Massively Parallel Sequencing: Successes, Limitations and the Future for Inborn Errors of Metabolism

Inborn errors of metabolism (IEM) are a diverse group of inherited diseases from a presentation, natural history and diagnostic perspective [1]. They remain one of the few groups of primary genetic diseases where treatment options are available and established. The management of IEM varies based on the associated dysfunctional metabolic pathway, and central to the management of IEM is multi-disciplinary team care. Amongst others, this includes medical, nursing, dietetics, social work and genetic counselling [2].

Common presentations of IEM include acute small molecule intoxication, multi-system malformation disorders [3], global developmental delay and developmental regression [2]. Given the broad nature of these disorders, the expansion of genomics with massively parallel sequencing (MPS) has revolutionised some aspects of IEM investigation and management [4] with the highest yield applying to multi-system malformation or complex molecule disorders. The most notable of these is the investigation of mitochondrial respiratory chain (MRC) defects. For these disorders, MPS has become the first-line clinical and health economic approach and has almost made the use of invasive tissue biopsies redundant [5, 6]. The clinical presentations of MRC defects are heterogeneous but commonly include global developmental delay, developmental regression, cardiomyopathy, lactic acidosis, liver failure or facial dysmorphism [7], many of which may be first referred for general paediatric review.

Genomics with MPS includes exome sequencing (ES) and whole genome sequencing (WGS). ES is limited to exonic (protein-coding) information but is cheaper and faster to perform. WGS is more sensitive with full genome coverage, including coding and non-coding information, but is more costly, slower and can result in more challenging data interpretation with respect to relevant findings [7]. In Australia, ES is currently more accessible than WGS, but WGS is increasingly utilised overseas [6].

Through a series of cases, we aim to describe how MPS is influencing the diagnosis and management of IEM, including successes, limitations and looking to the future.

MPS has revolutionised the diagnostic yield in some areas of paediatric care and reduced the diagnostic odyssey for many families, particularly those presenting with multi-system disorders [7]. Should families wish to pursue this, a genetic diagnosis can provide clarity, optimise management through established evidence, allow families to connect with support/family groups and provide timely reproductive planning information [8]. Dignity in a diagnosis is an important factor for families, as is reproductive confidence. The turnaround time for MPS has considerably improved, and options such as rapid and ultra-rapid ES have become more accessible in Australia. This has reduced the turnaround time to, in some cases, as fast as 2–5 days, opening early diagnostic possibilities in the appropriate setting [9].

As a result of reduced cost and improved technology, there has been rapid expansion in accessing MPS in general paediatric clinical practice. In Australia, in consultation with a clinical geneticist, a Medicare Benefits Schedule (MBS) item number for trio (parents and child) WGS or ES with mitochondrial DNA sequencing is now available to specialist paediatricians for paediatric patients younger than 11 years with multi-system disease and/or moderate to severe global developmental delay or intellectual disability [8]. An MBS item number is also available for suspected mitochondrial disease through WGS or ES and mitochondrial DNA sequencing.

The expansion of MPS into general paediatric care highlights the critical need for the integration of genetic counsellors into the paediatric multi-disciplinary care team [8, 10], as the expertise and understanding of the broader implications for families with a new genetic diagnosis is critical [11]. Genetic counsellors bring a deep understanding of the broader implications for families receiving a new genetic diagnosis, and their role is pivotal in facilitating comprehensive discussions regarding reproductive planning options [10]. This is arguably the area with the greatest impact after a new genetic diagnosis in a family. Reproductive planning options might include preimplantation genetic testing or targeted invasive testing of subsequent pregnancies. This may influence pregnancy management or provide an antenatal genetic diagnosis, which allows for preparation for an appropriate delivery environment or potential postnatal complications for an affected newborn [12, 13].

This is described in Section 2.1.

Despite the potential for improvement in diagnostic capabilities, the role of rapid MPS is limited in some IEM. This is most apparent in acute small molecule intoxication disorders, such as urea cycle disorders and organic acidurias, where metabolic biochemical investigations provide the most rapid diagnosis [4]. Management needs to be instigated well prior to even the speediest of genetic testing results. In these disorders, point-of-care metabolic investigations remain critical in providing fast and accurate diagnoses, which facilitate urgent management. These investigations might include venous blood gas, plasma amino acids, plasma acylcarnitine profile, plasma ammonia level and a urine metabolic screen including organic acids and amino acids.

MPS comes with its own inherent limitations, including current genetic understanding or knowledge and the identification of inconclusive findings such as variants of uncertain significance (VUS) [7]. Caution should be advised as medical teams and families may place additional weight on MPS results in the hope of finding a clear cause of a presentation, which may ultimately yield a negative or inconclusive result [8]. This may delay important and timely clinical management decisions. Additionally, a clear genetic diagnosis should not solely influence the offering of an acute intervention, making deferral of management decisions unnecessary whilst awaiting genetic testing results [14]. It is critical that families are aware of these limitations through the consent process before genetic testing is requested [8]. Genetic counsellors hold key skills in these areas [11, 15]. This is described in Section 3.1.

In summary, the expansion of MPS has revolutionised many parts of paediatric practice and will continue to play a key role in diagnosis in IEM, but is limited in some settings, such as in acute small molecule intoxication. Diagnosis of IEM includes a combination of clinical, phenotypic, biochemical and genetic information with a ‘multi-omics’ diagnostic approach complementing genomic findings and providing unique diagnostic information [7]. In this expanding use of MPS, remaining cognisant of limitations is important, including possible inconclusive and negative results [8]. This highlights the value of having genetic counsellors embedded into the relevant multi-disciplinary team, especially as a substantial benefit of MPS in IEM is the potential utility for reproductive planning [10].

IEM are the main beneficiaries of newborn screening, and the translation of gNBS has the potential to augment the clinical utility of current screening [29]. Care and consultation with key stakeholders, health services and patient groups are needed to delineate what is a genuinely treatable disorder for gNBS targets and to ensure due consideration of the relevant ethical implications of gNBS [14, 21]. Most importantly, the key focus for the future of IEM will be in access and equitable expansion of preconception reproductive carrier screening.

The authors declare no conflicts of interest.