ArticleFrontiers in immunology2014
Targeted NGS: A Cost-Effective Approach to Molecular Diagnosis of PIDs.
Article in Frontiers in immunology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers, 2 of them syntheses that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
54 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Monogenic etiologies of persistent human papillomavirus infections: A comprehensive systematic review.Genetics in medicine : official journal of the American College of Medical Genetics · 2024Pooled it
- Diagnostic Yield of Next Generation Sequencing in Genetically Undiagnosed Patients with Primary Immunodeficiencies: a Systematic Review.Journal of clinical immunology · 2019Pooled it
- The human mycobiome: a critical yet understudied component of health and disease.Microbiology (Reading, England) · 2025Review
- Targeted Next-Generation Sequencing in the Molecular Diagnosis of Severe Combined Immunodeficiency.Medicina (Kaunas, Lithuania) · 2025Article
- Framework for Race-Specific Prostate Cancer Detection Using Machine Learning Through Gene Expression Data: Feature Selection Optimization Approach.JMIR bioinformatics and biotechnology · 2025Article
- Contribution of next generation sequencing to the diagnosis of inborn errors of immunity in a pediatric cohort.Frontiers in immunology · 2025Article
- Diagnostic tests for primary immunodeficiency disorders: Classic and genetic testing.Allergy and asthma proceedings · 2024Review
- Enrichment of Immune Dysregulation Disorders in Adult Patients with Human Inborn Errors of Immunity.Journal of clinical immunology · 2024Article
- Evaluation and pilot testing of a multidisciplinary model of care to mainstream genomic testing for paediatric inborn errors of immunity.European journal of human genetics : EJHG · 2023Article
- Application of next-generation sequencing to identify different pathogens.Frontiers in microbiology · 2023Review
- Seed management using NGS technology to rapidly eliminate a deleterious allele from rice breeder seeds.Breeding science · 2022Article
- Diagnostic Yield and Therapeutic Consequences of Targeted Next-Generation Sequencing in Sporadic Primary Immunodeficiency.International archives of allergy and immunology · 2022Article
- Real-World Data and Budget Impact Analysis (BIA): Evaluation of a Targeted Next-Generation Sequencing Diagnostic Approach in Two Orthopedic Rare Diseases.Frontiers in pharmacology · 2022Article
- Genetic Analysis of a Cohort of 275 Patients with Hyper-IgE Syndromes and/or Chronic Mucocutaneous Candidiasis.Journal of clinical immunology · 2021Article
- Next-Generation Sequencing in the Field of Primary Immunodeficiencies: Current Yield, Challenges, and Future Perspectives.Clinical reviews in allergy & immunology · 2021Review
- Targeted NGS Yields Plentiful Ultra-Rare Variants in Inborn Errors of Immunity Patients.Genes · 2021Article
- Beyond monogenetic rare variants: tackling the low rate of genetic diagnoses in predominantly antibody deficiency.Cellular & molecular immunology · 2021Review
- Establishing the Molecular Diagnoses in a Cohort of 291 Patients With Predominantly Antibody Deficiency by Targeted Next-Generation Sequencing: Experience From a Monocentric Study.Frontiers in immunology · 2021Observational
- Implementation of Early Next-Generation Sequencing for Inborn Errors of Immunity: A Prospective Observational Cohort Study of Diagnostic Yield and Clinical Implications in Dutch Genome Diagnostic Centers.Frontiers in immunology · 2021Observational
- Primary Immunodeficiencies: Diseases of Children and Adults - A Review.Advances in experimental medicine and biology · 2021Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
backgroundPrimary immunodeficiencies (PIDs) are a diverse group of disorders caused by multiple genetic defects. Obtaining a molecular diagnosis for PID patients using a phenotype-based approach is often complex, expensive, and not always successful. Next-generation sequencing (NGS) methods offer an unbiased genotype-based approach, which can facilitate molecular diagnostics.
objectiveTo develop an efficient NGS method to identify variants in PID-related genes.
methodsWe performed HaloPlex custom target enrichment and NGS using the Ion Torrent PGM to screen 173 genes in 11 healthy controls, 13 PID patients previously evaluated with either an identified mutation or SNP, and 120 patients with undiagnosed PIDs. Sensitivity and specificity were determined by comparing NGS and Sanger sequencing results for 33 patients. Run metrics and coverage analyses were done to identify systematic deficiencies.
resultsA molecular diagnosis was identified for 18 of 120 patients who previously lacked a genetic diagnosis, including 9 who had atypical presentations and extensive previous genetic and functional studies. Our NGS method detected variants with 98.1% sensitivity and >99.9% specificity. Uniformity was variable (72-89%), and we were not able to reliably sequence 45 regions (45/2455 or 1.8% of total regions) due to low (<20) average read depth or <90% region coverage; thus, we optimized probe hybridization conditions to improve read-depth and coverage for future analyses, and established criteria to help identify true positives.
conclusionWhile NGS methods are not as sensitive as Sanger sequencing for individual genes, targeted NGS is a cost-effective, first-line genetic test for the evaluation of patients with PIDs. This approach decreases time to diagnosis, increases diagnostic rate, and provides insight into the genotype-phenotype correlation of PIDs in a cost-effective way.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.