Dataset Information

Future of Dutch NGS-Based Newborn Screening: Exploring the Technical Possibilities and Assessment of a Variant Classification Strategy.

ABSTRACT: In this study, we compare next-generation sequencing (NGS) approaches (targeted panel (tNGS), whole exome sequencing (WES), and whole genome sequencing (WGS)) for application in newborn screening (NBS). DNA was extracted from dried blood spots (DBS) from 50 patients with genetically confirmed inherited metabolic disorders (IMDs) and 50 control samples. One hundred IMD-related genes were analyzed. Two data-filtering strategies were applied: one to detect only (likely) pathogenic ((L)P) variants, and one to detect (L)P variants in combination with variants of unknown significance (VUS). The variants were filtered and interpreted, defining true/false positives (TP/FP) and true/false negatives (TN/FN). The variant filtering strategies were assessed in a background cohort (BC) of 4833 individuals. Reliable results were obtained within 5 days. TP results (47 patient samples) for tNGS, WES, and WGS results were 33, 31, and 30, respectively, using the (L)P filtering, and 40, 40, and 38, respectively, when including VUS. FN results were 11, 13, and 14, respectively, excluding VUS, and 4, 4, and 6, when including VUS. The remaining FN were mainly samples with a homozygous VUS. All controls were TN. Three BC individuals showed a homozygous (L)P variant, all related to a variable, mild phenotype. The use of NGS-based workflows in NBS seems promising, although more knowledge of data handling, automated variant interpretation, and costs is needed before implementation.

SUBMITTER: Kiewiet G

PROVIDER: S-EPMC10971161 | biostudies-literature | 2024 Mar

REPOSITORIES: biostudies-literature

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Future of Dutch NGS-Based Newborn Screening: Exploring the Technical Possibilities and Assessment of a Variant Classification Strategy.

Kiewiet Gea G Westra Dineke D de Boer Eddy N EN van Berkel Emma E Hofste Tom G J TGJ van Zweeden Martine M Derks Ronny C RC Leijsten Nico F A NFA Ruiterkamp-Versteeg Martina H A MHA Charbon Bart B Johansson Lennart L Bos-Kruizinga Janneke J Veenstra Inge J IJ de Sain-van der Velden Monique G M MGM Voorhoeve Els E Heiner-Fokkema M Rebecca MR van Spronsen Francjan F Sikkema-Raddatz Birgit B Nelen Marcel M

International journal of neonatal screening 20240307 1

In this study, we compare next-generation sequencing (NGS) approaches (targeted panel (tNGS), whole exome sequencing (WES), and whole genome sequencing (WGS)) for application in newborn screening (NBS). DNA was extracted from dried blood spots (DBS) from 50 patients with genetically confirmed inherited metabolic disorders (IMDs) and 50 control samples. One hundred IMD-related genes were analyzed. Two data-filtering strategies were applied: one to detect only (likely) pathogenic ((L)P) variants, ...[more]

PMID: 38535124

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Project description:Background and objectivesProjections that 60 transformative cell and gene therapies could be approved by the U.S. Food and Drug Administration (FDA) within 10 years underscore an urgent need to modernize the newborn screening (NBS) system. This study convened expert stakeholders to assess challenges to the NBS system and propose solutions for its modernization.MethodsNBS stakeholders (researchers, clinicians, state NBS leaders, advocates, industry professionals, and current/former advisory committee members) participated in one of five mixed-stakeholder panel discussions. Prior to panels, participants completed a survey in which they reviewed and ranked NBS challenges generated from relevant literature. During panels, participants deliberated on challenges and explored potential solutions. Pre-panel survey data were analyzed descriptively. Data from panel discussions were analyzed using a rapid qualitative analysis.ResultsMedian scores of the ranked challenges (1 = most important) reveal the top three most important barriers to address: critical missing data for NBS decision-making (Median = 2), burden on state NBS laboratories (Median = 3), and the amount of time required for state-level implementation of screening for new conditions (Median = 4). Panel discussions were rooted in recurring themes: the infant's well-being should be the focal point; the transformative therapy pipeline, although undeniably positive for individuals with rare diseases, is a threat to NBS capacity; decisions about modernizing NBS should be evidence-based; additional financial support is required but not sufficient for modernization; and modernization will require participation of multiple NBS stakeholders. This final overarching theme is reported in depth, including expertise, coordination, and collaboration challenges facing NBS and novel approaches to oversight, partnership, and coordination that were suggested by participants.ConclusionsThis study engaged representatives from multiple stakeholder groups to generate potential solutions to challenges facing NBS in the United States. These solutions provide a rich starting point for policy makers and other stakeholders who desire to maximize the impact of new transformative therapies for babies, families, and society.

Project description:BackgroundMultiplatform molecular subtyping has been put into clinical practice as an alternative for The Cancer Genome Atlas (TCGA)-based classification for endometrial cancer (EC), which proved a tool for predicting prognosis and guiding treatment. The traditional methods for the molecular classification of EC only based on pathological indicators are not accurate. The present study aimed to classify EC on a molecular level and explored the possibility of a one-time solution to guide clinical treatment and prognosis determination by utilizing data from a next-generation sequencing (NGS) panel. The ultimate aim was to utilize multiplatform testing to overcome disadvantages of long detection periods and limitations in the information regarding genetic variation.MethodsAn NGS-panel was produced using FFPE samples isolated from 86 patients pathologically diagnosed with EC, and molecular subtyping was performed according to the recommended criteria. In addition, 45 matched samples from 86 patients were randomly selected for immunohistochemical (IHC) staining of P53, MLH1, MSH2, PMS2, and MSH6. Another 41 samples were not analyzed due to incomplete IHC staining results. SPSS (V26.0; IBM Corp., Armonk, NY, USA) was used for receiver operating characteristic (ROC) curve analysis.ResultsThe molecular typing ratio of the 86 cases of endometrial carcinoma was calculated to be 16.28% for POLE type, 17.44% for MSI-H type, 47.67% for CN-L type, 12.79% for CN-H type, 5.81% for unclassified case. A comparison between IHC ProMisE-based subtyping and NGS-based subtyping of the 45 cases revealed that 3 cases were classified as MSI-H by IHC but as MSS by NGS. Among these cases, 1 case was deficient in MLH1 expression and PMS2 protein expression but had wild-type P53 protein, and the P53 sequencing data of this sample showed a missense mutation. Good overall consistency between the 2 determination methods was shown. Receiver operating characteristic (ROC) analysis showed that NGS had particularly high specificity and sensitivity for detecting the MSI and CN subtypes [area under the curve (AUC) =0.893>0.5, P=0.000029<0.01].ConclusionsThe present study suggested that NGS-based subtyping could serve as an effective approach for the molecular typing of EC. Both NGS and IHC bear their own unique advantages and challenges in clinical practice.

Dataset Information

Future of Dutch NGS-Based Newborn Screening: Exploring the Technical Possibilities and Assessment of a Variant Classification Strategy.

Publications

Future of Dutch NGS-Based Newborn Screening: Exploring the Technical Possibilities and Assessment of a Variant Classification Strategy.

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