Rapid Targeted Sequencing Using Dried Blood Spot Samples for Patients With Suspected Actionable Genetic Diseases

Abstract

Background: New genome sequencing technologies with enhanced diagnostic efficiency have emerged. Rapid and timely diagnosis of treatable rare genetic diseases can alter their medical management and clinical course. However, multiple factors, including ethical issues, must be considered. We designed a targeted sequencing platform to avoid ethical issues and reduce the turnaround time.Methods: We designed an automated sequencing platform using dried blood spot samples and a NEOseq_ACTION panel comprising 254 genes associated with Mendelian diseases having curable or manageable treatment options. Retrospective validation was performed using data from 24 genetically and biochemically confirmed patients. Prospective validation was performed using data from 111 patients with suspected actionable genetic diseases.Results: In prospective clinical validation, 13.5% patients presented with medically actionable diseases, including short-or medium-chain acyl-CoA dehydrogenase deficiencies (N = 6), hyperphenylalaninemia (N = 2), mucopolysaccharidosis type IVA (N = 1), alpha thalassemia (N = 1), 3-methylcrotonyl-CoA carboxylase 2 deficiency (N = 1), propionic acidemia (N = 1), glycogen storage disease, type IX(a) (N = 1), congenital myasthenic syndrome (N = 1), and citrullinemia, type II (N = 1). Using the automated analytic pipeline, the turnaround time from blood collection to result reporting was < 4 days.Conclusions: This pilot study evaluated the possibility of rapid and timely diagnosis of treatable rare genetic diseases using a panel designed by a multidisciplinary team. The automated analytic pipeline maximized the clinical utility of rapid targeted sequencing for medically actionable genes, providing a strategy for appropriate and timely treatment of rare genetic diseases.

Current State and Innovations in Newborn Screening: Continuing to Do Good and Avoid Harm

“…An example is the use of qPCR to identify both SMA and SCID from a single assay. In a diagnostic setting, these panels have already been used [ 65 , 66 ]; however, they have not yet in a screening setting.…”

Rapid Targeted Genomic Testing: A Powerful Tool for Diagnostic Evaluation of Critically Ill Neonates and Infants With Suspected Genetic Diseases

“…However, widespread deployment of rapid WGS or WES has led to several ethical issues pertaining to the interpretation of variants of uncertain significance (VUS), discovery of incidental findings related to adult-onset conditions by examining sequence information of the whole genome or exome, and implementation of medical therapies with minimal information on risks and benefits [9,13]. Time is another essential factor when treating critically ill children in neonatal and pediatric intensive care units, limiting In this issue of Annals of Laboratory Medicine, Kim and colleagues [14] report the design of a rapid targeted sequencing panel called NEOseq_ACTION containing 254 actionable genes with therapeutic options to meet clinical needs and overcome ethical concerns. They further developed a machine learningbased prediction model to support variant interpretation, which is expected to shorten the TAT and efficiently predict the pathogenicity of VUS [14].…”

“…Time is another essential factor when treating critically ill children in neonatal and pediatric intensive care units, limiting In this issue of Annals of Laboratory Medicine, Kim and colleagues [14] report the design of a rapid targeted sequencing panel called NEOseq_ACTION containing 254 actionable genes with therapeutic options to meet clinical needs and overcome ethical concerns. They further developed a machine learningbased prediction model to support variant interpretation, which is expected to shorten the TAT and efficiently predict the pathogenicity of VUS [14]. Prospective validation tests were performed using dried blood spot samples from critically ill neonates and infants with suspected genetic diseases based on abnormal neonatal screening findings, neonatal hypotonia, seizures, complex metabolic phenotypes, skeletal dysplasia or joint problems, and neurodevelopmental delays.…”

“…In this study of 111 children who underwent NEOseq_ACTION panel sequencing, 13.5% (15/111) had a genetic diagnosis, including 14 patients with autosomal recessive disease and one patient with X-linked recessive disease. The majority of patients (11/15) who received a genetic diagnosis were asymptomatic and showed abnormal findings in neonatal screening [14]. The average time from blood collection to reporting was 3.4 days, and medical management was applied for all patients (15/15) with a diagnosis [14].…”

“…The majority of patients (11/15) who received a genetic diagnosis were asymptomatic and showed abnormal findings in neonatal screening [14]. The average time from blood collection to reporting was 3.4 days, and medical management was applied for all patients (15/15) with a diagnosis [14].…”