Project Baby Bear: Rapid precision care incorporating rWGS in 5 California children's hospitals demonstrates improved clinical outcomes and reduced costs of care

Hypotonia in the Neonatal Intensive Care Unit

Hypotonia is a common presenting symptom in the neonatal intensive care unit (NICU). Hypotonia can be a manifestation of an underlying systemic illness, a primary nervous system disease, or a peripheral nervous system disease. Examination and history can suggest specific causes, but rapid and accurate diagnosis remains challenging due to the broad spectrum of causes. Options for disease-targeted therapies have increased the importance of early diagnosis. This article focuses on the evaluation and diagnostic approach of the hypotonic newborn in the NICU, with an emphasis on rapid identification of treatable conditions and updated recommendations on the utilization of genetic testing.

Precision medicine in the pediatric and neonatal intensive care units through genomics

PURPOSE OF REVIEW

Genome-wide sequencing technologies have revolutionized the understanding of human disorders and advanced precision medicine, especially for pediatric disorders. Here, we discuss the utility of genomic technologies in advancing the care of children admitted to the pediatric and neonatal intensive care units.

RECENT FINDINGS

Rapid molecular diagnosis permitted by genomic medicine has yielded clinically actionable findings that influence decision-making and facilitate timely therapeutic interventions. Identifying a genetic association provides a causal anchor to understanding disease biology at the single nucleotide resolution, revealing hidden biological heterogeneity that may be obscured by traditional imaging, laboratory, and pathological workup. The importance of a genetic diagnosis is further highlighted by the promise of gene therapy to correct the underlying genetic perturbation, as evidenced by the recent emergence of FDA-approved gene therapies for childhood genetic conditions.

SUMMARY

We predict that whole-genome sequencing, in conjunction with other omic technologies, will become critical diagnostic adjuncts in the clinical workup of critically ill children.

Untargeted proteomics enables ultra-rapid variant prioritisation in mitochondrial and other rare diseases

BACKGROUND

Only half of individuals with suspected rare diseases receive a genetic diagnosis following genomic testing. A genetic diagnosis allows access to appropriate care, restores reproductive confidence and reduces the number of potentially unnecessary interventions. A major barrier is the lack of disease agnostic functional tests suitable for implementation in routine diagnostics that can provide evidence supporting pathogenicity of novel variants, especially those refractory to RNA sequencing.

METHODS

Focusing on mitochondrial disease, we describe an untargeted mass-spectrometry based proteomics pipeline that can quantify proteins encoded by > 50% of Mendelian disease genes and > 80% of known mitochondrial disease genes in clinically relevant sample types, including peripheral blood mononuclear cells (PBMCs). In total we profiled > 90 individuals including undiagnosed individuals suspected of mitochondrial disease and a supporting cohort of disease controls harbouring pathogenic variants in nuclear and mitochondrial genes. Proteomics data were benchmarked against pathology accredited respiratory chain enzymology to assess the performance of proteomics as a functional test. Proteomics testing was subsequently applied to individuals with suspected mitochondrial disease, including a critically ill infant with a view toward rapid interpretation of variants identified in ultra-rapid genome sequencing.

RESULTS

Proteomics testing provided evidence to support variant pathogenicity in 83% of individuals in a cohort with confirmed mitochondrial disease, outperforming clinical respiratory chain enzymology. Freely available bioinformatic tools and criteria developed for this study ( https://rdms.app/ ) allow mitochondrial dysfunction to be identified in proteomics data with high confidence. Application of proteomics to undiagnosed individuals led to 6 additional diagnoses, including a mitochondrial phenocopy disorder, highlighting the disease agnostic nature of proteomics. Use of PBMCs as a sample type allowed rapid return of proteomics data supporting pathogenicity of novel variants identified through ultra-rapid genome sequencing in as little as 54 h.

CONCLUSIONS

This study provides a framework to support the integration of a single untargeted proteomics test into routine diagnostic practice for the diagnosis of mitochondrial and potentially other rare genetic disorders in clinically actionable timelines, offering a paradigm shift for the functional validation of genetic variants.

Benefits and barriers to broad implementation of genomic sequencing in the NICU

Genome (GS) and exome (ES) sequencing as first-tier diagnostic tests have the potential to increase rates of genetic diagnoses and acutely change the management of neonates in the neonatal intensive care unit (NICU). However, the widespread implementation of genomic sequencing has been limited by several barriers. In this systematic review, we analyze the current literature on the utilization of GS and ES in infants in the NICU to identify the benefits, barriers, and components of successful implementation. Across the 42 studies that discussed GS and ES in the NICU setting, six themes were identified: disease detection, timeliness of results, cost, provider attitudes, parental attitudes, and equitable access. Benefits of GS and ES include high disease detection rates, timely results, and possible reduction in healthcare costs by reducing time spent in the NICU. Additionally, clinicians find GS/ES to be important and useful, and parents and caregivers largely perceive GS/ES to be beneficial. Barriers to widespread GS/ES include availability of personnel to facilitate timely diagnosis and coverage of cost. Additionally, clinicians report worries about a lack of genetics knowledge, informed consent, results return, and potential harm. Parents consistently report low levels of anxiety, decisional conflict, harm, or regret. Finally, the lack of availability of translated consent documents limits the participation of families who do not speak English or Spanish. Continued work is essential to optimize these technologies and ensure equitable access.

How Neonatologists Use Genetic Information

OBJECTIVE

To delineate specific ways in which neonatologists integrate genetic information into their clinical decision making.

STUDY DESIGN

We employed chart-stimulated recall, in which neonatologists described how they used genetic tests in specific patient cases, as well as semi-structured questioning about genetic information.

RESULTS

Based on 28 interviews with neonatologists, we document 6 uses of genetic information: making a diagnosis, categorizing/stereotyping as "genetic," informing prognosis, influencing treatment, informing goals of care, and supporting accountability. Both specific genetic diagnoses as well as a general categorization as "genetic" help neonatologists make sense of unusual clinical situations and calibrate their predictions about the future. Predictions, in turn, inform goals of care decisions, the timing of medical technology placement, and neonatologists' self-evaluations. Diagnoses rarely influence day-to-day treatment directly. Neonatologists assign great value to improved prognostication, but simultaneously feel a responsibility to ensure that genetic information is not applied in ways that are overly deterministic or reflect ableism.

CONCLUSIONS

Frameworks for measuring successes and failures of genetic information in the neonatal intensive care unit need to be aligned with the ways neonatologists use this information. Understanding neonatologists' use creates opportunity to maximize benefit and reduce bias in applying this complex information.

First-Tier Versus Last-Tier Trio Whole-Genome Sequencing for the Diagnosis of Pediatric-Onset Rare Diseases

Despite advances in diagnostics, children with rare genetic disorders still face extended diagnostic odysseys, delaying appropriate clinical management, and placing burdens on families and healthcare resources. Whole-genome sequencing (WGS) offers a more comprehensive interrogation of the genome than other genetic tests, but its use in clinical practice remains limited. This study compared diagnostic rates, turnaround times, and clinical utility of first-tier versus last-tier trio-WGS for patients with suspected genetic pediatric-onset conditions, including 97 critical and 104 non-critical patients. Eighty-five patients (42.3%), including 57 (58.8%) critical and 28 (26.9%) non-critical patients, received a molecular diagnosis. The diagnostic rate was higher for first-tier (57%) than for last-tier (32.8%) trio-WGS. Of 121 causative variants identified, 19.8% would have been missed by whole-exome sequencing. Laboratory processing time was 4 days for all patients. The clinical setting had the greatest impact on time to reporting, averaging 5 days for critical patients versus 74 days for outpatients. WGS results impacted clinical decision-making for 34% of all critical and 14.3% of WGS-positive non-critical patients. This is the first Italian clinical study to demonstrate the diagnostic and clinical utility of a genome-first approach for both critical and non-critical patients with suspected genetic pediatric-onset disorders and feasibility in a public healthcare system.

Rapid Whole-Genome Sequencing as a First-Line Test Is Likely to Significantly Reduce the Cost of Acute Care in a Private Payer System

BACKGROUND

Genetic disorders are a leading contributor to morbidity and mortality in neonatal and pediatric intensive care units. Rapid whole-genome sequencing (rWGS) has demonstrated improved clinical outcomes and reduced costs of care. The objective of this study was to predict the effect of rWGS on healthcare spending if implemented as a first-line diagnostic test in the Blue Shield of California (BSC) private payer system.

METHODS

This study applied private payer reimbursement methods and rates to clinical outcomes of rWGS on pediatric inpatient care as determined by a previous study of publicly insured infants in Project Baby Bear. BSC patients who were clinically similar to the Project Baby Bear cohort were identified by matching on diagnosis-related group and severity of illness. Payment data from these BSC patients was used to estimate the financial impact of clinical outcomes resulting from rWGS testing in a commercially insured pediatric population.

RESULTS

The analysis estimated a reduction of $5.8 million to $7.8 million in inpatient payments due to an estimated 457 to 592 avoided inpatient days due to rWGS results. With an estimated cost of sequencing at $2.7 million for the entire cohort (n = 184), the financial impact of rWGS as a first-tier test in the intensive care unit resulted in estimated net savings to BSC of $16 730 to $28 061 per patient sequenced.

CONCLUSIONS

Implementation of rWGS using the protocols established in Project Baby Bear is likely to result in significant reductions in healthcare spending among privately insured patients.

A decade of whole-exome sequencing in Brazilian Neurology: from past insights to future perspectives

Over the last decade, whole-exome sequencing (WES) has become a standard diagnostic tool, significantly transforming the landscape of clinical genetics and playing a pivotal role in the diagnosis of neurogenetic diseases. This revolutionary shift has left a lasting impact on the field of neurology in Brazil. The current review article examines key developments and milestones achieved in Brazil through the application of WES in neurology and discusses forthcoming challenges and essential steps to advance molecular diagnosis. Several studies report the use of WES to diagnose genetic disorders with neurological manifestations in Brazil, underscoring the growing importance of molecular diagnosis in neurogenetics. These studies often provide detailed phenotypic analyses and clinical descriptions, offering valuable insights into the genetic underpinnings of several neurological conditions. Many reports highlight the use of WES in the investigation of complex neurological conditions in Brazil, such as neurodevelopmental disorders, hereditary spastic paraplegia, movement disorders, and ataxia. The discovery of new genes implicated in monogenic diseases with neurological manifestations through WES was a significant breakthrough. Despite these advances, the availability of large cohort studies on rare diseases in Brazil remains limited, hindering the ability to generalize findings and explore the full spectrum of genetic diversity. However, a few larger cohort studies have substantially contributed to our understanding of rare diseases and specific neurological disorders.While WES has limitations and may eventually be supplanted by more advanced diagnostic tools, it left a permanent mark on the neurology field in Brazil. The field of neurogenetics is set to become increasingly important in the future.

Clinical utility of rapid whole genome sequencing in neonatal patients receiving extracorporeal membrane oxygenation (ECMO)

OBJECTIVE

The objective of this study is to describe the impact of rapid and ultra-rapid whole genome sequencing (rWGS/urWGS) on the care of neonatal intensive care (NICU) patients who require extracorporeal membrane oxygenation (ECMO).

STUDY DESIGN

This is a retrospective cohort study at a single-center NICU in a tertiary children's hospital. The study population includes NICU patients treated with ECMO from May 2017 to September 2023. Patients were evaluated for whether whole genome was completed, speed of testing (rapid vs. ultra-rapid), diagnostic rate, and clinical utility.

RESULT

Twenty-six (72%) patients had rWGS/urWGS. A diagnosis associated with the patient's phenotype was made in 12 patients (46%). A change in clinical management was made due to rWGS/urWGS in 10 patients (38%) including avoidance of imaging studies, decisions regarding goals of care, and screening studies.

CONCLUSION

This study demonstrates a high diagnostic rate and clinical utility of rWGS/urWGS for NICU patients requiring ECMO.

Rapid Whole-Genome Sequencing in Critically Ill Infants and Children with Suspected, Undiagnosed Genetic Diseases: Evolution to a First-Tier Clinical Laboratory Test in the Era of Precision Medicine

The completion of the Human Genome Project in 2003 has led to significant advances in patient care in medicine, particularly in diagnosing and managing genetic diseases and cancer. In the realm of genetic diseases, approximately 15% of critically ill infants born in the U.S.A. are diagnosed with genetic disorders, which comprise a significant cause of mortality in neonatal and pediatric intensive care units. The introduction of rapid whole-genome sequencing (rWGS) as a first-tier test in critically ill children with suspected, undiagnosed genetic diseases is a breakthrough in the diagnosis and subsequent clinical management of such infants and older children in intensive care units. Rapid genome sequencing is currently being used clinically in the USA, the UK, the Netherlands, Sweden, and Australia, among other countries. This review is intended for students and clinical practitioners, including non-experts in genetics, for whom it provides a historical background and a chronological review of the relevant published literature for the progression of pediatric diagnostic genomic sequencing leading to the development of pediatric rWGS in critically ill infants and older children with suspected but undiagnosed genetic diseases. Factors that will help to develop rWGS as a clinical test in critically ill infants and the limitations are briefly discussed, including an evaluation of the clinical utility and accessibility of genetic testing, education for parents and providers, cost-effectiveness, ethical challenges, consent issues, secondary findings, data privacy concerns, false-positive and false-negative results, challenges in variant interpretation, costs and reimbursement, the limited availability of genetic counselors, and the development of evidence-based guidelines, which would all need to be addressed to facilitate the implementation of pediatric genomic sequencing in an effective widespread manner in the era of precision medicine.

The Utah NeoSeq Project: a collaborative multidisciplinary program to facilitate genomic diagnostics in the neonatal intensive care unit

Rapid genomic diagnostics in the Neonatal Intensive Care Unit represents a paradigm shift in medicine with increasing evidence of the utility of early diagnosis, impacting management. The goal of the Utah NeoSeq Project was to implement and evaluate a multidisciplinary and longitudinal rapid sequencing program while transitioning to CLIA-certified sequencing. Enrollment of 65 infants resulted in 26 (40%) with a diagnostic variant(s) and 7 (11%) harboring a strong candidate. This includes re-analyses resulting in four additional diagnoses. Parental surveys indicated that 7% (4/59) of parents had a decisional conflict after consent, and 3% (2/59) experienced decisional regret after the results. Fifty-two provider surveys were conducted. Seventy-nine percent (41/52) of results and 86% (19/22) of diagnostic results were "very useful" or "useful" and associated with management changes. The NeoSeq Project demonstrates that a multidisciplinary collaborative approach to diagnosis is feasible. We have developed a generalizable, collaborative protocol that addresses the need for expedited genetic evaluation with emerging technologies.

SeqFirst: Building equity access to a precise genetic diagnosis in critically ill newborns

Access to a precise genetic diagnosis (PrGD) in critically ill newborns is limited and inequitable because the complex inclusion criteria used to prioritize testing eligibility omit many patients at high risk for a genetic condition. SeqFirst-neo is a program to test whether a genotype-driven workflow using simple, broad exclusion criteria to assess eligibility for rapid genome sequencing (rGS) increases access to a PrGD in critically ill newborns. All 408 newborns admitted to a neonatal intensive care unit between January 2021 and February 2022 were assessed, and of 240 eligible infants, 126 were offered rGS (i.e., intervention group [IG]) and compared to 114 infants who received conventional care in parallel (i.e., conventional care group [CCG]). A PrGD was made in 62/126 (49.2%) IG neonates compared to 11/114 (9.7%) CCG infants. The odds of receiving a PrGD were ∼9 times greater in the IG vs. the CCG, and this difference was maintained at 12 months follow-up. Access to a PrGD in the IG vs. CCG differed significantly between infants identified as non-White (34/74, 45.9% vs. 6/29, 20.7%; p = 0.024) and Black (8/10, 80.0% vs. 0/4; p = 0.015). Neonatologists were significantly less successful at predicting a PrGD in non-White than non-Hispanic White infants. The use of a standard workflow in the IG with a PrGD revealed that a PrGD would have been missed in 26/62 (42%) infants. The use of simple, broad exclusion criteria that increase access to genetic testing significantly increases access to a PrGD, improves access equity, and results in fewer missed diagnoses.

Omics and rare diseases: challenges, applications, and future perspectives

INTRODUCTION

Rare diseases (RDs) are a heterogeneous group of diseases recognized as a relevant global health priority but posing aspects of complexity, such as geographical scattering of affected individuals, improper/late diagnosis, limited awareness, difficult surveillance and monitoring, limited understanding of natural history, and lack of treatment. Usually, RDs have a pediatric onset and are life-long, multisystemic, and associated with a poor prognosis.

AREAS COVERED

In this work, we review how high-throughput omics technologies such as genomics, transcriptomics, proteomics, metabolomics, epigenomics, and other well-established omics, which are increasingly more affordable and efficient, can be applied to the study of RDs promoting diagnosis, understanding of pathological mechanisms, biomarker discovery, and identification of treatments.

EXPERT OPINION

RDs, despite their challenges, offer a niche where collaborative efforts and personalized treatment strategies might be feasible using omics technologies. Specialized consortia fostering multidisciplinary collaboration, data sharing, and the development of biobanks and registries can be built; multi-omics approaches, including so far less exploited omics technologies, along with the implementation of AI tools can be undertaken to deepen our understanding of RDs, driving biomarker discovery and clinical interventions. Nevertheless, technical, ethical, legal, and societal issues must be clearly defined and addressed.

A meta-analysis of diagnostic yield and clinical utility of genome and exome sequencing in pediatric rare and undiagnosed genetic diseases

PURPOSE

To systematically evaluate the diagnostic yield and clinical utility of genome sequencing (GS) and exome sequencing (ES; genome-wide sequencing [GWS]) in pediatric patients with rare and undiagnosed genetic diseases.

METHODS

We conducted a meta-analysis of studies published between 2011 and 2023. To address study heterogeneity, comparative analyses included within-cohort studies using random-effects models.

RESULTS

We identified 108 studies including 24,631 probands with diverse clinical indications. The pooled diagnostic yield among within-cohort studies (N = 13) for GWS was 34.2% (95% CI: 27.6-41.5; I2: 86%) vs 18.1% (95% CI: 13.1-24.6; I2: 89%) for non-GWS, with 2.4-times odds of diagnosis (95% CI: 1.40-4.04; P < .05). The pooled diagnostic yield among within-cohort studies (N = 3) for GS was 30.6% (95% CI: 18.6-45.9; I2: 79%) vs 23.2% (95% CI: 18.5-28.7; I2: 58%) for ES, with 1.7-times the odds of diagnosis (95% CI: 0.94-2.92; P = .13). In first-line testing, the diagnostic yield tended to be higher for GS than for ES across clinical subgroups. The pooled clinical utility among patients with a positive diagnosis was 58.7% (95% CI: 47.3-69.2; I2: 81%) for GS and 54.5% (95% CI: 40.7-67.6; I2: 87%) for ES.

CONCLUSION

GS appears to have a higher diagnostic yield than ES, with similar clinical utility per positive diagnosis.

The "genetic test request": A genomic stewardship intervention for inpatient exome and genome orders at a tertiary pediatric hospital

PURPOSE

Exome sequencing (ES) and genome sequencing (GS) are useful tests to diagnose rare diseases in pediatric patients in critical care settings. Genomic test stewardship can increase the appropriate use of these tests leading to improved diagnostics and cost savings.

METHODS

A mandatory review of ES and GS orders for admitted patients was implemented in March 2023. Outcomes of the reviews, cost analysis, and subsequent test results through February 2024 were analyzed with descriptive statistics.

RESULTS

There were 444 genetic test request orders placed for 412 unique patients. Of these, 81 (18.2%) were redirected and 57 (12.8%) required modification after approval, leading to an overall cost savings of $345,821.00 or $778.88 per order. The combined diagnostic rate was 28.2% in this patient population.

CONCLUSION

Stewardship of ES/GS orders for pediatric inpatients is an effective tool to improve the appropriate usage of these genomic tests. Additional collaboration with stakeholders and expansion of genomic stewardship initiatives may shorten the diagnostic odyssey for critically ill pediatric patients and result in cost savings.

A machine learning decision support tool optimizes WGS utilization in a neonatal intensive care unit

The Mendelian Phenotype Search Engine (MPSE), a clinical decision support tool using Natural Language Processing and Machine Learning, helped neonatologists expedite decisions to whole genome sequencing (WGS) to diagnose patients in the neonatal intensive care unit. After the MPSE was introduced, utilization of WGS increased, time to ordering WGS decreased, and WGS diagnostic yield increased.

Breaking barriers: fostering equitable access to pediatric genomics through innovative care models and technologies

The integration of genomic medicine into pediatric clinical practice is a critical need that remains largely unmet, especially in socioeconomically challenged and rural areas where healthcare disparities are most pronounced. This review seeks to summarize the barriers responsible for delayed diagnosis and treatment, and examines diverse care models, technological innovations, and strategies for dissemination and implementation aimed at addressing the evolving genomic needs of pediatric populations. Through a comprehensive review of the literature, we explore proposed methodologies to bridge this gap in pediatric healthcare, with a specific emphasis on understanding and speeding implementation approaches and technologies to mitigate disparities in underserved populations, including rural and marginalized communities. There are both external and internal factors to consider in demographic and social determinants when evaluating patient access. To address these barriers, potential solutions include telegenetic services, alternative care delivery models, pediatric subspecialist expansion, and non-genetic provider education. By improving access to pediatric genomic services, therapeutic interventions will also be more available to all pediatric patients. IMPACT STATEMENT: Genomic testing has clinical utility in pediatric populations but access for people from diverse demographic and social-economic groups is problematic. Understanding barriers responsible for delayed genetic diagnosis and treatment in pediatric populations will improve reach, adoption, implementation, and maintenance of genomic medicine in pediatric healthcare context. Innovative care models, adaptation of appropriate technologies, and strategies aimed at addressing pediatric genomic needs are needed.

Exome and Genome Sequencing to Diagnose the Genetic Basis of Neonatal Hypotonia: An International Consortium Study

BACKGROUND AND OBJECTIVES

Hypotonia is a relatively common finding among infants in the neonatal intensive care unit (NICU). Consideration of genetic testing is recommended early in the care of infants with unexplained hypotonia. We aimed to assess the diagnostic yield and overall impact of exome and genome sequencing (ES and GS).

METHODS

Consecutive infants with hypotonia were identified from research and clinical databases across 5 teaching hospitals in United States, Canada, United Kingdom, and Australia. Inclusion criteria included NICU admission and genetic evaluation. Infants with a known explanation for hypotonia were excluded. Data regarding infant characteristics, genetic testing, and diagnoses were collected. The primary outcome was identification of a molecular diagnosis. Impact on care was a secondary outcome. The Fisher exact and Wilcoxon rank-sum tests were used for statistical analysis.

RESULTS

We identified 147 infants with unexplained hypotonia. The median gestational age was 39 weeks (interquartile range [IQR] 36-42 weeks), 77 (52%) were female, and the median age was 8 days at the time of evaluation (IQR 2-19 days). Eighty (54%) had hypotonia as the main clinical feature while 67 (46%) had additional multisystem involvement. Seventy-five (51%) underwent rapid ES, 44 (30%) rapid GS, 2 (1%) both ES and GS, and 26 (18%) were admitted before ES or GS became available. Of the 121 infants who underwent ES and/or GS, 72 (60%) had the primary outcome of a molecular diagnosis. In addition, 2 infants with mitochondrial genome variants were diagnosed by mitochondrial GS after negative ES, and one infant needed targeted testing to identify a short tandem repeat expansion missed by GS. The proportion diagnosed by ES and GS was not different between infants with hypotonia as the primary finding (37/56, 66%) and infants with multisystemic symptoms (35/65, 54%, odds ratio [OR] 1.7, CI 0.8-3.7, p value = 0.20). Testing was more likely to have an impact on care for infants receiving a genetic diagnosis (57/66 vs 14/33, OR 8.4, CI 2.9-26.1, p = 1.0E-05).

DISCUSSION

Rapid ES and GS provided a molecular diagnosis for most of the infants with unexplained hypotonia who underwent testing. Further studies are needed to assess the generalizability of these findings as increased access to genetic testing becomes available.

CLASSIFICATION OF EVIDENCE

This study provides Class IV evidence that in unexplained neonatal hypotonia, rapid ES or GS adds diagnostic specificity.

Interstitial lung disease in the newborn

Although relatively rare, interstitial lung diseases may present with respiratory distress in the newborn period. Most commonly these include developmental and growth disorders, disorders of surfactant synthesis and homeostasis, pulmonary interstitial glycogenosis, and neuroendocrine cell hyperplasia of infancy. Although the diagnosis of these disorders is sometimes made based on clinical presentation and imaging, due to the significant overlap between disorders and phenotypic variability, lung biopsy or, increasingly genetic testing is needed for diagnosis. These diseases may result in significant morbidity and mortality. Effective medical treatment options are in some cases limited and/or invasive. The genetic basis for some of these disorders has been identified, and with increased utilization of exome and whole genome sequencing even before lung biopsy, further insights into their genetic etiologies should become available.

Critically unwell infants and children with mitochondrial disorders diagnosed by ultrarapid genomic sequencing

PURPOSE

To characterize the diagnostic and clinical outcomes of a cohort of critically ill infants and children with suspected mitochondrial disorders (MD) undergoing ultrarapid genomic testing as part of a national program.

METHODS

Ultrarapid genomic sequencing was performed in 454 families (genome sequencing: n = 290, exome sequencing +/- mitochondrial DNA sequencing: n = 164). In 91 individuals, MD was considered, prompting analysis using an MD virtual gene panel. These individuals were reviewed retrospectively and scored according to modified Nijmegen Mitochondrial Disease Criteria.

RESULTS

A diagnosis was achieved in 47% (43/91) of individuals, 40% (17/43) of whom had an MD. Seven additional individuals in whom an MD was not suspected were diagnosed with an MD after broader analysis. Gene-agnostic analysis led to the discovery of 2 novel disease genes, with pathogenicity validated through targeted functional studies (CRLS1 and MRPL39). Functional studies enabled diagnosis in another 4 individuals. Of the 24 individuals ultimately diagnosed with an MD, 79% had a change in management, which included 53% whose care was redirected to palliation.

CONCLUSION

Ultrarapid genetic diagnosis of MD in acutely unwell infants and children is critical for guiding decisions about the need for additional investigations and clinical management.

Genome-based newborn screening for severe childhood genetic diseases has high positive predictive value and sensitivity in a NICU pilot trial

Large prospective clinical trials are underway or planned that examine the clinical utility and cost effectiveness of genome-based newborn screening (gNBS). One gNBS platform, BeginNGS, currently screens 53,575 variants for 412 severe childhood genetic diseases with 1,603 efficacious therapies. Retrospective evaluation of BeginNGS in 618,290 subjects suggests adequate sensitivity and positive predictive value (PPV) to proceed to prospective studies. To inform pivotal clinical trial design, we undertook a pilot clinical trial. We enrolled 120 infants in a regional neonatal intensive care unit (NICU) who were not under consideration for rapid diagnostic genome sequencing (RDGS). Each enrollee received BeginNGS and two index tests (California state NBS and RDGS). California NBS identified 4 of 4 true positive (TP) findings (TP rate 3.6%, sensitivity 100%) and 11 false positive (FP) findings (PPV 27%). RDGS identified 41 diagnostic findings in 36 neonates (diagnostic rate 30%). BeginNGS identified 5 of 6 on-target TP disorders (TP rate 4.2%, 95% confidence interval 1%-8%, sensitivity 83%) and no FPs (PPV 100%). Changes in management were anticipated following the return of 27 RDGS results in 25 enrollees (clinical utility [CU] 21%), 3 of 4 NBS TPs (CU 2.7%), and all BeginNGS TPs (CU 4.2%). The incidence of actionable genetic diseases in NICU infants not being considered for RDGS suggests (1) performance of RDGS in ∼20% of admissions misses many genetic diagnoses, (2) NICU enrollment in gNBS trials will greatly increase power to test endpoints, and (3) NICUs may be attractive for early implementation of consented BeginNGS screening.

Hospital-wide access to genomic data advanced pediatric rare disease research and clinical outcomes

Boston Children's Hospital has established a genomic sequencing and analysis research initiative to improve clinical care for pediatric rare disease patients. Through the Children's Rare Disease Collaborative (CRDC), the hospital offers CLIA-grade exome and genome sequencing, along with other sequencing types, to patients enrolled in specialized rare disease research studies. The data, consented for broad research use, are harmonized and analyzed with CRDC-supported variant interpretation tools. Since its launch, 66 investigators representing 26 divisions and 45 phenotype-based cohorts have joined the CRDC. These studies enrolled 4653 families, with 35% of analyzed cases having a finding either confirmed or under further investigation. This accessible and harmonized genomics platform also supports additional institutional data collections, research and clinical, and now encompasses 13,800+ patients and their families. This has fostered new research projects and collaborations, increased genetic diagnoses and accelerated innovative research via integration of genomics research with clinical care.

Impact of prenatal genomics on clinical genetics practice

Genetic testing for prenatal diagnosis in the pre-genomic era primarily focused on detecting common fetal aneuploidies, using methods that combine maternal factors and imaging findings. The genomic era, ushered in by the emergence of new technologies like chromosomal microarray analysis and next-generation sequencing, has transformed prenatal diagnosis. These new tools enable screening and testing for a broad spectrum of genetic conditions, from chromosomal to monogenic disorders, and significantly enhance diagnostic precision and efficacy. This chapter reviews the transition from traditional karyotyping to comprehensive sequencing-based genomic analyses. We discuss both the clinical utility and the challenges of integrating prenatal exome and genome sequencing into prenatal care and underscore the need for ethical frameworks, improved prenatal phenotypic characterization, and global collaboration to further advance the field.

Genome Sequencing is Critical for Forecasting Outcomes Following Congenital Cardiac Surgery

While exome and whole genome sequencing have transformed medicine by elucidating the genetic underpinnings of both rare and common complex disorders, its utility to predict clinical outcomes remains understudied. Here, we used artificial intelligence (AI) technologies to explore the predictive value of genome sequencing in forecasting clinical outcomes following surgery for congenital heart defects (CHD). We report results for a cohort of 2,253 CHD patients from the Pediatric Cardiac Genomics Consortium with a broad range of complex heart defects, pre- and post-operative clinical variables and exome sequencing. Damaging genotypes in chromatin-modifying and cilia-related genes were associated with an elevated risk of adverse post-operative outcomes, including mortality, cardiac arrest and prolonged mechanical ventilation. The impact of damaging genotypes was further amplified in the context of specific CHD phenotypes, surgical complexity and extra-cardiac anomalies. The absence of a damaging genotype in chromatin-modifying and cilia-related genes was also informative, reducing the risk for adverse postoperative outcomes. Thus, genome sequencing enriches the ability to forecast outcomes following congenital cardiac surgery.

Benchmarking nanopore sequencing and rapid genomics feasibility: validation at a quaternary hospital in New Zealand

Approximately 200 critically ill infants and children in New Zealand are in high-dependency care, many suspected of having genetic conditions, requiring scalable genomic testing. We adopted an acute care genomics protocol from an accredited laboratory and established a clinical pipeline using Oxford Nanopore Technologies PromethION 2 solo system and Fabric GEM™ software. Benchmarking of the pipeline was performed using Global Alliance for Genomics and Health benchmarking tools and Genome in a Bottle samples (HG002-HG007). Evaluation of single nucleotide variants resulted in a precision and recall of 0.997 and 0.992, respectively. Small indel identification approached a precision of 0.922 and recall of 0.838. Large genomic variations from Coriell Copy Number Variation Reference Panel 1 were reliably detected with ~2 M long reads. Finally, we present results obtained from fourteen trio samples, ten of which were processed in parallel with a clinically accredited short-read rapid genomic testing pipeline (Newborn Genomics Programme; NCT06081075; 2023-10-12).

Exploring the Role of Genetic Testing in Decisions to Redirect Care in Critically Ill Infants

OBJECTIVE

Genetic disorders are a major determinant of morbidity and mortality within neonatal intensive care units (NICUs). Studies have found genetic testing in critically ill infants may lead to changes in clinical decisions such as pursuing end of life care. This study surveyed palliative care providers to explore the influence of genetic testing on decisions to redirect care in critically ill infants.

METHODS

This study was conducted retrospectively on cases who were admitted to the Level IV NICU at Primary Children's Hospital, underwent redirection to end of life care, and whose death date was between 2019-2023. A review of the case's electronic medical record was performed to construct a clinical case summary. The clinical summary and questionnaire were sent to the case's palliative care provider.

RESULTS

Fifty-six cases were included in this study and 73% had genetic testing completed. Our results suggest the information from genetic testing played a relatively minor role in the decision to redirect care for cases with negative or uncertain genetic testing and positive genetic testing results, although the influence appeared higher in the latter group.

CONCLUSION

Our results suggest the assumptions of several studies that genetic testing is responsible for changes in clinical management and cost savings, especially in cases of redirection of care may have been overestimated. Our results fill a critical gap in current literature and demonstrate the need for further investigation to clarify the direct role of genetic testing in clinical decisions in the NICU, especially related to redirection of care.

Early Intervention services in the era of genomic medicine: setting a research agenda

Newborn genomic sequencing (NBSeq) has the potential to substantially improve early detection of rare genetic conditions, allowing for pre-symptomatic treatment to optimize outcomes. Expanding conceptions of the clinical utility of NBSeq include earlier access to behavioral early intervention to support the acquisition of core motor, cognitive, communication, and adaptive skills during critical windows in early development. However, important questions remain about equitable access to early intervention programs for the growing number of infants identified with a genetic condition via NBSeq. We review the current NBSeq public health, clinical, and research landscape, and highlight ongoing international research efforts to collect population-level data on the utility of NBSeq for healthy newborns. We then explore the challenges facing a specific Early Intervention (EI) system-the US federally supported "Part C" system-for meeting the developmental needs of young children with genetic diagnoses, including structural limitations related to funding, variable eligibility criteria, and lack of collaboration with newborn screening programs. We conclude with a set of questions to guide future research at the intersection of NBSeq, newborn screening, and EI, which once answered, can steer future policy to ensure that EI service systems can optimally support the developmental needs of infants impacted by broader implementation of NBSeq. IMPACT: Existing literature on the clinical benefits of genome sequencing in newborns tends to focus on earlier provision of medical interventions, with less attention to the ongoing developmental needs of very young children with genetic conditions. This review outlines the developmental needs of a growing number of children diagnosed with genetic conditions in infancy and describes the strengths and limitations of the United States Early Intervention system (IDEA Part C) for meeting those needs.

Potential clinical applications of advanced genomic analysis in cerebral palsy

Cerebral palsy (CP) has historically been attributed to acquired insults, but emerging research suggests that genetic variations are also important causes of CP. While microarray and whole-exome sequencing based studies have been the primary methods for establishing new CP-gene relationships and providing a genetic etiology for individual patients, the cause of their condition remains unknown for many patients with CP. Recent advancements in genomic technologies offer additional opportunities to uncover variations in human genomes, transcriptomes, and epigenomes that have previously escaped detection. In this review, we outline the use of these state-of-the-art technologies to address the molecular diagnostic challenges experienced by individuals with CP. We also explore the importance of identifying a molecular etiology whenever possible, given the potential for genomic medicine to provide opportunities to treat patients with CP in new and more precise ways.

Rapid Whole-Genome Sequencing and Clinical Management in the PICU: A Multicenter Cohort, 2016-2023

OBJECTIVES

Analysis of the clinical utility of rapid whole-genome sequencing (rWGS) outside of the neonatal period is lacking. We describe the use of rWGS in PICU and cardiovascular ICU (CICU) patients across four institutions.

DESIGN

Ambidirectional multisite cohort study.

SETTING

Four tertiary children's hospitals.

PATIENTS

Children 0-18 years old in the PICU or CICU who underwent rWGS analysis, from May 2016 to June 2023.

INTERVENTIONS

None.

MEASUREMENTS AND MAIN RESULTS

A total of 133 patients underwent clinical, phenotype-driven rWGS analysis, 36 prospectively. A molecular diagnosis was identified in 79 patients (59%). Median (interquartile range [IQR]) age was 6 months (IQR 1.2 mo-4.6 yr). Median time for return of preliminary results was 3 days (IQR 2-4). In 79 patients with a molecular diagnosis, there was a change in ICU management in 19 patients (24%); and some change in clinical management in 63 patients (80%). Nondiagnosis changed management in 5 of 54 patients (9%). The clinical specialty ordering rWGS did not affect diagnostic rate. Factors associated with greater odds ratio (OR [95% CI]; OR [95% CI]) of diagnosis included dysmorphic features (OR 10.9 [95% CI, 1.8-105]) and congenital heart disease (OR 4.2 [95% CI, 1.3-16.8]). Variables associated with greater odds of changes in management included obtaining a genetic diagnosis (OR 16.6 [95% CI, 5.5-62]) and a shorter time to genetic result (OR 0.8 [95% CI, 0.76-0.9]). Surveys of pediatric intensivists indicated that rWGS-enhanced clinical prognostication ( p < 0.0001) and contributed to a decision to consult palliative care ( p < 0.02).

CONCLUSIONS

In this 2016-2023 multiple-PICU/CICU cohort, we have shown that timely genetic diagnosis is feasible across institutions. Application of rWGS had a 59% (95% CI, 51-67%) rate of diagnostic yield and was associated with changes in critical care management and long-term patient management.

Genomic testing and molecular diagnosis among infants with congenital heart disease in the neonatal intensive care unit

OBJECTIVE

To evaluate patterns of genetic testing among infants with CHD at a tertiary care center.

STUDY DESIGN

We conducted a retrospective observational cohort study of infants in the NICU with suspicion of a genetic disorder. 1075 of 7112 infants admitted to BCH had genetic evaluation including 329 with CHD and 746 without CHD. 284 of 525 infants with CHD admitted to CMHH had genetic evaluation. Patterns of testing and diagnoses were compared.

RESULTS

The rate of diagnosis after testing was similar for infants with or without CHD (38% [121/318] vs. 36% [246/676], p = 0.14). In a multiple logistic regression, atrioventricular septal defects were most high associated with genetic diagnosis (odds ratio 29.99, 95% confidence interval 2.69-334.12, p < 0.001).

CONCLUSIONS

Infants with suspicion of a genetic disorder with CHD had similar rates of molecular diagnosis as those without CHD. These results support a role for genetic testing among NICU infants with CHD.

Non-Genetic Healthcare Providers' Experiences and Perspectives with Rapid Genome-Wide Sequencing in Canadian Neonatal Intensive Care Units

BACKGROUND/OBJECTIVES

Rapid genome-wide sequencing (rGWS) continues to transform the care provided to infants with genetic conditions in neonatal intensive care units (NICUs). Previous research has demonstrated that rGWS has immense benefits on patient care; however, little is known about non-genetic healthcare providers' (HCPs) experiences and perspectives of working with rGWS and supporting families through the rGWS testing process in Canadian NICU facilities. To address this gap, we surveyed and conducted semi-structured interviews with non-genetic HCPs of diverse professions from NICUs in British Columbia.

METHODS

An interpretive description approach was used to analyze interview transcripts to identify patterns and variations in non-genetic HCPs' experiences and perceptions with rGWS.

RESULTS

Participants had varying degrees of exposure to rGWS and levels of comfort with the testing process. Numerous barriers affecting the implementation of rGWS were identified, including low levels of comprehension of rGWS, longer turn-around times than expected, and having to apply for provincial government approval to access testing. Participants desired more education on rGWS, clear guidelines on the use of rGWS in NICUs, and resources for non-genetic HCPs and parents to support implementation.

CONCLUSIONS

The results from this study can inform the development of workflows and educational resources on the use of rGWS in NICUs, helping to ensure that the NICU team is supported to optimize rGWS implementation.

A Machine Learning Decision Support Tool Optimizes Whole Genome Sequencing Utilization in a Neonatal Intensive Care Unit

The Mendelian Phenotype Search Engine (MPSE), a clinical decision support tool using Natural Language Processing and Machine Learning, helped neonatologists expedite decisions to whole genome sequencing (WGS) to diagnose patients in the Neonatal Intensive Care Unit. After the MPSE was introduced, utilization of WGS increased, time to ordering WGS decreased, and WGS diagnostic yield increased.

Clinical exome sequencing uncovers genetic disorders in neonates with suspected hypoxic-ischemic encephalopathy: A retrospective analysis

Hypoxic-ischemic encephalopathy (HIE) occurs in up to 7 out of 1000 births and accounts for almost a quarter of neonatal deaths worldwide. Despite the name, many newborns with HIE have little evidence of perinatal hypoxia. We hypothesized that some infants with HIE have genetic disorders that resemble encephalopathy. We reviewed genetic results for newborns with HIE undergoing exome or genome sequencing at a clinical laboratory (2014-2022). Neonates were included if they had a diagnosis of HIE and were delivered ≥35 weeks. Neonates were excluded for cardiopulmonary pathology resulting in hypoxemia or if neuroimaging suggested postnatal hypoxic-ischemic injury. Of 24 patients meeting inclusion criteria, six (25%) were diagnosed with a genetic condition. Four neonates had variants at loci linked to conditions with phenotypic features resembling HIE, including KIF1A, GBE1, ACTA1, and a 15q13.3 deletion. Two additional neonates had variants in genes not previously associated with encephalopathy, including DUOX2 and PTPN11. Of the six neonates with a molecular diagnosis, two had isolated HIE without apparent comorbidities to suggest a genetic disorder. Genetic diagnoses were identified among neonates with and without sentinel labor events, abnormal umbilical cord gasses, and low Apgar scores. These results suggest that genetic evaluation is clinically relevant for patients with perinatal HIE.

NeoGx: Machine-Recommended Rapid Genome Sequencing for Neonates

Background

Genetic disease is common in the Level IV Neonatal Intensive Care Unit (NICU), but neonatology providers are not always able to identify the need for genetic evaluation. We trained a machine learning (ML) algorithm to predict the need for genetic testing within the first 18 months of life using health record phenotypes.

Methods

For a decade of NICU patients, we extracted Human Phenotype Ontology (HPO) terms from clinical text with Natural Language Processing tools. Considering multiple feature sets, classifier architectures, and hyperparameters, we selected a classifier and made predictions on a validation cohort of 2,241 Level IV NICU admits born 2020-2021.

Results

Our classifier had ROC AUC of 0.87 and PR AUC of 0.73 when making predictions during the first week in the Level IV NICU. We simulated testing policies under which subjects begin testing at the time of first ML prediction, estimating diagnostic odyssey length both with and without the additional benefit of pursuing rGS at this time. Just by using ML to accelerate initial genetic testing (without changing the tests ordered), the median time to first genetic test dropped from 10 days to 1 day, and the number of diagnostic odysseys resolved within 14 days of NICU admission increased by a factor of 1.8. By additionally requiring rGS at the time of positive ML prediction, the number of diagnostic odysseys resolved within 14 days was 3.8 times higher than the baseline.

Conclusions

ML predictions of genetic testing need, together with the application of the right rapid testing modality, can help providers accelerate genetics evaluation and bring about earlier and better outcomes for patients.

The Multi-Omic Approach to Newborn Screening: Opportunities and Challenges

Newborn screening programs have seen significant evolution since their initial implementation more than 60 years ago, with the primary goal of detecting treatable conditions within the earliest possible timeframe to ensure the optimal treatment and outcomes for the newborn. New technologies have driven the expansion of screening programs to cover additional conditions. In the current era, the breadth of screened conditions could be further expanded by integrating omic technologies such as untargeted metabolomics and genomics. Genomic screening could offer opportunities for lifelong care beyond the newborn period. For genomic newborn screening to be effective and ready for routine adoption, it must overcome barriers such as implementation cost, public acceptability, and scalability. Metabolomics approaches, on the other hand, can offer insight into disease phenotypes and could be used to identify known and novel biomarkers of disease. Given recent advances in metabolomic technologies, alongside advances in genomics including whole-genome sequencing, the combination of complementary multi-omic approaches may provide an exciting opportunity to leverage the best of both approaches and overcome their respective limitations. These techniques are described, along with the current outlook on multi-omic-based NBS research.

Neonatal Seizures: New Evidence, Classification, and Guidelines

Neonates are susceptible to seizures due to their unique physiology and combination of risks associated with gestation, delivery, and the immediate postnatal period. Advances in neonatal care have improved outcomes for some of our most fragile patients, but there are persistent challenges for epileptologists in identifying neonatal seizures, diagnosing etiologies, and providing the most appropriate care, with an ultimate goal to maximize patient outcomes. In just the last few years, there have been critical advances in the state of the science, as well as new evidence-based guidelines for diagnosis, classification, and treatment of neonatal seizures. This review will provide updated knowledge about the pathophysiology of neonatal seizures, classification of the provoked seizures and neonatal epilepsies, state of the art guidance on EEG monitoring in the neonatal ICU, current treatment guidelines for neonatal seizures, and potential for future advancement in treatment.

Rapid Whole Genome Sequencing: It Is Feasible! When Can We Implement It?

Evaluation of the Feasibility, Diagnostic Yield, and Clinical Utility of Rapid Genome Sequencing in Infantile Epilepsy (Gene-STEPS): An International, Multicentre, Pilot Cohort Study D’Gama AM, Mulhern S, Sheidley BR, Boodhoo F, Buts S, Chandler NJ, Cobb J, Curtis M, Higginbotham EJ, Holland J, Khan T, Koh J, Liang NSY, McRae L, Nesbitt SE, Oby BT, Paternoster B, Patton A, Rose G, Scotchman E, Valentine R, Wiltrout KN; Gene-STEPS Study Group; IPCHiP Executive Committee; Hayeems RZ, Jain P, Lunke S, Marshall CR, Rockowitz S, Sebire NJ, Stark Z, White SM, Chitty LS, Cross JH, Scheffer IE, Chau V, Costain G, Poduri A, Howell KB, McTague A. Lancet Neurol. 2023;22(9):812-825. doi:10.1016/S1474-4422(23)00246-6 Background: Most neonatal and infantile-onset epilepsies have presumed genetic aetiologies, and early genetic diagnoses have the potential to inform clinical management and improve outcomes. We therefore aimed to determine the feasibility, diagnostic yield, and clinical utility of rapid genome sequencing in this population. Methods: We conducted an international, multicentre, cohort study (Gene-STEPS), which is a pilot study of the International Precision Child Health Partnership (IPCHiP). IPCHiP is a consortium of four paediatric centres with tertiary-level subspecialty services in Australia, Canada, the UK, and the USA. We recruited infants with new-onset epilepsy or complex febrile seizures from IPCHiP centres, who were younger than 12 months at seizure onset. We excluded infants with simple febrile seizures, acute provoked seizures, known acquired cause, or known genetic cause. Blood samples were collected from probands and available biological parents. Clinical data were collected from medical records, treating clinicians, and parents. Trio genome sequencing was done when both parents were available, and duo or singleton genome sequencing was done when one or neither parent was available. Site-specific protocols were used for DNA extraction and library preparation. Rapid genome sequencing and analysis was done at clinically accredited laboratories, and results were returned to families. We analysed summary statistics for cohort demographic and clinical characteristics and the timing, diagnostic yield, and clinical impact of rapid genome sequencing. Findings: Between Sept 1, 2021, and Aug 31, 2022, we enrolled 100 infants with new-onset epilepsy, of whom 41 (41%) were girls and 59 (59%) were boys. Median age of seizure onset was 128 days (IQR 46-192). For 43 (43% [binomial distribution 95% CI 33-53]) of 100 infants, we identified genetic diagnoses, with a median time from seizure onset to rapid genome sequencing result of 37 days (IQR 25-59). Genetic diagnosis was associated with neonatal seizure onset versus infantile seizure onset (14 [74%] of 19 vs 29 [36%] of 81; p = 0.0027), referral setting (12 [71%] of 17 for intensive care, 19 [44%] of 43 non-intensive care inpatient, and 12 [28%] of 40 outpatient; p = 0.0178), and epilepsy syndrome (13 [87%] of 15 for self-limited epilepsies, 18 [35%] of 51 for developmental and epileptic encephalopathies, 12 [35%] of 34 for other syndromes; p = 0.001). Rapid genome sequencing revealed genetic heterogeneity, with 34 unique genes or genomic regions implicated. Genetic diagnoses had immediate clinical utility, informing treatment (24 [56%] of 43), additional evaluation (28 [65%]), prognosis (37 [86%]), and recurrence risk counselling (all cases). Interpretation: Our findings support the feasibility of implementation of rapid genome sequencing in the clinical care of infants with new-onset epilepsy. Longitudinal follow-up is needed to further assess the role of rapid genetic diagnosis in improving clinical, quality-of-life, and economic outcomes.

Newborn Screening Has Moved Way Beyond PKU

Nurses need to understand how clinical genetic and genomic applications affect newborn screening and advocate for parents and newborns.

Wales Infants' and childreN's Genome Service (WINGS): providing rapid genetic diagnoses for unwell children

INTRODUCTION

This study reviews the first 3 years of delivery of the first National Health Service (NHS)-commissioned trio rapid whole genome sequencing (rWGS) service for acutely unwell infants and children in Wales.

METHODS

Demographic and phenotypic data were prospectively collected as patients and their families were enrolled in the Wales Infants' and childreN's Genome Service (WINGS). These data were reviewed alongside trio rWGS results.

RESULTS

From April 2020 to March 2023, 82 families underwent WINGS, with a diagnostic yield of 34.1%. The highest diagnostic yields were noted in skeletal dysplasias, neurological or metabolic phenotypes. Mean time to reporting was 9 days.

CONCLUSION

This study demonstrates that trio rWGS is having a positive impact on the care of acutely unwell infants and children in an NHS setting. In particular, the study shows that rWGS can be applied in an NHS setting, achieving a diagnostic yield comparable with the previously published diagnostic yields achieved in research settings, while also helping to improve patient care and management.

Time to diagnosis in rapid exome/genome sequencing in the clinical inpatient setting

Exome and genome sequencing are clinically available, with many laboratories offering expedited testing (e.g., "rapid" and "ultra-rapid"). With the increase in uptake of expedited testing, there is a need for the development of inpatient protocols for best practices based on real-life data. A retrospective 2-year review (October 2019-November 2021) of the utilization of rapid exome and genome sequencing for inpatient cases at a tertiary care center using a utilization management tracking database with subsequent chart review was performed. Thirty-three expedited "rapid/priority" exome/genome tests were performed clinically. The average total turnaround time (TAT) was 17.88 days (5-43 days) with an average TAT of 13.97 days (3-41 days) for the performing laboratory. There were 5 positive diagnostic results (15.2%), 3 likely positive diagnostic results (9%), 2 noncontributory results (6%), and 26 nondiagnostic results (69.7%). Real-life data suggest that there is an approximately 3.91-day lag in getting samples to the performing laboratory. Although laboratories may advertise their expected TAT, a number of factors can potentially impact the actual time from test order placement to communication of the results for clinical use. Understanding the points of delay will enable the development of internal protocols and policies to improve time to diagnosis.

Universal Exome Sequencing in Critically Ill Adults: A Diagnostic Yield of 25% and Race-Based Disparities in Access to Genetic Testing

Numerous studies have underscored the diagnostic and therapeutic potential of exome or genome sequencing in critically ill pediatric populations. However, an equivalent investigation in critically ill adults remains conspicuously absent. We retrospectively analyzed whole exome sequencing (WES) data available through the PennMedicine Biobank (PMBB) from all 365 young adult patients, aged 18-40 years, with intensive care unit (ICU) admissions at the University of Pennsylvania Health System who met inclusion criteria for our study. For each participant, two Medical Genetics and Internal Medicine-trained clinicians reviewed WES reports and patient charts for variant classification, result interpretation, and identification of genetic diagnoses related to their critical illness. Of the 365 individuals in our study, 90 (24.7%) were found to have clearly diagnostic results on WES; an additional 40 (11.0%) had a suspicious variant of uncertain significance (VUS) identified; and an additional 16 (4.4%) had a medically actionable incidental finding. The diagnostic rate of exome sequencing did not decrease with increasing patient age. Affected genes were primarily involved in cardiac function (18.8%), vascular health (16.7%), cancer (16.7%), and pulmonary disease (11.5%). Only half of all diagnostic findings were known and documented in the patient chart at the time of ICU admission. Significant disparities emerged in subgroup analysis by EHR-reported race, with genetic diagnoses known/documented for 63.5% of White patients at the time of ICU admission but only for 28.6% of Black or Hispanic patients. There was a trend towards patients with undocumented genetic diagnoses having a 66% increased mortality rate, making these race-based disparities in genetic diagnosis even more concerning. Altogether, universal exome sequencing in ICU-admitted adult patients was found to yield a new definitive diagnosis in 11.2% of patients. Of these diagnoses, 76.6% conferred specific care-altering medical management recommendations. Our study suggests that the diagnostic utility of exome sequencing in critically ill young adults is similar to that observed in neonatal and pediatric populations and is age-independent. The high diagnostic rate and striking race-based disparities we find in genetic diagnoses argue for broad and universal approaches to genetic testing for critically ill adults. The widespread implementation of comprehensive genetic sequencing in the adult population promises to enhance medical care for all individuals and holds the potential to rectify disparities in genetic testing referrals, ultimately promoting more equitable healthcare delivery.

Applications of genome sequencing as a single platform for clinical constitutional genetic testing

The number of human disease genes has dramatically increased over the past decade, largely fueled by ongoing advances in sequencing technologies. In parallel, the number of available clinical genetic tests has also increased, including the utilization of exome sequencing for undiagnosed diseases. Although most clinical sequencing tests have been centered on enrichment-based multigene panels and exome sequencing, the continued improvements in performance and throughput of genome sequencing suggest that this technology is emerging as a potential platform for routine clinical genetic testing. A notable advantage is a single workflow with the opportunity to reflexively interrogate content as clinically indicated; however, challenges with implementing routine clinical genome sequencing still remain. This review is centered on evaluating the applications of genome sequencing as a single platform for clinical constitutional genetic testing, including its potential utility for diagnostic testing, carrier screening, cytogenomic molecular karyotyping, prenatal testing, mitochondrial genome interrogation, and pharmacogenomic and polygenic risk score testing.

Genomes in clinical care

In the era of precision medicine, genome sequencing (GS) has become more affordable and the importance of genomics and multi-omics in clinical care is increasingly being recognized. However, how to scale and effectively implement GS on an institutional level remains a challenge for many. Here, we present Genome First and Ge-Med, two clinical implementation studies focused on identifying the key pillars and processes that are required to make routine GS and predictive genomics a reality in the clinical setting. We describe our experience and lessons learned for a variety of topics including test logistics, patient care processes, data reporting, and infrastructure. Our model of providing clinical care and comprehensive genomic analysis from a single source may be used by other centers with a similar structure to facilitate the implementation of omics-based personalized health concepts in medicine.

A Children's Rights Framework for Genomic Medicine: Newborn Screening as a Use Case

The year 2023 marked the 60th anniversary of screening newborns in the United States for diseases that benefit from early identification and intervention. All around the world, the goal of NBS is to facilitate timely diagnosis and management to improve individual health outcomes in all newborns regardless of their place of birth, economic circumstances, ability to pay for treatment, and access to healthcare. Advances in technology to screen and treat disease have led to a rapid increase in the number of screened conditions, and innovations in genomics are expected to exponentially expand this number further. A system where all newborns are screened, coupled with rapid technological innovation, provides a unique opportunity to improve pediatric health outcomes and advance children's rights, including the unique rights of sick and disabled children. This is especially timely as we approach the 100th anniversary of the 1924 Geneva Declaration of the Rights of the Child, which includes children's right to healthcare, and the 1989 United Nations Convention on the Rights of the Child that expanded upon this aspect and affirmed each child's right to the highest attainable standard of health. In this manuscript, we provide background on the evolving recognition of the rights of children and the foundational rights to healthcare and non-discrimination, provide two examples that highlight issues to access and equity in newborn screening that may limit a child's right to healthcare and best possible outcomes, detail ways the current approach to newborn screening advances the rights of the child, and finally, propose that the incorporation of genomics into newborn screening presents a useful case study to recognize and uphold the rights of every child.

A Practical Guide to Whole Genome Sequencing in the NICU

The neonatal period is a peak time for the presentation of genetic disorders that can be diagnosed using whole genome sequencing (WGS). While any one genetic disorder is individually rare, they collectively contribute to significant morbidity, mortality, and health-care costs. As the cost of WGS continues to decline and becomes increasingly available, the ordering of rapid WGS for NICU patients with signs or symptoms of an underlying genetic condition is now feasible. However, many neonatal clinicians are not comfortable with the testing, and unfortunately, there is a dearth of geneticists to facilitate testing for every patient that needs it. Here, we will review the science behind WGS, diagnostic capabilities, limitations of testing, time to consider testing, test initiation, interpretation of results, developing a plan of care that incorporates genomic information, and returning WGS results to families.

The Multiple Odysseys in Research and Clinical Care for Neurogenetic Conditions

Neurogenetic conditions (NGC; e.g., fragile X, Angelman, Prader-Willi syndromes) represent the cause for intellectual or developmental disabilities in up to 60% of cases. With expanded diagnostic options and an increasing focus on the development of gene therapies comes the potential of improved quality of life for individuals with NGCs and their families. However, these emerging initiatives also bring new challenges and considerations for NGC researchers and clinicians, including considerations for supporting caregivers and assuring outcome measures for clinical trials adequately reflect the lived experiences of people with NGCs. This paper summarizes the advances and current and future challenges of research and clinical service provision for people with NGCs and their caregivers.

Rapid genomic sequencing for genetic disease diagnosis and therapy in intensive care units: a review

Single locus (Mendelian) diseases are a leading cause of childhood hospitalization, intensive care unit (ICU) admission, mortality, and healthcare cost. Rapid genome sequencing (RGS), ultra-rapid genome sequencing (URGS), and rapid exome sequencing (RES) are diagnostic tests for genetic diseases for ICU patients. In 44 studies of children in ICUs with diseases of unknown etiology, 37% received a genetic diagnosis, 26% had consequent changes in management, and net healthcare costs were reduced by $14,265 per child tested by URGS, RGS, or RES. URGS outperformed RGS and RES with faster time to diagnosis, and higher rate of diagnosis and clinical utility. Diagnostic and clinical outcomes will improve as methods evolve, costs decrease, and testing is implemented within precision medicine delivery systems attuned to ICU needs. URGS, RGS, and RES are currently performed in <5% of the ~200,000 children likely to benefit annually due to lack of payor coverage, inadequate reimbursement, hospital policies, hospitalist unfamiliarity, under-recognition of possible genetic diseases, and current formatting as tests rather than as a rapid precision medicine delivery system. The gap between actual and optimal outcomes in children in ICUs is currently increasing since expanded use of URGS, RGS, and RES lags growth in those likely to benefit through new therapies. There is sufficient evidence to conclude that URGS, RGS, or RES should be considered in all children with diseases of uncertain etiology at ICU admission. Minimally, diagnostic URGS, RGS, or RES should be ordered early during admissions of critically ill infants and children with suspected genetic diseases.

Evidence review and considerations for use of first line genome sequencing to diagnose rare genetic disorders

Early use of genome sequencing (GS) in the diagnostic odyssey can reduce suffering and improve care, but questions remain about which patient populations are most amenable to GS as a first-line diagnostic test. To address this, the Medical Genome Initiative conducted a literature review to identify appropriate clinical indications for GS. Studies published from January 2011 to August 2022 that reported on the diagnostic yield (DY) or clinical utility of GS were included. An exploratory meta-analysis using a random effects model evaluated DY based on cohort size and diagnosed cases per cohort. Seventy-one studies met inclusion criteria, comprising over 13,000 patients who received GS in one of the following settings: hospitalized pediatric patients, pediatric outpatients, adult outpatients, or mixed. GS was the first-line test in 38% (27/71). The unweighted mean DY of first-line GS was 45% (12-73%), 33% (6-86%) in cohorts with prior genetic testing, and 33% (9-60%) in exome-negative cohorts. Clinical utility was reported in 81% of first-line GS studies in hospitalized pediatric patients. Changes in management varied by cohort and underlying molecular diagnosis (24-100%). To develop evidence-informed points to consider, the quality of all 71 studies was assessed using modified American College of Radiology (ACR) criteria, with five core points to consider developed, including recommendations for use of GS in the N/PICU, in lieu of sequential testing and when disorders with substantial allelic heterogeneity are suspected. Future large and controlled studies in the pediatric and adult populations may support further refinement of these recommendations.

Multi-center implementation of rapid whole genome sequencing provides additional evidence of its utility in the pediatric inpatient setting

Objective

Multi-center implementation of rapid whole genome sequencing with assessment of the clinical utility of rapid whole genome sequencing (rWGS), including positive, negative and uncertain results, in admitted infants with a suspected genetic disease.

Study design

rWGS tests were ordered at eight hospitals between November 2017 and April 2020. Investigators completed a survey of demographic data, Human Phenotype Ontology (HPO) terms, test results and impacts of results on clinical care.

Results

A total of 188 patients, on general hospital floors and intensive care unit (ICU) settings, underwent rWGS testing. Racial and ethnic characteristics of the tested infants were broadly representative of births in the country at large. 35% of infants received a diagnostic result in a median of 6 days. The most common HPO terms for tested infants indicated an abnormality of the nervous system, followed by the cardiovascular system, the digestive system, the respiratory system and the head and neck. Providers indicated a major change in clinical management because of rWGS for 32% of infants tested overall and 70% of those with a diagnostic result. Also, 7% of infants with a negative rWGS result and 23% with a variant of unknown significance (VUS) had a major change in management due to testing.

Conclusions

Our study demonstrates that the implementation of rWGS is feasible across diverse institutions, and provides additional evidence to support the clinical utility of rWGS in a demographically representative sample of admitted infants and includes assessment of the clinical impact of uncertain rWGS results in addition to both positive and negative results.