Clinical evaluation of a hemochromatosis next-generation sequencing gene panel

Background:Systemic autoinflammatory diseases (sAID) are a group of conditions with recurrent episodes of inflammation in absence of infection or autoimmune response. Its physiopathology mainly lies on mono/poligenic mutations involving genes related to the innate immune system response. Next Generation Sequencing (NGS) platformss have been a big step forward on sAID diagnosis, although a clinical and genetic correlation is still needed.Objectives:To review the sAID related gene panel variants identified using NGS sAID gene panel on a cohort of adult patients screened for sAID from a referral third-level hospital.To correlate genetic and clinical findings for sAID related variants identified in order to the clinical suspicion diagnosis of sAID.Methods:A retrospective review of a cohort of adult (≥ 16 yo) patients with available NGS sAID related gene panel (MiSeq Illumina sequencing platform including intron and exon variants from up to 17 sAID genes, with coverage depth > x100) among 2014 and 2019 was performed.Demographic, clinical and genetic data were collected in a database.Genetic variants were classified according to the American College of Medical Genetics/Association for Molecular Pathology classification as benign/likely benign/variable of unknown significance (VUS)/likely pathogenic/pathogenic. In case of polymorphisms or lack of genetic data, the variants were named as unclassified.A description of the cohort and an analysis of the correlation assessment between clinical data and genetic findings were performed.Results:246 out of 299 (82%) patients with NGS sAID gene panel had clinical data available. 170/246 (69%) were adult patients. The medium age was 48 yo, and the M/F ratio was 2.46. 87/170 (51%) adult patients presented 122 variants involving sAID genes (60/87 patients with a single variant). All the variants out of 7 seven were heterozygous variants.Variants were classified according to ACMG/AMP as follow: pathogenic/probably pathogenic: 22/122 (18%), unknown significance: 74/122 (60.6%), benign/probably benign: 6/122 (4.91%). 20/122 (16.4%) were unclassified variants or polymorphisms.The most frequent variants identified involved MEFV (54/122), NOD2/CARD15 (18/122) and TNFRSF1A (17/122 including 12 p.Arg121Gln variants) genes.37/122 (30%) variants correlated with the clinical picture in 33 patients, allowing to confirm the suspected diagnosis. Among the 122 variants, 7 not previously communicated variants were identified.No somatic variants were found.Conclusion:NGS sAID related gene panel is a useful tool for sAID diagnosis. In this cohort of 170 adult patients from a referral third-level hospital, genetic tests identified sAID related variants in almost half of them.20% of patients who underwent genetic NGS sAID related gene panel studies were finally diagnosed with sAID.The identification of a genetic variant (even pathogenic / likely pathogenic variant) is not diagnostic for sAID if there is not a suggestive clinical picture.Despite genetic findings, a careful evaluation of clinical – genetic correlation is needed to confirm the suspicion diagnosis, especially for low penetrance variants like TNFRSF1A p. Arg121Gln.References:Diagnostic utility of a targeted next-generation sequencing gene panel in the clinical suspicion of systemic autoinflammatory diseases: a multi-center study. Karacan I, Balamir A, Uğurlu S, et al. . Rheumatol Int. 2019 May;39(5):911-919. doi: 10.1007/s00296-019-04252-5. Epub 2019 Feb 19.Disclosure of Interests:None declared

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Next generation sequencing-based gene panel tests for the management of solid tumors

Cancer Science ◽

10.1111/cas.13837 ◽

2018 ◽

Vol 110 (1) ◽

pp. 6-15 ◽

Cited By ~ 20

Author(s):

Masayuki Nagahashi ◽

Yoshifumi Shimada ◽

Hiroshi Ichikawa ◽

Hitoshi Kameyama ◽

Kazuaki Takabe ◽

...

Keyword(s):

Next Generation Sequencing ◽

Solid Tumors ◽

Gene Panel ◽

Next Generation ◽

Generation Sequencing

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Next-Generation Sequencing Approach to Non–Small Cell Lung Carcinoma Yields More Actionable Alterations

Archives of Pathology & Laboratory Medicine ◽

10.5858/arpa.2017-0046-oa ◽

2017 ◽

Vol 142 (3) ◽

pp. 353-357 ◽

Cited By ~ 12

Author(s):

Mitra Mehrad ◽

Somak Roy ◽

Humberto Trejo Bittar ◽

Sanja Dacic

Keyword(s):

Next Generation Sequencing ◽

Lung Adenocarcinoma ◽

Small Cell ◽

Gene Panel ◽

Next Generation ◽

Small Cell Lung ◽

Genomic Alterations ◽

Generation Sequencing ◽

Gene Alterations ◽

Cancer Panel

Context.— Different testing algorithms and platforms for EGFR mutations and ALK rearrangements in advanced-stage lung adenocarcinoma exist. The multistep approach with single-gene assays has been challenged by more efficient next-generation sequencing (NGS) of a large number of gene alterations. The main criticism of the NGS approach is the detection of genomic alterations of uncertain significance. Objective.— To determine the best testing algorithm for patients with lung cancer in our clinical practice. Design.— Two testing approaches for metastatic lung adenocarcinoma were offered between 2012–2015. One approach was reflex testing for an 8-gene panel composed of DNA Sanger sequencing for EGFR, KRAS, PIK3CA, and BRAF and fluorescence in situ hybridization for ALK, ROS1, MET, and RET. At the oncologist's request, a subset of tumors tested by the 8-gene panel was subjected to a 50-gene Ion AmpliSeq Cancer Panel. Results.— Of 1200 non–small cell lung carcinomas (NSCLCs), 57 including 46 adenocarcinomas and NSCLCs, not otherwise specified; 7 squamous cell carcinomas (SCCs); and 4 large cell neuroendocrine carcinomas (LCNECs) were subjected to Ion AmpliSeq Cancer Panel. Ion AmpliSeq Cancer Panel detected 9 potentially actionable variants in 29 adenocarcinomas that were wild type by the 8-gene panel testing (9 of 29, 31.0%) in the following genes: ERBB2 (3 of 29, 10.3%), STK11 (2 of 29, 6.8%), PTEN (2 of 29, 6.8%), FBXW7 (1 of 29, 3.4%), and BRAF G469A (1 of 29, 3.4%). Four SCCs and 2 LCNECs showed investigational genomic alterations. Conclusions.— The NGS approach would result in the identification of a significant number of actionable gene alterations, increasing the therapeutic options for patients with advanced NSCLCs.

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Clinical evaluation of a dedicated next generation sequencing panel for routine glioma diagnostics

Acta Neuropathologica Communications ◽

10.1186/s40478-018-0633-y ◽

2018 ◽

Vol 6 (1) ◽

Cited By ~ 11

Author(s):

Nathalie E. Synhaeve ◽

Martin J. van den Bent ◽

Pim J. French ◽

Winand N. M. Dinjens ◽

Peggy N. Atmodimedjo ◽

...

Keyword(s):

Next Generation Sequencing ◽

Clinical Evaluation ◽

Next Generation ◽

Generation Sequencing

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Targeted next generation sequencing with an extended gene panel does not impact variant detection in mitochondrial diseases

BMC Medical Genetics ◽

10.1186/s12881-018-0568-y ◽

2018 ◽

Vol 19 (1) ◽

Cited By ~ 10

Author(s):

Morgane Plutino ◽

Annabelle Chaussenot ◽

Cécile Rouzier ◽

Samira Ait-El-Mkadem ◽

Konstantina Fragaki ◽

...

Keyword(s):

Next Generation Sequencing ◽

Mitochondrial Diseases ◽

Gene Panel ◽

Next Generation ◽

Targeted Next Generation Sequencing ◽

Variant Detection ◽

Generation Sequencing

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Clinical evaluation of panel testing by next-generation sequencing (NGS) for gene mutations in myeloid neoplasms

Diagnostic Pathology ◽

10.1186/s13000-016-0456-8 ◽

2016 ◽

Vol 11 (1) ◽

Cited By ~ 45

Author(s):

Chun Hang Au ◽

Anna Wa ◽

Dona N. Ho ◽

Tsun Leung Chan ◽

Edmond S. K. Ma

Keyword(s):

Next Generation Sequencing ◽

Clinical Evaluation ◽

Gene Mutations ◽

Next Generation ◽

Panel Testing ◽

Myeloid Neoplasms ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

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Targeted Hotspot Gene Panel Using Massively Parallel Sequencing (Next Generation Sequencing)

Diagnostic Pathology: Molecular Oncology ◽

10.1016/b978-0-323-37678-5.50047-5 ◽

2016 ◽

pp. 4-20-4-21

Keyword(s):

Next Generation Sequencing ◽

Massively Parallel Sequencing ◽

Gene Panel ◽

Massively Parallel ◽

Next Generation ◽

Parallel Sequencing ◽

Generation Sequencing

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Early detection of lysosomal diseases by screening of cases of idiopathic splenomegaly and/or thrombocytopenia with a next‐generation sequencing gene panel

JIMD Reports ◽

10.1002/jmd2.12078 ◽

2019 ◽

Vol 51 (1) ◽

pp. 53-61

Author(s):

Gloria Muñoz ◽

David García‐Seisdedos ◽

Crina Ciubotariu ◽

Miguel Piris‐Villaespesa ◽

Marta Gandía ◽

...

Keyword(s):

Next Generation Sequencing ◽

Early Detection ◽

Gene Panel ◽

Next Generation ◽

Lysosomal Diseases ◽

Generation Sequencing

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Targeted Next-Generation Sequencing in a Large Cohort of Genetically Undiagnosed Patients with Neuromuscular Disorders in Spain

Genes ◽

10.3390/genes11050539 ◽

2020 ◽

Vol 11 (5) ◽

pp. 539

Author(s):

Lidia Gonzalez-Quereda ◽

Maria Jose Rodriguez ◽

Jordi Diaz-Manera ◽

Jorge Alonso-Perez ◽

Eduard Gallardo ◽

...

Keyword(s):

Next Generation Sequencing ◽

Neuromuscular Disorders ◽

Neuromuscular Disorder ◽

Gene Panel ◽

Muscular Dystrophies ◽

Next Generation ◽

Congenital Myasthenic Syndromes ◽

Targeted Next Generation Sequencing ◽

Generation Sequencing ◽

Myasthenic Syndromes

The term neuromuscular disorder (NMD) includes many genetic and acquired diseases and differential diagnosis can be challenging. Next-generation sequencing (NGS) is especially useful in this setting given the large number of possible candidate genes, the clinical, pathological, and genetic heterogeneity, the absence of an established genotype-phenotype correlation, and the exceptionally large size of some causative genes such as TTN, NEB and RYR1. We evaluated the diagnostic value of a custom targeted next-generation sequencing gene panel to study the mutational spectrum of a subset of NMD patients in Spain. In an NMD cohort of 207 patients with congenital myopathies, distal myopathies, congenital and adult-onset muscular dystrophies, and congenital myasthenic syndromes, we detected causative mutations in 102 patients (49.3%), involving 42 NMD-related genes. The most common causative genes, TTN and RYR1, accounted for almost 30% of cases. Thirty-two of the 207 patients (15.4%) carried variants of uncertain significance or had an unidentified second mutation to explain the genetic cause of the disease. In the remaining 73 patients (35.3%), no candidate variant was identified. In combination with patients’ clinical and myopathological data, the custom gene panel designed in our lab proved to be a powerful tool to diagnose patients with myopathies, muscular dystrophies and congenital myasthenic syndromes. Targeted NGS approaches enable a rapid and cost-effective analysis of NMD- related genes, offering reliable results in a short time and relegating invasive techniques to a second tier.

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