New Ratios for Performance Improvement for Identifying Acyl-CoA Dehydrogenase Deficiencies in Expanded Newborn Screening: A Retrospective Study

Newborn screening follow-up for very long-chain acyl-CoA dehydrogenase deficiency in Colorado: Working towards a standardized protocol

Very long chain acyl-CoA dehydrogenase deficiency (VLCADD) is an autosomal recessive fatty acid β-oxidation disorder that has been identified by newborn screening (NBS) in most states since the early 2000s. Despite over 20 years of experience, there are aspects of VLCADD NBS that remain challenging. We conducted a retrospective chart review of abnormal NBS for VLCADD in Colorado between 2017 and 2023. We analyzed confirmatory plasma acylcarnitine profiles (P-ACP), genetic sequencing of ACADVL, Collaborative Laboratory Integrated Reports (CLIR) scores, patient enzyme analysis of VLCAD, and cell-based variant expression analysis. A real-world "Clinical Designation" was then compared to a variety of algorithms trialed on the data. Of the 67 infants with abnormal screens during this timeframe, 5 (7 %) had a Clinical Designation of affected, 4 (6 %) remained unclassified, and 58 (87 %) were discharged based on a designation of unaffected. A Kruskal-Wallis rank sum test showed the biomarker with the best discrimination between affected and unaffected individuals was C14:1/C12:1 [chi-squared 10.4 (p = 0.001)]. The highest performing algorithm was (Molecular testing + cell-based expression) + (P-ACP C14:1 OR P-ACP C14:1/C12:1). Excluding the missing data, this algorithm showed 96 % (46 of 48) agreement with the Clinical Designation. We conclude that there is not a single biomarker that can specifically discern affected from unaffected individuals who screen positive on NBS for VLCADD. Thus, we developed a standardized diagnostic approach to more accurately classify patients that starts with the molecular findings and requires at least one of the P-ACP C14:1 or P-ACP C14:1/C12:1 to agree with molecular findings. The algorithm needs to be trialed with a different data set, and will advance the conversation around maximizing benefits and minimizing harms for infants who screen positive for VLCADD.

Genetic analyses of very long-chain acyl-coenzyme A dehydrogenase deficiency: A case report with a novel ACADVL variant

Background

Very long-chain acyl-coenzyme A dehydrogenase deficiency (VLCADD) is a rare autosomal recessive disease associated with variants in the ACADVL gene.

Methods

In December 2021, a neonate with VLCADD was identified via newborn screening in Xuzhou, China. Genetic testing and genetic family verification were performed via high-throughput sequencing combined with Sanger sequencing. The pathogenicity and functional impacts of novel variants were predicted using bioinformatics methods.

Results

Initial results obtained from tandem mass spectrometry blood screening were suggestive of VLCADD. Two compound heterozygous variants, c.753 T > G (p.S251R) and c.1276G > A (p.A426T), inherited from the father and mother, respectively, were detected in the ACADVL gene of this individual. The c.753 T > G variant is novel and unreported.

Conclusion

These findings broaden the known mutational spectrum of the ACADVL gene in a Chinese population.

Using the C14:1/Medium-Chain Acylcarnitine Ratio Instead of C14:1 to Reduce False-Positive Results for Very-Long-Chain Acyl-CoA Dehydrogenase Deficiency in Newborn Screening in Japan

Very-long-chain acyl-CoA dehydrogenase (VLCAD) deficiency is a long-chain fatty acid oxidation disorder that manifests as either a severe phenotype associated with cardiomyopathy, a hypoglycemic phenotype, or a myopathic phenotype. As the hypoglycemic phenotype can cause sudden infant death, VLCAD deficiency is included in newborn screening (NBS) panels in many countries. The tetradecenoylcarnitine (C14:1) level in dried blood specimens is commonly used as a primary marker for VLCAD deficiency in NBS panels. Its ratio to acetylcarnitine (C2) and various other acylcarnitines is used as secondary markers. In Japan, tandem mass spectrometry-based NBS, initially launched as a pilot study in 1997, was introduced to the nationwide NBS program in 2013. In the present study, we evaluated levels of acylcarnitine with various chain lengths (C18 to C2), free carnitine, and their ratios in 175 infants who tested positive for VLCAD deficiency with C14:1 and C14:1/C2 ratios. Our analyses indicated that the ratios of C14:1 to medium-chain acylcarnitines (C10, C8, and C6) were the most effective markers in reducing false-positive rates. Their use with appropriate cutoffs is expected to improve NBS performance for VLCAD deficiency.

Newborn screening for fatty acid oxidation disorders in a southern Chinese population

Background and aims

Fatty acid oxidation disorders (FAODs) are a group of autosomal recessive metabolic diseases included in many newborn screening (NBS) programs, but the incidence and disease spectrum vary widely between ethnic groups. We aimed to elucidate the incidence, disease spectrum, and genetic features of FAODs in a southern Chinese population.

Materials and methods

The FAODs screening results of 643,606 newborns from 2014 to 2022 were analyzed.

Results

Ninety-two patients were eventually diagnosed with FAODs, of which 61 were PCD, 20 were MADD, 5 were SCADD, 4 were VLCADD, and 2 were CPT-IAD. The overall incidence of FAODs was 1:6996 (95 % CI: 1:5814-1:8772) newborns. All PCD patients had low C0 levels during NBS, while nine patients (14.8 %) had normal C0 levels during the recall review. All but one MADD patients had elevated C8, C10, and C12 levels during NBS, while eight patients (40 %) had normal acylcarnitine levels during the recall review. The most frequent SLC22A5 variant was c.760C > T (p.R254*) with an allele frequency of 29.51 %, followed by c.51C > G (p.F17L) (17.21 %) and c.1400C > G (p.S467C) (16.39 %). The most frequent ETFDH variant was c.250G > A (p.A84T) with an allelic frequency of 47.5 %, followed by c.524G > A (R175H) (12.5 %), c.998A > G (p.Y333C) (12.5 %), and c.1657T > C (p.Y553H) (7.5 %).

Conclusion

The prevalence, disease spectrum, and genetic characteristics of FAODs in a southern Chinese population were clarified. PCD was the most common FAOD, followed by MADD. Hotspot variants were found in SLC22A5 and ETFDH genes, while the remaining FAODs showed great molecular heterogeneity. Incorporating second-tier genetic screening is critical for FAODs.

Butyrylcarnitine Elevation in Newborn Screening: Reducing False Positives and Distinguishing between Two Rare Diseases through the Evaluation of New Ratios

One of the main challenges of newborn screening programs, which screen for inherited metabolic disorders, is cutting down on false positives (FPs) in order to avoid family stresses, additional analyses, and unnecessary costs. False positives are partly caused by an insubstantial number of robust biomarkers in evaluations. Another challenge is how to distinguish between diseases which share the same primary marker and for which secondary biomarkers are just as highly desirable. Focusing on pathologies that involve butyrylcarnitine (C4) elevation, such as short-chain acylCoA dehydrogenase deficiency (SCADD) and isobutyrylCoA dehydrogenase deficiency (IBDD), we investigated the acylcarnitine profile of 121 newborns with a C4 increase to discover secondary markers to achieve two goals: reduce the FP rate and discriminate between the two rare diseases. Analyses were carried out using tandem mass spectrometry with whole blood samples spotted on filter paper. Seven new biomarkers (C4/C0, C4/C5, C4/C5DC\C6OH, C4/C6, C4/C8, C4/C14:1, C4/C16:1) were identified using a non-parametric ANOVA analysis. Then, the corresponding cut-off values were found and applied to the screening program. The seven new ratios were shown to be robust (p < 0.001 and p < 0.01, 0.0937 < ε2 < 0.231) in discriminating between FP and IBDD patients, FP and SCADD patients, or SCADD and IBDD patients. Our results suggest that the new ratios are optimal indicators for identifying true positives, distinguishing between two rare diseases that share the same primary biomarker, improving the predictive positive value (PPV) and reducing the false positive rate (FPR).

PRSS37 deficiency leads to impaired energy metabolism in testis and sperm revealed by DIA-based quantitative proteomic analysis

Our previous studies have reported that a putative trypsin-like serine protease, PRSS37, is exclusively expressed in testicular germ cells during late spermatogenesis and essential for sperm migration from the uterus into the oviduct and sperm-egg recognition via mediating the interaction between PDILT and ADAM3. In the present study, the global proteome profiles of wild-type (wt) and Prss37^-/- mice in testis and sperm were compared employing data independent acquisition (DIA) technology. Overall, 2506 and 459 differentially expressed proteins (DEPs) were identified in Prss37-null testis and sperm, respectively, when compared to control groups. Bioinformatic analyses revealed that most of DEPs were related to energy metabolism. Of note, the DEPs associated with pathways for the catabolism such as glucose via glycolysis, fatty acids via β-oxidation, and amino acids via oxidative deamination were significantly down-regulated. Meanwhile, the DEPs involved in the tricarboxylic acid cycle (TCA cycle) and oxidative phosphorylation (OXPHOS) were remarkably decreased. The DIA data were further confirmed by a markedly reduction of intermediate metabolites (citrate and fumarate) in TCA cycle and terminal metabolite (ATP) in OXPHOS system after disruption of PRSS37. These outcomes not only provide a more comprehensive understanding of the male fertility of energy metabolism modulated by PRSS37 but also furnish a dynamic proteomic resource for further reproductive biology studies.

Newborn screening and genetic variation of medium chain acyl-CoA dehydrogenase deficiency in the Chinese population

OBJECTIVES

Medium-chain acyl-CoA dehydrogenase deficiency (MCADD) is an autosomal recessive disorder of the fatty acid oxidative metabolism. This study aimed to investigate the epidemiological characteristics, the spectrum of variation, clinical phenotype, and prognosis of MCADD in Chinese newborns.

METHODS

We retrospectively analysed newborn screening (NBS) data in the Zibo area from January 2016 to March 2022 and summarized 42 cases recently reported in Chinese neonates. High-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) and next-generation sequencing (NGS) were used to detect the concentrations of carnitine in the blood spots and for diagnosis.

RESULTS

A total of 183,082 newborns were detected, and six patients were diagnosed with MCADD (1/3,0514). The primary octanoylcarnitine (C8) and the octanoylcarnitine/decanoylcarnitine ratio (C8/C10) were elevated in all patients. Gene analysis revealed four known and four novel variants of the ACADM gene. Five patients were asymptomatic and developed normally under dietary guidance. One child died of vaccination-induced MCADD, presenting with hypoglycemia and elevated acylcarnitines.

CONCLUSIONS

The incidence of MCADD in Chinese newborns varies geographically from 1/222,903 to 1/30,514, and the most common pathogenic variant is c.449_452 del CTGA (p. T150Rfs∗4) in ACADM gene with a frequency of 27.7%. HPLC-MS/MS and genetic analysis are beneficial for early prevention and good prognosis of MCADD.

Opportunities and challenges in machine learning-based newborn screening-A systematic literature review

The development and continuous optimization of newborn screening (NBS) programs remains an important and challenging task due to the low prevalence of screened diseases and high sensitivity requirements for screening methods. Recently, different machine learning (ML) methods have been applied to support NBS. However, most studies only focus on single diseases or specific ML techniques making it difficult to draw conclusions on which methods are best to implement. Therefore, we performed a systematic literature review of peer-reviewed publications on ML-based NBS methods. Overall, 125 related papers, published in the past two decades, were collected for the study, and 17 met the inclusion criteria. We analyzed the opportunities and challenges of ML methods for NBS including data preprocessing, classification models and pattern recognition methods based on their underlying approaches, data requirements, interpretability on a modular level, and performance. In general, ML methods have the potential to reduce the false positive rate and identify so far unknown metabolic patterns within NBS data. Our analysis revealed, that, among the presented, logistic regression analysis and support vector machines seem to be valuable candidates for NBS. However, due to the variety of diseases and methods, a general recommendation for a single method in NBS is not possible. Instead, these methods should be further investigated and compared to other approaches in comprehensive studies as they show promising results in NBS applications.

Investigating the Metabolic Model in Preterm Neonates by Tandem Mass Spectrometry: A Cohort Study

The changes of metabolite profiles in preterm birth have been demonstrated using newborn screening data. However, little is known about the holistic metabolic model in preterm neonates. The aim was to investigate the holistic metabolic model in preterm neonates. All metabolite values were obtained from a cohort data of routine newborn screening. A total of 261 758 newborns were recruited and randomly divided into a training subset and a testing subset. Using the training subset, 949 variates were considered to establish a logistic regression model for identifying preterm birth (<37 weeks) from term birth (≥37 weeks). Sventy-two variates (age at collection, TSH, 17α-OHP, proline, tyrosine, C16:1-OH, C18:2, and 65 ratios) entered into the final metabolic model for identifying preterm birth from term birth. Among the variates entering into the final model of PTB [Leucine+Isoleucine+Proline-OH)/Valine (OR=38.36], (C3DC+C4-OH)/C12 (OR=15.58), Valine/C5 (OR=6.32), [Leucine+isoleucine+Proline-OH)/Ornithine (OR=2.509)], and Proline/C18:1 (OR=2.465) have the top five OR values, and [Leucine+Isoleucine+Proline-OH)/C5 (OR=0.05)], [Leucine+Isoleucine+Proline-OH)/Phenylalanine (OR=0.214)], proline/valine (OR=0.230), C16/C18 (OR=0.259), and Alanine/free carnitine (OR=0.279) have the five lowest OR values. The final metabolic model had a capacity of identifying preterm infants with >80% accuracy in both the training and testing subsets. When identifying neonates ≤32 weeks from those >32 weeks, it had a robust performance with nearly 95% accuracy in both subsets. In summary, we have established an excellent metabolic model in preterm neonates. These findings could provide new insights for more efficient nutrient supplements and etiology of preterm birth.

Ethnic preference distribution of inborn errors of metabolism: A 4-year study in a multi-ethnic region of China

Chinese newborns have been screened for inborn errors of metabolism (IEM) for over 20 years. Although China features 56 different ethnic groups, there are no specific data describing the incidence of such genetic errors across difference ethnicities. To understand the ethnic preference distribution of the incidence and variants of IEM in the Ningxia Hui Autonomous Region of China, 189,354 newborns from 2016 to 2019 were screened by tandem mass spectrometry, including 87,482 from the Han ethnic population, 88,229 from the Hui population, 1,103 from other ethnicities, and 12,540 infants without ethnic registration. Suspected cases then underwent specific genetic profiling by targeted next generation sequencing. In total, 160 patients were diagnosed with 17 types of IEM, with a significant higher incidence in Hui infants (1/1,003) than in Han infants (1/1,232). Five diseases (eight patients) were specifically detected in Han infants, while three were exclusively diagnosed in six Hui infants. For shared diseases, the variants of keys genes also showed ethnic preference. Our findings enhance our understanding of the genetics underlying IEM, thus promoting the development of treatment plans for patients from different areas or ethnicities in China.

Neonatal Screening on Tandem Mass Spectrometry as a Powerful Tool for the Reassessment of the Prevalence of Underestimated Diseases in Newborns and Their Family Members: A Focus on Short Chain Acyl-CoA Dehydrogenase Deficiency

Early detection of disabling diseases, prior to clinical manifestations, is the primary goal of newborn screening (NS). Indeed, the required number of core and secondary conditions selected for screening panels is increasing in many countries. Furthermore, newborn screening can lead to diagnosis of maternal diseases such as vitamin B12 deficiency or 3-MethylcrotonylCoA-carboxylase deficiency (3MCC). NS became mandatory in Sicily in December 2017. Here we report NS data collected between December 2017 and April 2020. Our results show that tandem mass spectrometry is a powerful tool for discovery of underestimated disease in newborns and their family members. Our panel included short chain acyl-CoA dehydrogenase deficiency (SCADD). Here, we report that results of our investigation led to reassessment of SCADD prevalence in our population. The infant and adult patients diagnosed in our study had previously not shown overt symptoms.

Newborn screening and genetic characteristics of patients with short- and very long-chain acyl-CoA dehydrogenase deficiencies

BACKGROUND AND AIMS

Acyl-CoA dehydrogenase deficiencies are a group of mitochondrial fatty-acid oxidation disorders rarely reported in mainland China. We assessed the biochemical and genetic characteristics of patients with short- and very-long-chain-acyl-CoA dehydrogenase deficiencies (SCADD/VLCADD) discovered through newborn screening.

MATERIALS AND METHODS

We investigated the effects of genetic variations on protein function using in silico prediction and structural modelling.

RESULTS

Of 364,545 screened newborns, four were diagnosed with SCADD and four with VLCADD. SCADD and VLCADD incidences in our population were 1:91,136. All patients exhibited elevated C4 or C14:1 levels. Three SCADD patients had increased urinary ethylmalonic acid concentrations. Six ACADS and eight ACADVL variants were identified, with no hotspot variants, and five were unreported, including four missense variants and one splice site variant. ACADVL c.1434 + 2 T > C is a splice site variant that could affect splicing, leading to exon 14 skipping. In silico tools predicted the missense variants as pathogenic. Structural modelling confirmed that the missense variants may affect quaternary structures, causing protein instability.

CONCLUSIONS

Our findings expanded the ACADS and ACADVL mutational spectra. The combination of in silico prediction and structural modelling can improve our understanding of the pathogenicity of unreported genetic variants, providing an explanation for variant assessment.