scholarly journals A comparative study of mutation screening of sarcomeric genes ( MYBPC3 , MYH7 , TNNT2 ) using single gene approach versus targeted gene panel next generation sequencing in a cohort of HCM patients in Egypt

2017 ◽  
Vol 18 (4) ◽  
pp. 381-387
Author(s):  
Heba Sh. Kassem ◽  
Roddy Walsh ◽  
Paul J. Barton ◽  
Besra S. Abdelghany ◽  
Remon S. Azer ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Comparative Study ◽  
Single Gene ◽  
Mutation Screening ◽  
Gene Panel ◽  
Next Generation ◽  
Generation Sequencing ◽  
Sarcomeric Genes

scholarly journals A novel PKHD1 mutation identified in a family affected by ARPKD Ling Hou, Yue Du, Chengguang Zhao, Yubin Wu

2018 ◽  
Vol 2 (1) ◽  
Author(s):  
Ling Hou ◽  
Yue Du ◽  
Chengguang Zhao ◽  
Yubin Wu
Keyword(s):  
Next Generation Sequencing ◽  
Single Gene ◽  
Mutation Screening ◽  
Genetic Diagnosis ◽  
Compound Heterozygous ◽  
Next Generation ◽  
Blood Leukocytes ◽  
Gene Capture ◽  
Renal Cystic Disease ◽  
Generation Sequencing

Objective Autosomal recessive polycystic kidney disease (ARPKD) is a rare inherited renal cystic disease involving multiple organs. It is caused by mutations in the PKHD1 gene. Here, we investigate the gene mutations in a family affected by ARPKD. Methods Genomic DNA was extracted from peripheral blood leukocytes obtained from the subjects, by means of targeted gene capture and next generation sequencing technologies for mutation screening, and were confirmed by Sanger sequencing. Results Two heterozygous mutations of PKHD1, c.6890T>C (p.Ile2297Thr) and c.11215C>T (p.Arg3739Trp), located in exons 43 and 62, respectively, were identified in the patient. Furthermore, the father and mother were revealed to be carriers of heterozygous c.6890T>C (p.Ile2297Thr) and c.11215C>T (p.Arg3739Trp) mutations, respectively. Mutation of c.11215C>T (p.Arg3739Trp) has been found in the ARPKD Mutation Database (http://www.humgen.rwth-aachen.de) but mutation of c.6890T>C (p.Ile2297Thr) has not been reported. Conclusions Compound heterozygous PKHD1 mutations were elucidated to be the molecular basis of ARPKD in this patient. The newly identified c.6890T>C (p.Ile2297Thr) mutation in the patient expands the mutation spectrum of the PKHD1 gene. Targeted gene capture and next generation sequencing are suitable for genetic diagnosis of single-gene inherited diseases like ARPKD, in which the pathogenic gene is large.

Experience with the targeted next-generation sequencing in the diagnosis of hereditary hypophosphatemic rickets

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Ihsan Turan ◽  
Sevcan Erdem ◽  
Leman Damla Kotan ◽  
Semine Ozdemir Dilek ◽  
Mehmet Tastan ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Single Gene ◽  
Care Center ◽  
Tertiary Care ◽  
Gene Panel ◽  
Hypophosphatemic Rickets ◽  
Next Generation ◽  
Efficient Manner ◽  
Individual Gene ◽  
Generation Sequencing

Abstract Objectives Hereditary Hypophosphatemic Rickets (HHR) is a heterogeneous group of disorders characterized by hypophosphatemia. Although the X-linked dominant HHR is the most common form, the genetic etiology of HHR is variable. Recently, developed next-generation sequencing techniques may provide opportunities for making HHR diagnosis in a timely and efficient way. Methods We investigated clinical and genetic features for 18 consecutive probands and their 17 affected family members with HHR. All patient’s clinical and biochemical data were collected. We first analyzed a single gene with Next-generation sequencing if the patients have a strong clue for an individual gene. For the remaining cases, a Hypophosphatemic Rickets gene panel, including all known HHR genes by Next-generation sequencing, was employed. Results We were able to diagnosis all of the consecutive 35 patients in our tertiary care center. We detected nine novel and 10 previously described variants in PHEX (9; 50%), SLC34A3 (3; 17%), ENPP1 (3; 17%), SLC34A1 (1; 5%), CLCN5 (1; 5%), and DMP1 (1; 5%). Conclusions To delineate the etiology of HHR cases in a cost and time-efficient manner, we propose single gene analysis by next-generation sequencing if findings of patients indicate a strong clue for an individual gene. If that analysis is negative or for all other cases, a Next-generation Sequence gene panel, which includes all known HHR genes, should be employed.

scholarly journals Molecular Diagnostic of Solid Tumor Using a Next Generation Sequencing Custom-Designed Multi-Gene Panel

Diagnostics ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 250 ◽  
Author(s):  
Dario de Biase ◽  
Giorgia Acquaviva ◽  
Michela Visani ◽  
Viviana Sanza ◽  
Chiara M. Argento ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Solid Tumors ◽  
Single Gene ◽  
Gene Panel ◽  
Molecular Diagnostic ◽  
Analytical Sensitivity ◽  
Next Generation ◽  
Gene Characterization ◽  
Generation Sequencing ◽  
Oncosuppressor Genes

Next generation sequencing (NGS) allows parallel sequencing of multiple genes at a very high depth of coverage. The need to analyze a variety of targets for diagnostic/prognostic/predictive purposes requires multi-gene characterization. Multi-gene panels are becoming standard approaches for the molecular analysis of solid lesions. We report a custom-designed 128 multi-gene panel engineered to cover the relevant targets in 22 oncogene/oncosuppressor genes for the analysis of the solid tumors most frequently subjected to routine genotyping. A total of 1695 solid tumors were analyzed for panel validation. The analytical sensitivity is 5%. Analytical validation: (i) Accuracy: sequencing results obtained using the multi-gene panel are concordant using two different NGS platforms and single-gene approach sequencing (100% of 83 cases); (ii) Precision: consistent results are obtained in the samples analyzed twice with the same platform (100% of 20 cases). Clinical validation: the frequency of mutations identified in different tumor types is consistent with the published literature. This custom-designed multi-gene panel allows to analyze with high sensitivity and throughput 22 oncogenes/oncosuppressor genes involved in diagnostic/prognostic/predictive characterization of central nervous system tumors, non-small-cell lung carcinomas, colorectal carcinomas, thyroid nodules, pancreatic lesions, melanoma, oral squamous carcinomas and gastrointestinal stromal tumors.

scholarly journals Frequency detection of BRAF V600E mutation in a cohort of pediatric langerhans cell histiocytosis patients by next-generation sequencing

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Shunqiao Feng ◽  
Lin Han ◽  
Mei Yue ◽  
Dixiao Zhong ◽  
Jing Cao ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Langerhans Cell Histiocytosis ◽  
Mutation Screening ◽  
Langerhans Cell ◽  
Braf V600e ◽  
P Value ◽  
Type I ◽  
Next Generation ◽  
Mutation Status ◽  
Generation Sequencing

Abstract Background Langerhans cell histiocytosis (LCH) is a rare neoplastic disease that occurs in both children and adults, and BRAF V600E is detected in up to 64% of the patients. Several studies have discussed the associations between BRAF V600E mutation and clinicopathological manifestations, but no clear conclusions have been drawn regarding the clinical significance of the mutation in pediatric patients. Results We retrieved the clinical information for 148 pediatric LCH patients and investigated the BRAF V600E mutation using next-generation sequencing alone or with droplet digital PCR. The overall positive rate of BRAF V600E was 60/148 (41%). The type of sample (peripheral blood and formalin-fixed paraffin-embedded tissue) used for testing was significantly associated with the BRAF V600E mutation status (p-value = 0.000 and 0.000). The risk of recurrence declined in patients who received targeted therapy (p-value = 0.006; hazard ratio 0.164, 95%CI: 0.046 to 0.583). However, no correlation was found between the BRAF V600E status and gender, age, stage, specific organ affected, TP53 mutation status, masses close to the lesion or recurrence. Conclusions This is the largest pediatric LCH study conducted with a Chinese population to date. BRAF V600E in LCH may occur less in East Asian populations than in other ethnic groups, regardless of age. Biopsy tissue is a more sensitive sample for BRAF mutation screening because not all of circulating DNA is tumoral. Approaches with low limit of detection or high sensitivity are recommended for mutation screening to avoid type I and II errors.

scholarly journals Development of a Next-Generation Sequencing Method for BRCA Mutation Screening

2012 ◽  
Vol 14 (6) ◽  
pp. 602-612 ◽  
Author(s):  
Maurice Chan ◽  
Shen Mo Ji ◽  
Zhen Xuan Yeo ◽  
Linda Gan ◽  
Eric Yap ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Brca Mutation ◽  
Mutation Screening ◽  
Next Generation ◽  
Sequencing Method ◽  
Generation Sequencing ◽  
Next Generation Sequencing Method

SAT0531 NEXT GENERATION SEQUENCING AND AUTOINFLAMMATORY SYNDROMES: CLINICAL AND GENETICAL CORRELATION ON AN ADULT POPULATION FROM A REFERRAL THIRD-CARE CENTRE

2020 ◽  
Vol 79 (Suppl 1) ◽  
pp. 1223-1223
Author(s):  
J. R. Marques Soares ◽  
M. Antolin Mate ◽  
E. Garcia Arumi ◽  
E. Tizzano Ferrari ◽  
S. Bujan Rivas
Keyword(s):  
Next Generation Sequencing ◽  
Genetic Data ◽  
Clinical Suspicion ◽  
Gene Panel ◽  
Adult Patients ◽  
Next Generation ◽  
Related Gene ◽  
Unknown Significance ◽  
Level Hospital ◽  
Generation Sequencing

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

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

2018 ◽  
Vol 110 (1) ◽  
pp. 6-15 ◽  
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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