was a preterm infant presenting with several crises of dehydration, hypoglycaemia and hyponatremia together with nephrocalcinosis and hypertrophic cardiomyopathy. Whole genome sequencing was performed using a paired-end 2x75bp protocol. Sequencing data were exported after 50 sequencing cycles for a first analysis. After run completion, the rapid-sequencing protocol, a second analysis of the 2 x 75 paired-end run was performed. Both analyses comprised read-mapping and SNP-/indel calling on an on-site Edico Genome DRAGEN server, followed by functional annotation and pathogenicity prediction using in-house scripts. After the first analysis within 17 h, the emergency ultra-rapid protocol identified two novel compound heterozygous variants in the insulin receptor gene (INSR), pathogenic variants in which cause Donohue Syndrome. The genetic diagnosis could be confirmed by detection of hyperinsulinism and patient care adjusted. Nonetheless, we decided to pursue RNA studies, proving the functional effect of the novel splice variant and reduced expression levels of INSR in patients skin fibroblasts.

Seltene Erkrankungen in der Pädiatrie – von der Diagnostik und Behandlung einzelner Erkrankungen zum Aufbau von Netzwerkstrukturen

Die Versorgung von Menschen mit seltenen Erkrankungen (SE) stellt das Gesundheitssystem vor große Aufgaben. Dieses betrifft in besonderem Maße die Kinder- und Jugendmedizin, denn mehr als 80 % aller SE werden im Verlauf des Kindesalters symptomatisch. Oft fehlten und fehlen trotz rascher diagnostischer und therapeutischer Fortschritte belastbare Behandlungs- und Betreuungskonzepte mit ausreichender personeller Kontinuität und Expertise im ambulanten wie auch stationären Bereich.

Derzeit leben in Deutschland ca. 4 Mio. Patienten mit einer SE, und jeder Kinder- und Jugendmediziner, ob in der Praxis oder in der Spezialambulanz im Universitätsklinikum, wird immer wieder mit diesen Patienten beschäftigt sein. In den letzten Jahren konnten die diagnostischen und jetzt zunehmend auch ursächlich therapeutischen Möglichkeiten entscheidend verbessert werden. Dieser Prozess ist äußerst dynamisch, wie die aktuellen Entwicklungen und Diskussionen um die ursächlichen genetischen Therapien der spinalen Muskelatrophie zeigen. Zur erfolgreichen Umsetzung der medizinischen Fortschritte in unser Gesundheitssystem wurde unter entscheidender Einbeziehung der Selbsthilfe, die für die Betroffenen von SE und ihre Angehörigen essenzielle Arbeiten leistet, 2013 ein Nationaler Aktionsplan für Menschen mit Seltenen Erkrankungen erarbeitet und verabschiedet. Dieser sieht sektorenübergreifende Versorgungsstrukturen und die Strukturierung von Zentren für seltene Erkrankungen vor. Innovationsfondprojekte haben inzwischen konkrete Verbesserungen der Versorgung von Patienten mit SE erfolgreich erprobt, und die Deutsche Gesellschaft für Kinder- und Jugendmedizin (DGKJ) hat eine neue Kommission für SE unter Einbeziehung der Patientenvertretung Allianz Chronischer Seltener Erkrankungen (ACHSE) e. V. und der Deutschen Gesellschaft für Humangenetik eingerichtet. Diese soll sich dieser speziellen Thematik widmen sowie diese positiven Entwicklungen beratend unterstützen. Mit diesem Artikel nehmen wir eine aktuelle Standortbestimmung vor und geben Anregungen für Diskussionen.

Genetics and pediatric hospital admissions, 1985 to 2017

PURPOSE

To determine the prevalence and sociodemographic and hospitalization history of genetic conditions in a sample of inpatients in a pediatric hospital in 2017, and to compare results with unpublished studies from 1985, 1995, and 2007.

METHODS

Two weeks of admissions were classified according to a pre-existing categorization, based on genetic etiology, encompassing chromosomal and monogenic conditions, multifactorial (MF) conditions, and no known genetic cause.

RESULTS

In 2017, 299 (16%) patients had chromosomal or monogenic conditions, 6-7% more than 2007 and 1995, but similar to 1985. Autosomal dominant (AD) conditions increased from <2% previously to 6% in 2017 (p < 0.001). MF conditions comprised the majority throughout, increasing from 45% to 54%. Age at admission was highest in autosomal recessive (AR) and X-linked categories in 1995, 2007, and 2017, reflected in their high number of previous admissions, while the AD, MF, and nongenetic categories were the youngest with similar lengths of stay and previous admissions.

CONCLUSION

Conditions with a genetic contribution account for over half of pediatric inpatients. Since 1985, there have been many changes in age at admission and length of stay, but it is the increasing prevalence of AR, AD, and MF conditions that is important when considering future service provision.

Diagnosis of genetic diseases in seriously ill children by rapid whole-genome sequencing and automated phenotyping and interpretation

By informing timely targeted treatments, rapid whole-genome sequencing can improve the outcomes of seriously ill children with genetic diseases, particularly infants in neonatal and pediatric intensive care units (ICUs). The need for highly qualified professionals to decipher results, however, precludes widespread implementation. We describe a platform for population-scale, provisional diagnosis of genetic diseases with automated phenotyping and interpretation. Genome sequencing was expedited by bead-based genome library preparation directly from blood samples and sequencing of paired 100-nt reads in 15.5 hours. Clinical natural language processing (CNLP) automatically extracted children's deep phenomes from electronic health records with 80% precision and 93% recall. In 101 children with 105 genetic diseases, a mean of 4.3 CNLP-extracted phenotypic features matched the expected phenotypic features of those diseases, compared with a match of 0.9 phenotypic features used in manual interpretation. We automated provisional diagnosis by combining the ranking of the similarity of a patient's CNLP phenome with respect to the expected phenotypic features of all genetic diseases, together with the ranking of the pathogenicity of all of the patient's genomic variants. Automated, retrospective diagnoses concurred well with expert manual interpretation (97% recall and 99% precision in 95 children with 97 genetic diseases). Prospectively, our platform correctly diagnosed three of seven seriously ill ICU infants (100% precision and recall) with a mean time saving of 22:19 hours. In each case, the diagnosis affected treatment. Genome sequencing with automated phenotyping and interpretation in a median of 20:10 hours may increase adoption in ICUs and, thereby, timely implementation of precise treatments.

Developmental Support for Infants With Genetic Disorders

As the technical ability for genetic diagnosis continues to improve, an increasing number of diagnoses are made in infancy or as early as the neonatal period. Many of these diagnoses are known to be associated with developmental delay and intellectual disability, features that would not be clinically detectable at the time of diagnosis. Others may be associated with cognitive impairment, but the incidence and severity are yet to be fully described. These neonates and infants with genetic diagnoses therefore represent an emerging group of patients who are at high risk for neurodevelopmental disabilities. Although there are well-established developmental supports for high-risk infants, particularly preterm infants, after discharge from the NICU, programs specifically for infants with genetic diagnoses are rare. And although previous research has demonstrated the positive effect of early developmental interventions on outcomes among preterm infants, the impact of such supports for infants with genetic disorders who may be born term, remains to be understood. We therefore review the literature regarding existing developmental assessment and intervention approaches for children with genetic disorders, evaluating these in the context of current developmental supports postdischarge for preterm infants. Further research into the role of developmental support programs for early assessment and intervention in high-risk neonates diagnosed with rare genetic disorders is needed.

Exome sequencing compared with standard genetic tests for critically ill infants with suspected genetic conditions

PURPOSE

As exome sequencing (ES) is increasingly used as a diagnostic tool, we aimed to compare ES with status quo genetic diagnostic workup for infants with suspected genetic disorders in terms of identifying diagnoses, survival, and cost of care.

METHODS

We studied newborns and infants admitted to intensive care with a suspected genetic etiology within the first year of life at a US quaternary-referral children's hospital over 5 years. In this propensity-matched cohort study using electronic medical record data, we compared patients who received ES as part of a diagnostic workup (ES cohort, n = 368) with clinically similar patients who did not receive ES (No-ES cohort, n = 368).

RESULTS

Diagnostic yield (27.4% ES, 25.8% No-ES; p = 0.62) and 1-year survival (80.2% ES, 84.8% No-ES; p = 0.10) were no different between cohorts. ES cohort patients had higher cost of admission, diagnostic investigation, and genetic testing (all p < 0.01).

CONCLUSION

ES did not differ from status quo genetic testing collectively in terms of diagnostic yield or patient survival; however, it had high yield as a single test, led to complementary classes of diagnoses, and was associated with higher costs. Further work is needed to define the most efficient use of diagnostic ES for critically ill newborns and infants.

Diagnostic and service impact of genomic testing technologies in a neonatal intensive care unit

AIM

To investigate the diagnostic and service impact of chromosomal microarray and whole exome sequencing (WES) in a neonatal intensive care unit (NICU).

METHODS

This was a retrospective medical record review of NICU patients referred for genetics consultation at three time points over a 9-year period at a single centre to determine referral indications, genetic consultation outcomes and time to diagnosis.

RESULTS

The number of NICU patients referred for genetics consultation increased from 44 in 2007 to 95 in 2015. The proportion of NICU patients suspected of having a genetic condition following clinical geneticist assessment remained stable, averaging 5.3% of all admissions. The proportion of patients receiving a confirmed diagnosis rose from 21% in 2007 to 53% in 2015, with a shift from primarily chromosomal abnormalities to a broad range of monogenic disorders, increasingly diagnosed by WES as a first-tier test. The average age at diagnosis in 2015 was 19 days (range 12-38 days) for chromosomal abnormalities and 138 days (range 10-309 days) for monogenic conditions.

CONCLUSIONS

The adoption of new genetic technologies at our centre has increased the proportion of patients receiving a confirmed genetic diagnosis. This study provides important benchmark data to measure further improvements as turn-around times for genomic testing decrease.

A Randomized, Controlled Trial of the Analytic and Diagnostic Performance of Singleton and Trio, Rapid Genome and Exome Sequencing in Ill Infants

The second Newborn Sequencing in Genomic Medicine and Public Health study was a randomized, controlled trial of the effectiveness of rapid whole-genome or -exome sequencing (rWGS or rWES, respectively) in seriously ill infants with diseases of unknown etiology. Here we report comparisons of analytic and diagnostic performance. Of 1,248 ill inpatient infants, 578 (46%) had diseases of unknown etiology. 213 infants (37% of those eligible) were enrolled within 96 h of admission. 24 infants (11%) were very ill and received ultra-rapid whole-genome sequencing (urWGS). The remaining infants were randomized, 95 to rWES and 94 to rWGS. The analytic performance of rWGS was superior to rWES, including variants likely to affect protein function, and ClinVar pathogenic/likely pathogenic variants (p < 0.0001). The diagnostic performance of rWGS and rWES were similar (18 diagnoses in 94 infants [19%] versus 19 diagnoses in 95 infants [20%], respectively), as was time to result (median 11.0 versus 11.2 days, respectively). However, the proportion diagnosed by urWGS (11 of 24 [46%]) was higher than rWES/rWGS (p = 0.004) and time to result was less (median 4.6 days, p < 0.0001). The incremental diagnostic yield of reflexing to trio after negative proband analysis was 0.7% (1 of 147). In conclusion, rapid genomic sequencing can be performed as a first-tier diagnostic test in inpatient infants. urWGS had the shortest time to result, which was important in unstable infants, and those in whom a genetic diagnosis was likely to impact immediate management. Further comparison of urWGS and rWES is warranted because genomic technologies and knowledge of variant pathogenicity are evolving rapidly.

The burden of rare diseases

The subject of rare disease numbers is rife with misconceptions, not just in websites and other layman's literature, but also in the medical literature. Various websites mention numbers that are not validated by any solid data, while in turn the medical literature cites the aforementioned websites as sources, thus perpetuating a number of myths about rare diseases and their burden. We review the existing literature on rare disease numbers, in an attempt to demystify the subject. Specifically, we summarize data pertaining to: (a) known number and cumulative prevalence of rare diseases; (b) rare disease-associated mortality; (c) rare disease-associated morbidity, including numbers on health care services related to rare diseases; and (d) orphan drug numbers.

Genetic disorders and mortality in infancy and early childhood: delayed diagnoses and missed opportunities

PURPOSE

Infants admitted to a level IV neonatal intensive care unit (NICU) who do not survive early childhood are a population that is probably enriched for rare genetic disease; we therefore characterized their genetic diagnostic evaluation.

METHODS

This is a retrospective analysis of infants admitted to our NICU between 1 January 2011 and 31 December 2015 who were deceased at the time of records review, with age at death less than 5 years.

RESULTS

A total of 2,670 infants were admitted; 170 later died. One hundred six of 170 (62%) had an evaluation for a genetic or metabolic disorder. Forty-seven of 170 (28%) had laboratory-confirmed genetic diagnoses, although 14/47 (30%) diagnoses were made postmortem. Infants evaluated for a genetic disorder spent more time in the NICU (median 13.5 vs. 5.0 days; p = 0.003), were older at death (median 92.0 vs. 17.5 days; p < 0.001), and had similarly high rates of redirection of care (86% vs. 79%; p = 0.28).

CONCLUSION

Genetic disorders were suspected in many infants but found in a minority. Approximately one-third of diagnosed infants died before a laboratory-confirmed genetic diagnosis was made. This highlights the need to improve genetic diagnostic evaluation in the NICU, particularly to support end-of-life decision making.

Exome sequencing in neonates: diagnostic rates, characteristics, and time to diagnosis

PURPOSE

Neonatal patients are particularly appropriate for utilization of diagnostic exome sequencing (DES), as many Mendelian diseases are known to present in this period of life but often with complex, heterogeneous features. We attempted to determine the diagnostic rates and features of neonatal patients undergoing DES.

METHODS

The clinical histories and results of 66 neonatal patients undergoing DES were retrospectively reviewed.

RESULTS

Clinical DES identified potentially relevant findings in 25 patients (37.9%). The majority of patients had structural anomalies such as birth defects, dysmorphic features, cardiac, craniofacial, and skeletal defects. The average time for clinical rapid testing was 8 days.

CONCLUSION

Our observations demonstrate the utility of family-based exome sequencing in neonatal patients, including familial cosegregation analysis and comprehensive medical review.