Targeted next-generation sequencing: A novel diagnostic tool for primary immunodeficiencies

Nijman, Isaäc J; Montfrans, Joris M. van; Hoogstraat, Marlous; Boes, Marianne; Corput, Lisette van de; Renner, Ellen D.; Zon, P van; Lieshout, Stef van; Elferink, Martin; Burg, Mirjam van der; Vermont, Clementien; Zwaag, Bert van der; Janson, Esther; Cuppen, Edwin; Amstel, Johannes Kristian Ploos van; Gijn, Mariëlle van

doi:10.1016/j.jaci.2013.08.032

Cited by 136 publications

(118 citation statements)

References 22 publications

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“…Galactosialidosis was excluded by normal galactosidase activity (1,246 and 1,257 nmol/mg/h for patient 1 and 2, respectively; normal range: 600-1,650). Targeted next-generation sequencing (Nijman et al 2014) of NEU1 revealed two previously described compound heterozygous mutations (c.1195_1200dup p.His399_Tyr400dup; c.679G>A, p.Glu227Arg) in both patients, confirming neuraminidase deficiency (Bonten et al 2000;Lukong et al 2000). Nomenclature is according to HGVS guidelines and is based upon transcript NM 000434.3.…”

Section: Biochemical Phenotype and Genotypementioning

confidence: 86%

Pitfalls in Diagnosing Neuraminidase Deficiency: Psychosomatics and Normal Sialic Acid Excretion

et al. 2015

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Section: Biochemical Phenotype and Genotypementioning

confidence: 86%

Pitfalls in Diagnosing Neuraminidase Deficiency: Psychosomatics and Normal Sialic Acid Excretion

et al. 2015

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“…Increasingly extensive gene panels are used to interrogate the growing number of genes implicated in Mendelian diseases (1). However, such panels only modestly increase the number of high-confidence diagnostic results while identifying ever larger numbers of variants of uncertain significance (VUS) (2)(3)(4). The likelihood that a rare variant is indeed pathogenic depends on the pre-test probability that the patient has the relevant disease.…”

Section: [Main Text: ] Introductionmentioning

confidence: 99%

Reassessment of Mendelian gene pathogenicity using 7,855 cardiomyopathy cases and 60,706 reference samples

Walsh

Thomson

Ware

et al. 2016

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One Sentence Summary: Comparing the frequency of very rare variation between patient cohorts and very large genomic reference datasets enables the reliable re-evaluation of genes previously implicated in Mendelian disease and more accurate assessment of the likely pathogenicity of different classes of variants. Abstract:The accurate interpretation of variation in Mendelian disease genes has lagged behind data generation as sequencing has become increasingly accessible. Ongoing large sequencing efforts present huge interpretive challenges, but also provide an invaluable opportunity to characterize the spectrum and importance of rare variation. Here we analyze sequence data from 7,855 clinical cardiomyopathy cases and 60,706 ExAC reference samples to better understand genetic variation in a representative autosomal dominant disorder. We show that in some genes previously reported as important causes of a given cardiomyopathy, rare variation is not clinically informative and there is a high likelihood of false positive interpretation. By contrast, in other genes, we find that diagnostic laboratories may be overly conservative when assessing variant pathogenicity. We outline improved interpretation approaches for specific genes and variant classes and propose that these will increase the clinical utility of testing across a range of Mendelian diseases.All rights reserved. No reuse allowed without permission.

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“…Because of the low incidence and the fact that activation of the inflammatory response in AID is indistinguishable from pathogen-induced immune activation, it usually takes multiple cycles before the possibility of autoinflammation is recognized. Final diagnosis of hereditary AID can only be made by DNA analysis, such as by next-generation sequencing [12]. We think it is relevant to emphasize here the mechanistic distinction between AID and autoimmune diseases.…”

Section: Importance Of Mitochondria In Autoinflammatory Diseasementioning

confidence: 99%

Mitochondria in autoinflammation: cause, mediator or bystander?

Burgh

Boes

2015

Trends in Endocrinology & Metabolism

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Targeted next-generation sequencing: A novel diagnostic tool for primary immunodeficiencies

Cited by 136 publications

References 22 publications

Pitfalls in Diagnosing Neuraminidase Deficiency: Psychosomatics and Normal Sialic Acid Excretion

Pitfalls in Diagnosing Neuraminidase Deficiency: Psychosomatics and Normal Sialic Acid Excretion

Reassessment of Mendelian gene pathogenicity using 7,855 cardiomyopathy cases and 60,706 reference samples

Mitochondria in autoinflammation: cause, mediator or bystander?

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