Expanding the Australian Newborn Blood Spot Screening Program using genomic sequencing: do we want it and are we ready?

Effect of newborn genomic screening for lysosomal storage disorders: a cohort study in China

BACKGROUND

Lysosomal storage disorders (LSDs) have a relatively high incidence among rare diseases and can lead to severe consequences if not treated promptly. However, many countries and regions have not included these disorders in their newborn screening programs, resulting in missed early detection, underdiagnosis, and delayed treatment. Newborn genomic screening (NBGS) has shown good screening effectiveness for traditional biochemical screening diseases; however, its effectiveness for LSDs has not yet been evaluated in the general newborn population.

METHODS

To evaluate the outcome of NBGS for LSDs, a cohort study was conducted involving newborns recruited from Nanjing Women and Children's Healthcare Hospital in China from March 18, 2022, to September 21, 2023. All participants underwent NBGS of 15 LSDs (18 genes) via dried blood spots, followed by enzyme activity testing for NBGS-positive individuals. The study calculated the incidence and carrier rates for each LSD though NBGS, as well as the positive screening rate, the false positive rate and the positive predictive value of the screening process.

RESULTS

Among 22,687 newborns (11,996 males [52.88%]), 1344 (6.0%) were identified as carriers, and 30 (0.13%) were initially positive for LSDs. Of these, 4 were excluded, 15 were diagnosed as LSD-presymptomatic individuals based on enzyme deficiency and pathogenic variants conforming to inheritance patterns, and 11 remain under follow-up. The estimated combined birth incidence of LSDs in Nanjing was 1/1512, primarily including Fabry disease, Krabbe disease, glycogen storage disease type II, Niemann-Pick disease, and mucopolysaccharidosis type II. Rather than directly comparing NBGS and enzyme activity screening, this study evaluated two sequential screening strategies: (1) NBGS-first with reflex enzyme testing and (2) enzyme activity-first with reflex genomic testing. The NBGS-first strategy demonstrated higher sensitivity and specificity, with a significantly lower false positive rate and higher positive predictive values compared to the enzyme-first strategy (P < 0.05).

CONCLUSIONS

This study highlights the potential of NBGS to enhance early detection of presymptomatic LSD individuals, enabling timely interventions and improving newborn health outcomes. Integrating NBGS into routine newborn screening programs could provide an effective and proactive approach for LSD identification and management.

Diagnostic yield of cystic fibrosis from a South Australian monocentric cohort: a retrospective study

OBJECTIVES

To determine the diagnostic yield of cystic fibrosis (CF) using a two-tiered genetic testing approach. Although newborn screening includes CF, this typically only covers a selection of common genetic variants, and with over 2000 reported in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, we hypothesised that patients will be missed and present clinically later in life.

DESIGN

A retrospective study over a 5-year period (January 2018-December 2022).

SETTING

A single pathology service in South Australia.

PARTICIPANTS

A total of 1909 CF test referrals from patients with clinical suspicion indicated by respiratory and gastrointestinal manifestations, foetal echogenic bowel and male infertility and asymptomatic CF requests for reproductive carrier screening.

PRIMARY AND SECONDARY OUTCOME MEASURES

The number and type of CFTR gene variants detected in symptomatic and asymptomatic testing referrals.

RESULTS

A total of 25 patients were diagnosed with CF or CF-related disorders (2.5%) with gastrointestinal symptoms yielding the highest diagnostic rate of 4.4%. Additionally, a total of 79 carriers (4.1%) were identified uncovering a carrier frequency of 1 in 24, which is consistent with the 1 in 25 reported in the Caucasian population. CF was found to be causative of foetal echogenic bowel in 0.83% of cases.

CONCLUSIONS

This study highlights the importance of considering CF in symptomatic patients, even in a nation with >99% of newborns screened for CF. Additionally, the identification of CF in this population supports the recommendation for CF genetic testing in reproductive healthcare.

Prequalification of genome-based newborn screening for severe childhood genetic diseases through federated training based on purifying hyperselection

Genome-sequence-based newborn screening (gNBS) has substantial potential to improve outcomes in hundreds of severe childhood genetic disorders (SCGDs). However, a major impediment to gNBS is imprecision due to variants classified as pathogenic (P) or likely pathogenic (LP) that are not SCGD causal. gNBS with 53,855 P/LP variants, 342 genes, 412 SCGDs, and 1,603 therapies was positive in 74% of UK Biobank (UKB470K) adults, suggesting 97% false positives. We used the phenomenon of purifying hyperselection, which acts to decrease the frequency of SCGD causal diplotypes, to reduce false positives. Training of gene-disease-inheritance mode-diplotype tetrads in 618,290 control and affected subjects identified 293 variants or haplotypes and seven genes with variable inheritance contributing higher positive diplotype counts than consistent with purifying hyperselection and with little or no evidence of SCGD causality. With these changes, 2.0% of UKB470K adults were positive. In contrast, gNBS was positive in 7.2% of 3,118 critically ill children with suspected SCGDs and 7.9% of 705 infant deaths. When compared with rapid diagnostic genome sequencing (RDGS), gNBS had 99.1% recall. In eight true-positive children, gNBS was projected to decrease time to diagnosis by a median of 121 days and avoid life-threatening disease presentations in four children, organ damage in six children, ∼$1.25 million in healthcare cost, and ten (1.4%) infant deaths. Federated training predicated on purifying hyperselection provides a general framework to attain high precision in population screening. Federated training across many biobanks and clinical trials can provide a privacy-preserving mechanism for qualification of gNBS in diverse genetic ancestries.

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.

Key informant perspectives on implementing genomic newborn screening: a qualitative study guided by the Action, Actor, Context, Target, Time framework

Newborn screening (NBS) programmes are highly successful, trusted, public health interventions. Genomic sequencing offers the opportunity to increase the benefits of NBS by screening infants for a greater number and variety of childhood-onset conditions. This study aimed to describe who needs to do what, when, and for whom to deliver genomic newborn screening (gNBS) and capture perceived implementation barriers and enablers. 'Key informants' (individuals involved in the delivery of NBS) were interviewed. The Actor, Action, Context, Time and Target framework guided data collection and analysis. Participants (N = 20) identified new Actions required to deliver gNBS (educating healthcare providers, longitudinal psychosocial support), NBS Actions needing modification (obtaining consent) and NBS Actions that could be adopted for gNBS (prompt referral pathways). Obtaining consent in a prenatal Context was a source of some disagreement. The Time to disclose high chance results was raised as a key consideration in gNBS programme design. Genetic counsellors were identified as key Actors in results management, but workforce limitations may be a barrier. Online decision support tools were an enabler to offering gNBS. The implementation of gNBS will require behaviour changes from HCPs delivering NBS. Findings can inform how to deliver gNBS at population-scale.

Protocol for the Australian Type 1 Diabetes National Screening Pilot: Assessing the feasibility and acceptability of three general population screening models in children

AIM

One third of Australian children diagnosed with type 1 diabetes present with life-threatening diabetic ketoacidosis (DKA) at diagnosis. Screening for early-stage, presymptomatic type 1 diabetes, with ongoing follow-up, can substantially reduce this risk (<5% risk). Several screening models are being trialled internationally, without consensus on the optimal approach. This pilot study aims to assess three models for a routine, population-wide screening programme in Australia.

METHODS

An implementation science-guided pilot study to evaluate the feasibility, acceptability and costs of three screening models in children will be conducted between July 2022 and June 2024. These models are as follows: (1) Genetic risk-stratified screening using newborn heel prick dried bloodspots, followed by autoantibody testing from 11 months of age; (2) genetic risk-stratified screening of infant (6-12 months) saliva followed by autoantibody testing from 10 months of age; and (3) autoantibody screening using capillary dried bloodspots collected from children aged 2, 6 or 10 years. Cohorts for each model will be recruited from targeted geographic areas across Australia involving ≥2 states per cohort, with a recruitment target of up to 3000 children per cohort (total up to 9000 children). The primary outcome is screening uptake for each cohort. Secondary outcomes include programme feasibility, costs, parental anxiety, risk perception, satisfaction, well-being and quality of life, and health professional attitudes and satisfaction.

CONCLUSIONS

This pilot is the first direct comparison of three screening implementation models for general population screening. Findings will provide evidence to inform a potential national screening programme for Australian children.

TRIAL REGISTRATION

ACTRN12622000381785.

Newborn Genomic Sequencing Needs Confirmation but Not Repeating

Newborn screening (NBS) has been one of the big innovations in public health. It has grown over the decades, especially with the introduction of tandem mass spectrometry. However, it is likely to expand significantly in the coming decades with the introduction of genomic testing. Traditionally, in NBS, there has been a pattern of repeat testing for confirmation and follow-up diagnostic testing. This follow-up is critical as NBS is a screening program. This pathway is appropriate for low-cost tests, but if public health authorities are going to invest in high-cost screening such as whole-genome sequencing, they are likely to baulk at repeating these expensive tests in a diagnostic setting. Our study investigates whether screening-grade data from NBS can be transitioned into diagnostic-grade data using a panel of single-nucleotide variants (SNVs) on a diagnostic specimen. These SNVs could be used to link the diagnostic specimen with all of the provenance requirements associated with routine pathology and the NBS genomic data. This strategy has large cost benefits and opens up the rapid use of NBS genomic data should a child present in an acute care setting and a genetic diagnosis is suspected. This approach will greatly speed up the confirmation of positive NBS results and reduce family anxiety due to delayed diagnostic testing.

Co-Creating the Experience of Consent for Newborn Genome Sequencing: The Generation Study

INTRODUCTION

The Generation Study (GS) aims to recruit 100,000 newborns in England to evaluate the utility and feasibility of using whole genome sequencing to screen for rare conditions that can be treated in early childhood; enable wider research to support further discovery in genomics and health; and explore the potential of storing an individual's genome over their lifetime. The GS incorporates complexities of consent in newborn screening, genomic medicine, and healthcare research, and there is a gap in exploring how to implement existing recommendations. Participant involvement has been shown to improve the implementation of processes and materials in healthcare. This paper describes how the GS team leveraged this through Design Research (DR) methodologies to develop the GS consent experience.

METHODS

Over a 2-year period, 9 rounds of DR were undertaken with expectant and recent parents and a chosen partner (n = 105). Each round consisted of semi-structured interviews and a range of co-design and usability testing activities.

RESULTS

DR activities highlighted areas for consideration for consent materials and processes. We describe common barriers and enablers across three stages of consent: awareness, consideration, and making an informed decision. As well as ensuring participants fully understand pros and cons of taking part, materials should consider pre-existing assumptions or misconceptions which may discourage parents from learning about the GS.

CONCLUSION

Involving parents in co-creation has broadened the perspective of what constitutes informed decision-making for newborn genome sequencing. Iterative rounds of research and design can provide tangible paths forward, supporting the successful implementation of informed decision-making.

Perceptions of genomic newborn screening: a cross-sectional survey conducted with UK medical students

BACKGROUND

With the potential to identify a vast number of rare diseases soon after birth, genomic newborn screening (gNBS) could facilitate earlier interventions and improve health outcomes. Designing a gNBS programme will involve balancing stakeholders' opinions and addressing concerns. The views of medical students-future clinicians who would deliver gNBS-have not yet been explored.

METHODS

We conducted a nationwide online survey of UK medical students via the REDCap platform. Perceptions of gNBS, including scope of testing and potential benefits and drawbacks, were explored using a mix of multiple-choice questions, Likert scales, visual analogue scales and free-text questions.

RESULTS

In total, 116 medical students across 16 universities participated. Overall, 45% supported gNBS, with a positively skewed mean support score of 3.24 (SD 1.26, range: 1.0-5.0), and 55% felt it relevant to their future practice. Almost all agreed that infant-onset and childhood-onset diseases and conditions with effective treatments should be included. Most felt that earlier interventions and personalised care would be the most important benefit of gNBS. Other perceived benefits included earlier diagnoses, diagnosing more patients and enabling research for new treatments. However, several perceived challenges were highlighted: risk of genomic discrimination, incidental or uncertain findings, data security and breaching children's future autonomy. Students expressed conflicting opinions on the psychological impact on families, but most were concerned about a lack of support due to current resource limitations in health services. Students frequently reported having insufficient knowledge to form an opinion, which may reflect gaps in genomics education at medical school and the current lack of evidence base for gNBS.

CONCLUSION

Although some support for gNBS was demonstrated, ethicolegal and social challenges were raised, emphasising a need for ongoing discussions about the implications of gNBS.

Genetic counselors' perspectives on genomic screening of apparently healthy newborns in the United States

Purpose

There is growing international interest in using genomic sequencing to screen newborns and children for treatable genomic conditions. Although recent research has demonstrated increasing support for using genomic sequencing to screen newborns and children for treatable genomic conditions among various stakeholders, little is known about the perspectives of genetic counselors (GCs) in the United States, who are frequently engaged in the disclosure of positive newborn screening results and coordination of follow-up testing and management.

Methods

This study utilized a cross-sectional 3-section survey to explore GCs' perspectives on the benefits, limitations, and ethical and practical considerations of genomic sequencing in newborns as an adjunct screen to standard newborn screening (NBS). Additionally, we evaluated GCs' views on specific genes that could be added to NBS via sequencing.

Results

Of 176 GCs who participated in the study, most endorsed the addition of NBSeq for conditions that typically manifest in childhood and have a well-defined treatment or management protocol. Some perspectives, such as attitudes toward health inequity, varied by practice region. Most respondents endorsed 13 of 25 specific genetic conditions for inclusion in NBSeq.

Conclusion

Our findings demonstrate GCs' support for the expansion of NBS using genomic sequencing in the United States and the need for ongoing investigation of ethical and practical concerns related to its implementation.

Newborn Screening: Current Practice and Our Journey over the Last 60 Years

BACKGROUND

Inborn errors of metabolism comprise a set of more than 2000 known disorders which can result in significant morbidity and may be rapidly fatal. Diagnosing these disorders at birth and treating immediately, however, may often result in a normal to near-normal life for the affected infant. Thus, newborn screening (NBS) has saved or improved the lives of countless individuals since its inception in the 1960s.

CONTENT

This review covers NBS, from its early beginnings up to the current day practice. We follow the evolution of NBS, as well as describe the need and how disorders are added to NBS programs, the testing and how its performance is monitored, and the follow-up to the testing. We also briefly touch on NBS outside the United States.

SUMMARY

Newborn screening in the United States is a major public health success story and it continues to grow and evolve to cover more disorders and utilize new technological advances.

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.

Current Status of Newborn Bloodspot Screening Worldwide 2024: A Comprehensive Review of Recent Activities (2020-2023)

Newborn bloodspot screening (NBS) began in the early 1960s based on the work of Dr. Robert "Bob" Guthrie in Buffalo, NY, USA. His development of a screening test for phenylketonuria on blood absorbed onto a special filter paper and transported to a remote testing laboratory began it all. Expansion of NBS to large numbers of asymptomatic congenital conditions flourishes in many settings while it has not yet been realized in others. The need for NBS as an efficient and effective public health prevention strategy that contributes to lowered morbidity and mortality wherever it is sustained is well known in the medical field but not necessarily by political policy makers. Acknowledging the value of national NBS reports published in 2007, the authors collaborated to create a worldwide NBS update in 2015. In a continuing attempt to review the progress of NBS globally, and to move towards a more harmonized and equitable screening system, we have updated our 2015 report with information available at the beginning of 2024. Reports on sub-Saharan Africa and the Caribbean, missing in 2015, have been included. Tables popular in the previous report have been updated with an eye towards harmonized comparisons. To emphasize areas needing attention globally, we have used regional tables containing similar listings of conditions screened, numbers of screening laboratories, and time at which specimen collection is recommended. Discussions are limited to bloodspot screening.

'Integrating Ethics and Equity with Economics and Effectiveness for newborn screening in the genomic age: A qualitative study protocol of stakeholder perspectives

BACKGROUND

Newborn bloodspot screening is a well-established population health initiative that detects serious, childhood-onset, treatable conditions to improve health outcomes. With genomic technologies advancing rapidly, many countries are actively discussing the introduction of genomic assays into newborn screening programs. While adding genomic testing to Australia's newborn screening program could improve outcomes for infants and families, it must be considered against potential harms, ethical, legal, equity and social implications, and economic and health system impacts. We must ask not only 'can' we use genomics to screen newborns?' but 'should we'?' and 'how much should health systems invest in genomic newborn screening?'.

METHODS

This study will use qualitative methods to explore understanding, priorities, concerns and expectations of genomic newborn screening among parents/carers, health professionals/scientists, and health policy makers across Australia. In-depth, semi-structured interviews will be held with 30-40 parents/carers recruited via hospital and community settings, 15-20 health professionals/scientists, and 10-15 health policy makers. Data will be analysed using inductive content analysis. The Sydney Children's Hospital Network Human Research Ethics Committee approved this study protocol [2023/ETH02371]. The Standards for Reporting Qualitative Research will guide study planning, conduct and reporting.

DISCUSSION

Few studies have engaged a diverse range of stakeholders to explore the implications of genomics in newborn screening in a culturally and genetically diverse population, nor in a health system underpinned by universal health care. As the first study within a multi-part research program, findings will be used to generate new knowledge on the risks and benefits and importance of ethical, legal, social and equity implications of genomic newborn screening from the perspective of key stakeholders. As such it will be the foundation on which child and family centered criteria can be developed to inform health technology assessments and drive efficient and effective policy decision-making on the implementation of genomics in newborn screening.

Evaluating a Novel Newborn Screening Methodology: Combined Genetic and Biochemical Screenings

PURPOSE

Analysis of four newborn screening modes using newborn genomic sequencing (nGS) and traditional biochemical screening (TBS).

METHODS

Prospective clinical study with a total of 1,012 newborn samples from retrospective TBS. Three independent groups performed the study under strict double-blind conditions according to the screening modes: independent biochemical (IBS), independent NeoSeq (INS), sequential (SS), and combined (CS) screening. Using targeted sequencing, the NeoSeq panel included 154 pathogenic genes covering 86 diseases.

RESULTS

Of the 1,012 newborns, 120 were diagnosed were diagnosed with genetic diseases Among them, 52 cases were within the scope of TBS and 68 additional cases were identified through nGS. The number of cases detected per screening mode was 50, 113, 56, and 119 for IBS, INS, SS, and CS, respectively. CS was the most satisfactory screening mode, with the detection rate of 99.17%, the specificity and positive predictive value of 100%, and the negative predictive value of 99.89%. In addition, of the 68 cases identified by nGS (96 variants in 31 pathogenic genes), only four participants (5.9%) had clinical manifestations consistent with the disease. The experimental reporting cycles of CS and INS were the shortest.

CONCLUSIONS

CS was the most satisfactory method for newborn screening, which combined nGS with TBS to improve early diagnosis.

Australian Public Perspectives on Genomic Newborn Screening: Risks, Benefits, and Preferences for Implementation

Recent dramatic reductions in the timeframe in which genomic sequencing can deliver results means its application in time-sensitive screening programs such as newborn screening (NBS) is becoming a reality. As genomic NBS (gNBS) programs are developed around the world, there is an increasing need to address the ethical and social issues that such initiatives raise. This study therefore aimed to explore the Australian public's perspectives and values regarding key gNBS characteristics and preferences for service delivery. We recruited English-speaking members of the Australian public over 18 years of age via social media; 75 people aged 23-72 participated in 1 of 15 focus groups. Participants were generally supportive of introducing genomic sequencing into newborn screening, with several stating that the adoption of such revolutionary and beneficial technology was a moral obligation. Participants consistently highlighted receiving an early diagnosis as the leading benefit, which was frequently linked to the potential for early treatment and intervention, or access to other forms of assistance, such as peer support. Informing parents about the test during pregnancy was considered important. This study provides insights into the Australian public's views and preferences to inform the delivery of a gNBS program in the Australian context.

Australian parental perceptions of genomic newborn screening for non-communicable diseases

Background: Newborn bloodspot screening (NBS) programs have improved neonatal healthcare since the 1960s. Genomic sequencing now offers potential to generate polygenic risk score (PRS) that could be incorporated into NBS programs, shifting the focus from treatment to prevention of future noncommunicable disease (NCD). However, Australian parents' knowledge and attitudes regarding PRS for NBS is currently unknown. Methods: Parents with at least one Australian-born child under 18 years were invited via social media platforms to complete an online questionnaire aimed at examining parents' knowledge of NCDs, PRS, and precision medicine, their opinions on receiving PRS for their child, and considerations of early-intervention strategies to prevent the onset of disease. Results: Of 126 participants, 90.5% had heard the term "non-communicable disease or chronic condition," but only 31.8% and 34.4% were aware of the terms "polygenic risk score" and "precision medicine" respectively. A large proportion of participants said they would consider screening their newborn to receive a PRS for allergies (77.9%), asthma (81.0%), cancer (64.8%), cardiovascular disease (65.7%), mental illness (56.7%), obesity (49.5%), and type 2 diabetes (66.7%). Additionally, participants would primarily consider diet and exercise as interventions for specific NCDs. Discussion: The results from this study will inform future policy for genomic NBS, including expected rate of uptake and interventions that parents would consider employing to prevent the onset of disease.