Design and Validation of a Custom NGS Panel Targeting a Set of Lysosomal Storage Diseases Candidate for NBS Applications

Detection of Single-Nucleotide and Copy Number Defects Underlying Hyperphenylalaninemia by Next-Generation Sequencing

Hyperphenylalaninemia (HPA) is the most common inherited amino acid metabolism disorder characterized by serious clinical manifestations, including irreversible brain damage, intellectual deficiency and epilepsy. Due to its extensive genic and allelic heterogeneity, next-generation sequencing (NGS) technology may help to identify the molecular basis of this genetic disease. Herein, we describe the development and validation of a targeted NGS (tNGS) approach for the simultaneous detection of single-nucleotide changes and copy number variations (CNVs) in genes associated with HPA (PAH, GCH1, PTS, QDPR, PCBD1, DNAJC12) or useful for its differential diagnosis (SPR). Our tNGS approach offers the possibility to detail, with a high accuracy and in a single workflow, the combined effect of a broader spectrum of genomic variants in a comprehensive view, providing a significant step forward in the development of optimized patient care and management.

Consensus clinical management guidelines for acid sphingomyelinase deficiency (Niemann-Pick disease types A, B and A/B)

BACKGROUND

Acid Sphingomyelinase Deficiency (ASMD) is a rare autosomal recessive disorder caused by mutations in the SMPD1 gene. This rarity contributes to misdiagnosis, delayed diagnosis and barriers to good care. There are no published national or international consensus guidelines for the diagnosis and management of patients with ASMD. For these reasons, we have developed clinical guidelines that defines standard of care for ASMD patients.

METHODS

The information contained in these guidelines was obtained through a systematic literature review and the experiences of the authors in their care of patients with ASMD. We adopted the Appraisal of Guidelines for Research and Evaluation (AGREE II) system as method of choice for the guideline development process.

RESULTS

The clinical spectrum of ASMD, although a continuum, varies substantially with subtypes ranging from a fatal infantile neurovisceral disorder to an adult-onset chronic visceral disease. We produced 39 conclusive statements and scored them according to level of evidence, strengths of recommendations and expert opinions. In addition, these guidelines have identified knowledge gaps that must be filled by future research.

CONCLUSION

These guidelines can inform care providers, care funders, patients and their carers about best clinical practice and leads to a step change in the quality of care for patients with ASMD with or without enzyme replacement therapy (ERT).

Pompe disease ascertained through The Lantern Project, 2018-2021: Next-generation sequencing and enzymatic testing to overcome obstacles to diagnosis

The Lantern Project is an ongoing complimentary diagnostic program for patients in the United States sponsored by Sanofi and implemented by PerkinElmer Genomics. It combines specific enzymatic, biomarker, and genetic testing to facilitate rapid, accurate laboratory diagnosis of Pompe disease and several other lysosomal storage diseases, and a multigene next-generation sequencing panel including Pompe disease, LGMD, and other neuromuscular disorders. This article reports data for Pompe disease collected from October 2018 through December 2021, including acid α-glucosidase (GAA) enzyme assay and GAA sequencing (standard or expedited for positive newborn screening [NBS] to rule out infantile-onset Pompe disease [IOPD]) and the Focused Neuromuscular Panel, which includes GAA. One hundred forty patients (12 received only GAA enzyme testing, 128 had GAA sequencing alone or in addition to enzyme assay) have been confirmed with Pompe disease in this project. Eight of the 140 had a variant of unknown significance, but GAA activity ≤2.10 μmol/L/h, thus were confirmed with Pompe disease. Three diagnosed patients 0-2 years old had cross-reactive immunologic material (CRIM)-negative GAA variants and thus IOPD. One additional infant with presumptive IOPD had a homozygous frameshift c.1846del, likely CRIM-negative; symptoms were not provided. Among the 128 patients with molecular results, the c.-32-13T>G splice variant was homozygous in 11, compound-heterozygous in 98, and absent in 19. Proximal muscle weakness (58 patients) was the most common sign reported at testing; elevated creatine kinase (29 patients) was the most common laboratory result. The most common symptom categories were muscular (73 patients), musculoskeletal (13 patients), and respiratory (23 patients). Clinical information was not available for 42 samples, and 17 infants had only "abnormal NBS" or "low GAA" reported. Cardiac symptoms in 7 included potentially age-related conditions in five c.-32-13T>G-compound-heterozygous adults (myocardial infarction, heart murmur/palpitations, congestive heart failure: 1 each; 2 with atrial fibrillation) and hypertrophic cardiomyopathy in 2 children (1 and 2 years old) with presumptive IOPD. One novel GAA variant was observed in a patient with enzyme activity 0.31 μmol/L/h: c.1853_1854ins49, a frameshift pathogenic variant. The Lantern Project demonstrates the combinatorial utility of enzyme assay, targeted single-gene testing, and a focused neuromuscular next-generation sequencing panel in diagnosing Pompe disease.

The modern face of newborn screening

Newborn screening (NBS) has been developed for years to identify newborns with severe but treatable conditions. Taiwan's NBS system, after the initial setup for a total coverage of newborns in 1990s, was later optimized to ensure the timely return of results in infants with abnormal results. Advancements in techniques such as Tandem mass spectrometry enable the screening into a multiplex format and increase the conditions to be screened. Furthermore, advances in therapies, such as enzyme replacement therapy, stem cell transplantation, and gene therapy, significantly expand the needs for newborn screening. Advances in genomics and biomarkers discovery improve the test accuracy with the assistance of second-tier tests, and have the potential to be the first-tier test in the future. Therefore, challenge of NBS now is the knowledge gap, including the evidence of the long-term clinical benefits in large cohorts especially in conditions with new therapies, phenotypic variations and the corresponding management of some screened diseases, and cost-effectiveness of extended NBS programs. A short-term and a long-term follow-up program should be implemented to gather those outcomes better especially in the genomic era. Ethical and psychosocial issues are also potentially encountered frequently. Essential education and better informed consent should be considered fundamental to parallel those new tests into future NBS.

Detection of Structural Variants by NGS: Revealing Missing Alleles in Lysosomal Storage Diseases

Lysosomal storage diseases (LSDs) are a heterogeneous group of rare multisystem metabolic disorders occurring mostly in infancy and childhood, characterized by a gradual accumulation of non-degraded substrates inside the cells. Although biochemical enzymatic assays are considered the gold standard for diagnosis of symptomatic patients, genotyping is a requirement for inclusion in enzyme replacement programs and is a prerequisite for carrier tests in relatives and DNA-based prenatal diagnosis. The emerging next-generation sequencing (NGS) technologies are now offering a powerful diagnostic tool for genotyping LSDs patients by providing faster, cheaper, and higher-resolution testing options, and are allowing to unravel, in a single integrated workflow SNVs, small insertions and deletions (indels), as well as major structural variations (SVs) responsible for the pathology. Here, we summarize the current knowledge about the most recurrent and private SVs involving LSDs-related genes, review advantages and drawbacks related to the use of the NGS in the SVs detection, and discuss the challenges to bring this type of analysis in clinical diagnostics.

Second-tier strategies in newborn screening - potential and limitations

Newborn screening (NBS) is a public health measure to identify children with treatable disorders within the first days of life allowing presymptomatic treatment. It is the most successful measure of secondary medical prevention and part of public health programs in many countries worldwide. Application of second-tier strategies in NBS allows for increased specificity and consecutively a higher positive predictive value. Second-tier strategies can include analysis of specific biomarkers for a target disorder or may be based on molecular genetic analyses. Improving the quality of NBS, for example by second-tier strategies, is of utmost importance to maintain the high acceptance of NBS by families - especially as an increasing number of target disorders is being consecutively included into NBS programs.

The Utility of Genomic Testing for Hyperphenylalaninemia

Hyperphenylalaninemia (HPA), the most common amino acid metabolism disorder, is caused by defects in enzymes involved in phenylalanine metabolism, with the consequent accumulation of phenylalanine and its secondary metabolites in body fluids and tissues. Clinical manifestations of HPA include mental retardation, and its early diagnosis with timely treatment can improve the prognosis of affected patients. Due to the genetic complexity and heterogeneity of HPA, high-throughput molecular technologies, such as next-generation sequencing (NGS), are becoming indispensable tools to fully characterize the etiology, helping clinicians to promptly identify the exact patients’ genotype and determine the appropriate treatment. In this review, after a brief overview of the key enzymes involved in phenylalanine metabolism, we represent the wide spectrum of genes and their variants associated with HPA and discuss the utility of genomic testing for improved diagnosis and clinical management of HPA.

A cartridge-based device for automated analyses of solid matrices by online sample prep-capillary LC-MS/MS

Sample preparation is an essential step focused on eliminating interfering compounds while pre-concentrating the analytes. However, its multiple steps are laborious, time-consuming, and a source of errors. Currently, automated approaches represent a promising alternative to overcome these drawbacks. Similarly, miniaturisation has been considered an ideal strategy for creating greener analytical workflows. The combination of these concepts is currently highly desired by analytical chemists. However, most automated and miniaturised sample preparation techniques are primarily concerned with liquid samples, while solids are frequently overlooked. We present an approach based on a cartridge packed with solids (soil samples) coupled with a capillary LC-MS, combining sample preparation and analytical steps into a unique platform. As a proof-of-concept, nine pesticides used in sugarcane crops were extracted and analysed by our proposed method. For optimisation, a fractional factorial design (2^5-1) was performed with the following variables: aqueous dilution of the sample (V₁), extraction strength (V₂), matrix washing time (V₃), extraction flow (V₄), and analytical flow (V₅). After, the most influential ones (V₁, V₂, and V₃) were taken into a central composite design (2³) to select their best values. Under optimised conditions, the method reported linear ranges between 10 and 125 ng g^-1 with R² > 0.985. Accuracy and precision were in accordance with the values established by the International Council for Harmonisation (Q2(R1)). Therefore, the proposed approach was effective in extracting and analysing selected pesticides in soil samples. Also, we carried out initial qualitative tests for pesticides in honeybees to see if there is the possibility to apply our method in other solids.

A Comprehensive, Targeted NGS Approach to Assessing Molecular Diagnosis of Lysosomal Storage Diseases

With over 60 different disorders and a combined incidence occurring in 1:5000-7000 live births, lysosomal storage diseases (LSDs) represent a major public health problem and constitute an enormous burden for affected individuals and their families. Several reasons make the diagnosis of LSDs an arduous task for clinicians, including the phenotype and penetrance variability, the shared signs and symptoms, and the uncertainties related to biochemical enzymatic assay results. Developing a powerful diagnostic tool based on next generation sequencing (NGS) technology may help reduce the delayed diagnostic process for these families, leading to better outcomes for current therapies and providing the basis for more appropriate genetic counseling. Herein, we employed a targeted NGS-based panel to scan the coding regions of 65 LSD-causative genes. A reference group sample (n = 26) with previously known genetic mutations was used to test and validate the entire workflow. Our approach demonstrated elevated analytical accuracy, sensitivity, and specificity. We believe the adoption of comprehensive targeted sequencing strategies into a routine diagnostic route may accelerate both the identification and management of LSDs with overlapping clinical profiles, producing a significant reduction in delayed diagnostic response with beneficial results in the treatment outcome.