Reclassification of the Etiology of Infant Mortality With Whole-Genome Sequencing

Errors in genome sequencing result disclosures: A randomized controlled trial comparing neonatology non-genetics healthcare professionals and genetic counselors

PURPOSE

We compared the rate of errors in genome sequencing (GS) result disclosures by genetic counselors (GC) and trained non-genetics healthcare professionals (NGHPs) in SouthSeq, a randomized trial utilizing GS in critically ill infants.

METHODS

Over 400 recorded GS result disclosures were analyzed for major and minor errors. We used Fisher's exact test to compare error rates between GCs and NGHPs and performed a qualitative content analysis to characterize error themes.

RESULTS

Major errors were identified in 7.5% of disclosures by NGHPs and in no disclosures by GCs. Minor errors were identified in 32.1% of disclosures by NGHPs and in 11.4% of disclosures by GCs. Although most disclosures lacked errors, NGHPs were significantly more likely to make any error than GCs for all result types (positive, negative, or uncertain). Common major error themes include omission of critical information, overstating a negative result, and overinterpreting an uncertain result. The most common minor error was failing to disclose negative secondary findings.

CONCLUSION

Trained NGHPs made clinically significant errors in GS result disclosures. Characterizing common errors in result disclosure can illuminate gaps in education to inform the development of future genomics training and alternative service delivery models.

QAFI: a novel method for quantitative estimation of missense variant impact using protein-specific predictors and ensemble learning

Next-generation sequencing (NGS) has revolutionized genetic diagnostics, yet its application in precision medicine remains incomplete, despite significant advances in computational tools for variant annotation. Many variants remain unannotated, and existing tools often fail to accurately predict the range of impacts that variants have on protein function. This limitation restricts their utility in relevant applications such as predicting disease severity and onset age. In response to these challenges, a new generation of computational models is emerging, aimed at producing quantitative predictions of genetic variant impacts. However, the field is still in its early stages, and several issues need to be addressed, including improved performance and better interpretability. This study introduces QAFI, a novel methodology that integrates protein-specific regression models within an ensemble learning framework, utilizing conservation-based and structure-related features derived from AlphaFold models. Our findings indicate that QAFI significantly enhances the accuracy of quantitative predictions across various proteins. The approach has been rigorously validated through its application in the CAGI6 contest, focusing on ARSA protein variants, and further tested on a comprehensive set of clinically labeled variants, demonstrating its generalizability and robust predictive power. The straightforward nature of our models may also contribute to better interpretability of the results.

Genomic testing in neonates

Recent technological advances have led to the expansion of testing options for newborns with suspected rare genetic conditions, particularly in high-income healthcare settings. This article summarises the key genomic testing approaches, their indications and potential limitations.

Genomic sequencing for newborn screening: current perspectives and challenges

Traditional newborn screening (NBS) serves as a critical tool in identifying conditions that may impact a child's health from an early stage. Newborn sequencing (NBSeq), the comprehensive analysis of an infant's genome, holds immense promise for revolutionizing health care throughout the lifespan. NBSeq allows for early detection of genetic disease risk and precision personalized medicine. The rapid evolution of DNA sequencing technologies and increasing affordability have spurred numerous endeavors to explore the potential of whole-genome sequencing in newborn screening. However, this transformative potential cannot be realized without challenges. Ethical aspects must be carefully navigated to safeguard individual rights and maintain public trust. Moreover, genomic data interpretation poses complex challenges due to its amount, the presence of variants of uncertain significance, and the dynamic nature of our understanding of genetics. Implementation hurdles, including cost, infrastructure, and specialized expertise, also present barriers to the widespread adoption of NBSeq. Addressing these challenges requires collaboration among clinicians, researchers, policymakers, ethicists, and stakeholders across various sectors. Robust frameworks for informed consent, data protection, and governance are essential. Advances in bioinformatics, machine learning, and genomic interpretation are crucial for translation into actionable clinical insights. Scalability and improving downstream health care access are vital for equitability, particularly in underserved communities. By fostering interdisciplinary collaboration, advancing technology and infrastructure, and upholding ethical principles, we can unlock the full potential of NBSeq as a tool for precision medicine and pave the way toward a future where every child has the opportunity for a healthier, genomics-informed start to life.

Molecular autopsy by proxy: relevance for genetic counseling in rare genetic disorders

Background

Rare genetic disorders may result in death before a definitive clinical diagnosis is established.

Aim

This study aims to outline the processes and challenges in managing, from a genetic perspective, couples who lost children affected by rare genetic disorders.

Results

Six couples who experienced child loss due to rare genetic disorders, seen by the primary author at genetic evaluation and counseling sessions, were retrospectively analyzed. Four out of 6 couples reported consanguinity. Exome and genome sequencing were performed for the parents. Carrier status of two rare lethal metabolic disorders was confirmed in one consanguineous couple. Three couples were carriers of 3 other rare diseases. Variants of LYST, MPV17, HEXB, ITGB4, CD3E, ASPM, TK2, COL11A2, and LAMB3 genes were identified. Six out of 10 were pathogenic variants, out of which 4 correlated with the demised children's phenotypes. One couple was negative for pathogenic variants. The last couple did not undergo genetic testing since they were beyond the fertile window.

Conclusion

Appropriate parental genetic evaluation and counseling are mandatory for selecting the right genetic test to certify the diagnosis postmortem, by virtue of molecular autopsy by proxy. Clarifying a rare disorder diagnosis can help couples to avoid recurrence and plan early for their next pregnancies.

Palliative Care in the Neonatal Intensive Care Unit: An Evolutionary Concept Analysis of Uncertainty in Anticipated Loss

BACKGROUND

Although the concepts of uncertainty and anticipated loss have been explored in a variety of contexts, advances in genetic testing and life-sustaining technology rendered changes in the care of medically complex infants. The separate concepts no longer have the descriptive power to clarify new phenomena endured by parents in the changing neonatal landscape. A current concept analysis examining uncertainty in anticipated loss is necessary to generate knowledge concurrently with deviations observed in the neonatal intensive care unit.

PURPOSE

To explore the concept of uncertainty in anticipated loss among parents of infants with genetic disorders.

METHODS

Following Rodgers' method of concept analysis, the concept was named, surrogate terms, antecedents, attributes, and consequences were identified from the literature, and a model case was constructed. The databases CINAHL, PubMed, and PsycINFO were used to conduct the literature search.

RESULTS

Fifteen articles provided the data for this analysis. Uncertainty in anticipated loss is a complex, nonlinear, and multifaceted experience anteceded by an ultimately terminal diagnosis, an ambiguous prognosis, and a lack of clear knowledge to guide treatment. Its attributes include a loss of control, assumptive world remodeling, role/identity confusion, and prolonged emotional complexity that consequently leads to a cyclical pattern of positive and negative outcomes.

IMPLICATIONS

This newly defined concept empowers neonatal nurses to provide care that includes a holistic understanding of the experience of uncertainty in anticipated loss . Nurses are ideally positioned and have the responsibility to utilize this concept to become better advocates for infants and facilitators of parental wellness.

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.

Validated WGS and WES protocols proved saliva-derived gDNA as an equivalent to blood-derived gDNA for clinical and population genomic analyses

BACKGROUND

Whole exome sequencing (WES) and whole genome sequencing (WGS) have become standard methods in human clinical diagnostics as well as in population genomics (POPGEN). Blood-derived genomic DNA (gDNA) is routinely used in the clinical environment. Conversely, many POPGEN studies and commercial tests benefit from easy saliva sampling. Here, we evaluated the quality of variant call sets and the level of genotype concordance of single nucleotide variants (SNVs) and small insertions and deletions (indels) for WES and WGS using paired blood- and saliva-derived gDNA isolates employing genomic reference-based validated protocols.

METHODS

The genomic reference standard Coriell NA12878 was repeatedly analyzed using optimized WES and WGS protocols, and data calls were compared with the truth dataset published by the Genome in a Bottle Consortium. gDNA was extracted from the paired blood and saliva samples of 10 participants and processed using the same protocols. A comparison of paired blood-saliva call sets was performed in the context of WGS and WES genomic reference-based technical validation results.

RESULTS

The quality pattern of called variants obtained from genomic-reference-based technical replicates correlates with data calls of paired blood-saliva-derived samples in all levels of tested examinations despite a higher rate of non-human contamination found in the saliva samples. The F1 score of 10 blood-to-saliva-derived comparisons ranged between 0.8030-0.9998 for SNVs and between 0.8883-0.9991 for small-indels in the case of the WGS protocol, and between 0.8643-0.999 for SNVs and between 0.7781-1.000 for small-indels in the case of the WES protocol.

CONCLUSION

Saliva may be considered an equivalent material to blood for genetic analysis for both WGS and WES under strict protocol conditions. The accuracy of sequencing metrics and variant-detection accuracy is not affected by choosing saliva as the gDNA source instead of blood but much more significantly by the genomic context, variant types, and the sequencing technology used.

Prenatal and postnatal genetic testing toward personalized care: The non-invasive perinatal testing

This article investigates how non-invasive prenatal testing and the incorporation of genomic sequencing into newborn screening postnatally are transforming perinatal care. They improve the accuracy of prenatal and neonatal screening, allowing for early interventions and personalized therapies. Non-invasive prenatal testing before birth and saliva-sample-based newborn genomic sequencing after birth can be collectively referred to as non-invasive perinatal testing. Non-invasive prenatal testing is particularly useful for aneuploidy, whereas performance markers worsen as DNA abnormalities shrink in size. Screening for clinically actionable diseases in childhood would be crucial to personalized medical therapy, as the postnatal period remains appropriate for screening for the great majority of monogenic disorders. While genomic data can help diagnose uncommon diseases, challenges like ethics and equity necessitate joint approaches for appropriate integration in this revolutionary journey toward personalized care.

Genomic newborn screening for rare diseases

Rare diseases are a leading cause of infant mortality and lifelong disability. To improve outcomes, timely diagnosis and effective treatments are needed. Genomic sequencing has transformed the traditional diagnostic process, providing rapid, accurate and cost-effective genetic diagnoses to many. Incorporating genomic sequencing into newborn screening programmes at the population scale holds the promise of substantially expanding the early detection of treatable rare diseases, with stored genomic data potentially benefitting health over a lifetime and supporting further research. As several large-scale newborn genomic screening projects launch internationally, we review the challenges and opportunities presented, particularly the need to generate evidence of benefit and to address the ethical, legal and psychosocial issues that genomic newborn screening raises.

Prevalence and Clinical Significance of Commonly Diagnosed Genetic Disorders in Preterm Infants

Background and Objectives

Preterm infants (<34 weeks' gestation) experience high rates of morbidity and mortality before hospital discharge. Genetic disorders substantially contribute to morbidity and mortality in related populations. The prevalence and clinical impact of genetic disorders is unknown in this population. We sought to determine the prevalence of commonly diagnosed genetic disorders in preterm infants, and to determine the association of disorders with morbidity and mortality.

Methods

This was a retrospective multicenter cohort study of infants born from 23 to 33 weeks' gestation between 2000 and 2020. Genetic disorders were abstracted from diagnoses present in electronic health records. We excluded infants transferred from or to other health care facilities prior to discharge or death when analyzing clinical outcomes. We determined the adjusted odds of pre-discharge morbidity or mortality after adjusting for known risk factors.

Results

Of 320,582 infants, 4196 (1.3%) had genetic disorders. Infants with trisomy 13, 18, 21, or cystic fibrosis had greater adjusted odds of severe morbidity or mortality. Of the 17,427 infants who died, 566 (3.2%) had genetic disorders. Of the 65,968 infants with a severe morbidity, 1319 (2.0%) had genetic disorders.ConclusionsGenetic disorders are prevalent in preterm infants, especially those with life-threatening morbidities. Clinicians should consider genetic testing for preterm infants with severe morbidity and maintain a higher index of suspicion for life-threatening morbidities in preterm infants with genetic disorders. Prospective genomic research is needed to clarify the prevalence of genetic disorders in this population, and the contribution of genetic disorders to preterm birth and subsequent morbidity and mortality.

Article Summary

Genetic disorders were found in 1.3% of preterm infants and at a higher rate (2.0%) in infants who died or developed severe morbidity.

What’s Known on This Subject

Previous research described the prevalence and associated short-term morbidity and mortality of trisomy 13, 18, and 21 in preterm infants. The prevalence of other commonly diagnosed genetic disorders and associated short-term morbidity and mortality in preterm infants is unknown.

What This Study Adds

In a multicenter, retrospective cohort of 320,582 preterm (<34 weeks' gestation) infants, we found that 1.3% had genetic disorders diagnosed through standard care. Multiple disorders were associated with increased adjusted odds of morbidities or mortality prior to hospital discharge.

Contributors Statement Page

Selin S. Everett conceptualized and designed the study, conducted analyses, drafted the initial manuscript, and critically reviewed and revised the manuscript.Dr. Thomas Hays conceptualized and designed the study, drafted the initial manuscript, and critically reviewed and revised the manuscript.Miles Bomback conceptualized and designed the study and critically reviewed and revised the manuscript.Drs. Veeral N. Tolia and Reese H. Clark coordinated and supervised data collection and critically reviewed and revised the manuscript.Dr. Rakesh Sahni conceptualized and designed the study and critically reviewed and revised the manuscript.Dr. Alex Lyford conducted analyses and critically reviewed and revised the manuscript. Dr. Ronald J. Wapner reviewed and critically revised the manuscript.All authors approved the final manuscript as submitted and agree to be accountable for all aspects of the work.

Exploring collaboration models between geneticists and intensivists for implementing rapid genome sequencing in critical care settings

The availability of rapid genome sequencing (rGS) for children in a critical-care setting is increasing. This study explored the perspectives of geneticists and intensivists on optimal collaboration and division of roles when implementing rGS in neonatal and pediatric intensive care units (ICUs). We conducted an explanatory mixed methods study involving a survey embedded within an interview with 13 genetics and intensive care providers. Interviews were recorded, transcribed, and coded. Geneticists endorsed higher confidence in performing a physical exam and interpreting/communicating positive results. Intensivists endorsed highest confidence in determining whether genetic testing was appropriate, communicating negative results, and consenting. Major qualitative themes that emerged were: (1) concerns with both "genetics-led" and "intensivist-led" models with workflows and sustainability (2) shift the role of determining rGS eligibility to ICU medical professionals, (3) continued role of geneticists to assess phenotype, and (4) include genetic counselors (GCs) and neonatal nurse practitioners to enhance workflow and care. All geneticists supported shifting decisions regarding eligibility for rGS to the ICU team to minimize time cost for the genetics workforce. Exploring models of geneticist-led phenotyping, intensivist-led phenotyping for some indications, and/or inclusion of a dedicated inpatient GC may help offset the time burden of consenting and other tasks associated with rGS.

The fundamental need for unifying phenotypes in sudden unexpected pediatric deaths

A definitive, authoritative approach to evaluate the causes of unexpected, and ultimately unexplained, pediatric deaths remains elusive, relegating final conclusions to diagnoses of exclusion in the vast majority of cases. Research into unexplained pediatric deaths has focused primarily on sudden infant deaths (under 1 year of age) and led to the identification of several potential, albeit incompletely understood, contributory factors: nonspecific pathology findings, associations with sleep position and environment that may not be uniformly relevant, and the elucidation of a role for serotonin that is practically difficult to estimate in any individual case. Any assessment of progress in this field must also acknowledge the failure of current approaches to substantially decrease mortality rates in decades. Furthermore, potential commonalities with pediatric deaths across a broader age spectrum have not been widely considered. Recent epilepsy-related observations and genetic findings, identified post-mortem in both infants and children who died suddenly and unexpectedly, suggest a role for more intense and specific phenotyping efforts as well as an expanded role for genetic and genomic evaluation. We therefore present a new approach to reframe the phenotype in sudden unexplained deaths in the pediatric age range, collapsing many distinctions based on arbitrary factors (such as age) that have previously guided research in this area, and discuss its implications for the future of postmortem investigation.

Diagnostic genomic sequencing in critically ill children

Rare genetic diseases are a major cause of severe illnesses and deaths in new-borns and infants. Disease manifestation in critically ill children may be atypical or incomplete, making a monogenetic disease difficult to diagnose clinically. Rapid exome or genome ("genomic") sequencing in critically ill children demonstrated profound diagnostic and clinical value, and there is growing evidence that the faster a molecular diagnosis is established in such children, the more likely clinical management is influenced positively. An early molecular diagnosis enables treatment of critically ill children with precision medicine, has the potential to improve patient outcome and leads to healthcare cost savings. In this review, we outline the status quo of rapid genomic sequencing and possible future implications.

Intensive Care Clinicians' Perspectives on Ethical Challenges Raised by Rapid Genomic Testing in Critically Ill Infants

Rapid genomic testing (rGT) enables genomic information to be available in a matter of hours, allowing it to be used in time-critical settings, such as intensive care units. Although rGT has been shown to improve diagnostic rates in a cost-effective manner, it raises ethical questions around a range of different areas, including obtaining consent and clinical decision-making. While some research has examined the perspectives of parents and genetics health professionals, the attitudes of intensive care clinicians remain under-explored. To address this gap, we administered an online survey to English-speaking neonatal/paediatric intensivists in Europe, Australasia and North America. We posed two ethical scenarios: one relating to obtaining consent from the parents and the second assessing decision-making regarding the provision of life-sustaining treatments. Descriptive statistics were used to analyse the data. We received 40 responses from 12 countries. About 50-75% of intensivists felt that explicit parental consent was necessary for rGT. About 68-95% felt that a diagnosis from rGT should affect the provision of life-sustaining care. Results were mediated by intensivists' level of experience. Our findings show divergent attitudes toward ethical issues generated by rGT among intensivists and suggest the need for guidance regarding ethical decision-making for rGT.

A holistic approach to maximise diagnostic output in trio exome sequencing

Introduction

Rare genetic diseases are a major cause for severe illness in children. Whole exome sequencing (WES) is a powerful tool for identifying genetic causes of rare diseases. For a better and faster assessment of the vast number of variants that are identified in the index patient in WES, parental sequencing can be applied ("trio WES").

Methods

We assessed the diagnostic rate of routine trio WES including analysis of copy number variants in 224 pediatric patients during an evaluation period of three years.

Results

Trio WES provided a diagnosis in 67 (30%) of all 224 analysed children. The turnaround time of trio WES analysis has been reduced significantly from 41 days in 2019 to 23 days in 2021. Copy number variants could be identified to be causative in 10 cases (4.5%), underlying the importance of copy number variant analysis. Variants in three genes which were previously not associated with a clinical condition (GAD1, TMEM222 and ZNFX1) were identified using the matching tool GeneMatcher and were part of the first description of a new syndrome.

Discussion

Trio WES has proven to have a high diagnostic yield and to shorten the process of identifying the correct diagnosis in paediatric patients. Re-evaluation of all 224 trio WES 1-3 years after initial analysis did not establish new diagnoses. Initiating (trio) WES as a first-tier diagnostics including copy number variant detection should be considered as early as possible, especially for children treated in ICU, if a monogenetic disease is suspected.