Germline Pathogenic Variants Identified by Targeted Next-Generation Sequencing of Susceptibility Genes in Pheochromocytoma and Paraganglioma

The aim of this study was to evaluate germline variant frequencies of pheochromocytoma and paraganglioma targeted susceptibility genes with next-generation sequencing method. Germline DNA from 75 cases were evaluated with targeted next-generation sequencing on an Illumina NextSeq550 instrument. KIF1B, RET, SDHB, SDHD, TMEM127, and VHL genes were included in the study, and Sanger sequencing was used for verifying the variants. The pathogenic/likely pathogenic variants were in the VHL, RET, SDHB, and SDHD genes, and the diagnosis rate was 24% in this study. Three different novel pathogenic variants were determined in five cases. This is the first study from Turkey, evaluating germline susceptibility genes of pheochromocytoma and paraganglioma with a detection rate of 24% and three novel variants. All patients with pheochromocytoma and paraganglioma need clinical genetic testing with expanded targeted gene panels for higher diagnosis rates.

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Next-generation sequencing in the clinical genetic screening of patients with pheochromocytoma and paraganglioma

Endocrine Connections ◽

10.1530/ec-13-0009 ◽

2013 ◽

Vol 2 (2) ◽

pp. 104-111 ◽

Cited By ~ 32

Author(s):

Joakim Crona ◽

Alberto Delgado Verdugo ◽

Dan Granberg ◽

Staffan Welin ◽

Peter Stålberg ◽

...

Keyword(s):

Next Generation Sequencing ◽

Genetic Screening ◽

Bioinformatics Analysis ◽

Cost Effective ◽

Susceptibility Genes ◽

Next Generation ◽

Clinical Genetic ◽

Cost Effective Method ◽

Agilent Sureselect ◽

Generation Sequencing

BackgroundRecent findings have shown that up to 60% of pheochromocytomas (PCCs) and paragangliomas (PGLs) are caused by germline or somatic mutations in one of the 11 hitherto known susceptibility genes: SDHA, SDHB, SDHC, SDHD, SDHAF2, VHL, HIF2A (EPAS1), RET, NF1, TMEM127 and MAX. This list of genes is constantly growing and the 11 genes together consist of 144 exons. A genetic screening test is extensively time consuming and expensive. Hence, we introduce next-generation sequencing (NGS) as a time-efficient and cost-effective alternative.MethodsTumour lesions from three patients with apparently sporadic PCC were subjected to whole exome sequencing utilizing Agilent Sureselect target enrichment system and Illumina Hi seq platform. Bioinformatics analysis was performed in-house using commercially available software. Variants in PCC and PGL susceptibility genes were identified.ResultsWe have identified 16 unique genetic variants in PCC susceptibility loci in three different PCC, spending less than a 30-min hands-on, in-house time. Two patients had one unique variant each that was classified as probably and possibly pathogenic: NF1 Arg304Ter and RET Tyr791Phe. The RET variant was verified by Sanger sequencing.ConclusionsNGS can serve as a fast and cost-effective method in the clinical genetic screening of PCC. The bioinformatics analysis may be performed without expert skills. We identified process optimization, characterization of unknown variants and determination of additive effects of multiple variants as key issues to be addressed by future studies.

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Large next-generation sequencing gene panels in genetic heart disease: yield of pathogenic variants and variants of unknown significance

Netherlands Heart Journal ◽

10.1007/s12471-019-1250-5 ◽

2019 ◽

Vol 27 (6) ◽

pp. 304-309 ◽

Cited By ~ 8

Author(s):

F. H. M. van Lint ◽

O. R. F. Mook ◽

M. Alders ◽

H. Bikker ◽

R. H. Lekanne dit Deprez ◽

...

Keyword(s):

Heart Disease ◽

Next Generation Sequencing ◽

Next Generation ◽

Variants Of Unknown Significance ◽

Pathogenic Variants ◽

Unknown Significance ◽

Gene Panels ◽

Genetic Heart Disease ◽

Generation Sequencing

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Application of targeted next generation sequencing for the comprehensive analysis of pancreatitis susceptibility genes

Suizo ◽

10.2958/suizo.31.54 ◽

2016 ◽

Vol 31 (1) ◽

pp. 54-62 ◽

Cited By ~ 1

Author(s):

Eriko NAKANO ◽

Atsushi MASAMUNE ◽

Tetsuya NIIHORI ◽

Kiyoshi KUME ◽

Yoko AOKI ◽

...

Keyword(s):

Next Generation Sequencing ◽

Susceptibility Genes ◽

Comprehensive Analysis ◽

Next Generation ◽

Targeted Next Generation Sequencing ◽

Generation Sequencing

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Targeted Next-Generation Sequencing Identifies Pathogenic Variants in Familial Congenital Heart Disease

Journal of the American College of Cardiology ◽

10.1016/j.jacc.2014.09.048 ◽

2014 ◽

Vol 64 (23) ◽

pp. 2498-2506 ◽

Cited By ~ 50

Author(s):

Gillian M. Blue ◽

Edwin P. Kirk ◽

Eleni Giannoulatou ◽

Sally L. Dunwoodie ◽

Joshua W.K. Ho ◽

...

Keyword(s):

Congenital Heart Disease ◽

Heart Disease ◽

Next Generation Sequencing ◽

Congenital Heart ◽

Next Generation ◽

Targeted Next Generation Sequencing ◽

Pathogenic Variants ◽

Generation Sequencing

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Next-generation sequencing for endocrine cancers: Recent advances and challenges

Tumor Biology ◽

10.1177/1010428317698376 ◽

2017 ◽

Vol 39 (5) ◽

pp. 101042831769837 ◽

Cited By ~ 4

Author(s):

Padmanaban S Suresh ◽

Thejaswini Venkatesh ◽

Rie Tsutsumi ◽

Abhishek Shetty

Keyword(s):

Next Generation Sequencing ◽

Drug Targets ◽

Current View ◽

Endocrine Tumors ◽

Next Generation ◽

Clinical Genetic ◽

Clinical Genetic Testing ◽

Recent Advances ◽

Microarray Analyses ◽

Generation Sequencing

Contemporary molecular biology research tools have enriched numerous areas of biomedical research that address challenging diseases, including endocrine cancers (pituitary, thyroid, parathyroid, adrenal, testicular, ovarian, and neuroendocrine cancers). These tools have placed several intriguing clues before the scientific community. Endocrine cancers pose a major challenge in health care and research despite considerable attempts by researchers to understand their etiology. Microarray analyses have provided gene signatures from many cells, tissues, and organs that can differentiate healthy states from diseased ones, and even show patterns that correlate with stages of a disease. Microarray data can also elucidate the responses of endocrine tumors to therapeutic treatments. The rapid progress in next-generation sequencing methods has overcome many of the initial challenges of these technologies, and their advantages over microarray techniques have enabled them to emerge as valuable aids for clinical research applications (prognosis, identification of drug targets, etc.). A comprehensive review describing the recent advances in next-generation sequencing methods and their application in the evaluation of endocrine and endocrine-related cancers is lacking. The main purpose of this review is to illustrate the concepts that collectively constitute our current view of the possibilities offered by next-generation sequencing technological platforms, challenges to relevant applications, and perspectives on the future of clinical genetic testing of patients with endocrine tumors. We focus on recent discoveries in the use of next-generation sequencing methods for clinical diagnosis of endocrine tumors in patients and conclude with a discussion on persisting challenges and future objectives.

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Next-Generation Sequencing Improves Diagnosis, Prognosis and Clinical Management of Myeloid Neoplasms

Cancers ◽

10.3390/cancers11091364 ◽

2019 ◽

Vol 11 (9) ◽

pp. 1364 ◽

Cited By ~ 6

Author(s):

Diego Carbonell ◽

Julia Suárez-González ◽

María Chicano ◽

Cristina Andrés-Zayas ◽

Juan Carlos Triviño ◽

...

Keyword(s):

Next Generation Sequencing ◽

Copy Number Variants ◽

Genetic Alterations ◽

Next Generation ◽

Pathogenic Variants ◽

Myeloid Neoplasms ◽

Diagnostic Samples ◽

Gene Panels ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

Molecular diagnosis of myeloid neoplasms (MN) is based on the detection of multiple genetic alterations using various techniques. Next-generation sequencing (NGS) has been proved as a useful method for analyzing many genes simultaneously. In this context, we analyzed diagnostic samples from 121 patients affected by MN and ten relapse samples from a subset of acute myeloid leukemia patients using two enrichment-capture NGS gene panels. Pathogenicity classification of variants was enhanced by the development and application of a custom onco-hematology score. A total of 278 pathogenic variants were detected in 84% of patients. For structural alterations, 82% of those identified by cytogenetics were detected by NGS, 25 of 31 copy number variants and three out of three translocations. The detection of variants using NGS changed the diagnosis of seven patients and the prognosis of 15 patients and enabled us to identify 44 suitable candidates for clinical trials. Regarding AML, six of the ten relapsed patients lost or gained variants, comparing with diagnostic samples. In conclusion, the use of NGS panels in MN improves genetic characterization of the disease compared with conventional methods, thus demonstrating its potential clinical utility in routine clinical testing. This approach leads to better-adjusted treatments for each patient.

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Targeted next generation sequencing in patients with maturity-onset diabetes of the young (MODY)

Journal of Pediatric Endocrinology and Metabolism ◽

10.1515/jpem-2018-0184 ◽

2018 ◽

Vol 31 (12) ◽

pp. 1295-1304 ◽

Cited By ~ 6

Author(s):

Taha R. Özdemir ◽

Özgür Kırbıyık ◽

Bumin N. Dündar ◽

Ayhan Abacı ◽

Özge Ö. Kaya ◽

...

Keyword(s):

Next Generation Sequencing ◽

Maturity Onset Diabetes ◽

Next Generation ◽

Targeted Next Generation Sequencing ◽

Pathogenic Variants ◽

Onset Diabetes ◽

Frequent Mutations ◽

Standards And Guidelines ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

Abstract Background Maturity-onset diabetes of the young (MODY) is a common form of monogenic diabetes. Fourteen genes have been identified, each leading to cause a different type of MODY. The aims of this study were to reveal both known and novel variants in MODY genes in patients with MODY using targeted next generation sequencing (NGS) and to present the genotype-phenotype correlations. Methods Mutation analysis of MODY genes (GCK, HNF1A, HNF4A, HNF1B, ABCC8, INS and KCNJ11) was performed using targeted NGS in 106 patients with a clinical diagnosis of MODY. The variants were evaluated according to American College of Medical Genetics and Genomics (ACMG) Standards and Guidelines recommendations. Results A total of 18 (17%) variants were revealed among all patients. Seven variants in GCK, six in HNF4A, four in HNF1A and one in ABCC8 genes were found. Eight of them were previously published and 10 of them were assessed as novel pathogenic or likely pathogenic variants. Conclusions While the most frequent mutations are found in the HNF1A gene in the literature, most of the variants were found in the GCK gene in our patient group using the NGS method, which allows simultaneous analysis of multiple genes in a single panel.

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Genetic study of pediatric hypertrophic cardiomyopathy in Egypt

Cardiology in the Young ◽

10.1017/s1047951120003157 ◽

2020 ◽

Vol 30 (12) ◽

pp. 1910-1916

Author(s):

Rania K. Darwish ◽

Alireza Haghighi ◽

Zeinab S. Seliem ◽

Sonia A. El-Saiedi ◽

Nora H. Radwan ◽

...

Keyword(s):

Next Generation Sequencing ◽

Hypertrophic Cardiomyopathy ◽

Genetic Background ◽

Rare Variants ◽

National Study ◽

Next Generation ◽

Targeted Next Generation Sequencing ◽

Pathogenic Variants ◽

Egyptian Children ◽

Generation Sequencing

AbstractPaediatric cardiomyopathy is a progressive and often lethal disorder and the most common cause of heart failure in children. Despite their severe outcomes, their genetic etiology is still poorly characterised. The current study aimed at uncovering the genetic background of idiopathic primary hypertrophic cardiomyopathy in a cohort of Egyptian children using targeted next-generation sequencing. The study included 24 patients (15 males and 9 females) presented to the cardiomyopathy clinic of Cairo University Children’s Hospital with a median age of 2.75 (0.5–14) years. Consanguinity was positive in 62.5% of patients. A family history of hypertrophic cardiomyopathy was present in 20.8% of patients. Ten rare variants were detected in eight patients; two pathogenic variants (8.3%) in MBPC3 and MYH7, and eight variants of uncertain significance in MYBPC3, TTN, VCL, MYL2, CSRP3, and RBM20.Here, we report on the first national study in Egypt that analysed sarcomeric and non-sarcomeric variants in a cohort of idiopathic paediatric hypertrophic cardiomyopathy patients using next-generation sequencing. The current pilot study suggests that paediatric hypertrophic cardiomyopathy in Egypt might have a particular genetic background, especially with the high burden of consanguinity. Including the genetic testing in the routine diagnostic service is important for a better understanding of the pathophysiology of the disease, proper patient management, and at-risk detection. Genome-wide tests (whole exome/genome sequencing) might be better than the targeted sequencing approach to test primary hypertrophic cardiomyopathy patients in addition to its ability for the identification of novel genetic causes.

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