scholarly journals A Case of Next-generation Sequencing Gene Testing: Points to be Considered in Testing and Reporting

2022 ◽  
Vol 42 (2) ◽  
pp. 296-297
Author(s):  
Na-Kyoung Kim ◽  
Jong-Won Kim
Keyword(s):  
Next Generation Sequencing ◽  
Next Generation ◽  
Gene Testing ◽  
Generation Sequencing

Next Generation Sequencing May Be More Efficient and Economical Than Targeted Gene Testing in Patients with Primary Immune Deficiency (PID)

2013 ◽  
Vol 131 (2) ◽  
pp. AB52
Author(s):  
Talal Mousallem ◽  
Thomas J. Urban ◽  
Joseph L. Roberts ◽  
Roberta E. Parrott ◽  
David B. Goldstein ◽  
...  
Keyword(s):  
Immune Deficiency ◽  
Next Generation Sequencing ◽  
Primary Immune Deficiency ◽  
Next Generation ◽  
Gene Testing ◽  
Generation Sequencing

A pilot study of gene testing of genetic bone dysplasia using targeted next-generation sequencing

2015 ◽  
Vol 60 (12) ◽  
pp. 769-776 ◽  
Author(s):  
Huiwen Zhang ◽  
Rui Yang ◽  
Yu Wang ◽  
Jun Ye ◽  
Lianshu Han ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Pilot Study ◽  
Bone Dysplasia ◽  
Next Generation ◽  
Targeted Next Generation Sequencing ◽  
Gene Testing ◽  
Generation Sequencing

Analysis of a large cohort of non-small cell lung cancers submitted for somatic variant analysis demonstrates that targeted next-generation sequencing is fit for purpose as a molecular diagnostic assay in routine practice

2018 ◽  
Vol 71 (11) ◽  
pp. 1001-1006 ◽  
Author(s):  
David Allan Moore ◽  
Kevin Balbi ◽  
Alexander Ingham ◽  
Hendrik-Tobias Arkenau ◽  
Philip Bennett
Keyword(s):  
Next Generation Sequencing ◽  
Single Gene ◽  
Small Cell ◽  
Molecular Diagnostic ◽  
Next Generation ◽  
Small Cell Lung ◽  
Targeted Next Generation Sequencing ◽  
Gene Testing ◽  
The Impact ◽  
Generation Sequencing

AimsTargeted next-generation sequencing (tNGS) is increasingly being adopted as an alternative to single gene testing in some centres. Our aim was to assess the overall fitness and utility of tNGS as a routine clinical test in non-small cell lung cancer (NSCLC).MethodsAll NSCLC cases submitted to a single laboratory for tNGS analysis over a 3-year period were included. Rejection/failure rates and turnaround times were calculated. For reportable cases, data relating to observed genetic changes likely to be driving tumour growth and/or contributing to therapeutic resistance were extracted. The impact of varied referral site practices (tissue processing and sample format submitted) on analytical outcomes was also considered.ResultsA total of 2796 cases were submitted, of which 217 (7.8%) were rejected and 131 (5.1%) failed. The median turnaround time was seven working days. Of 2448 reported cases, KRAS, EGFR or other recognised driver mutations were observed in 35%, 17% and 5.4%, respectively. Of the remaining cases, 3.5% demonstrated significant incidental evidence of gene amplification. In 15% of EGFR-driven cases, evidence of an EGFR tyrosine kinase inhibitor resistance mechanism was observed. Potential concerns around the provision of slides or precut ‘rolls’ only (cf, formalin fixed paraffin embedded (FFPE) tissue blocks) as standard practice by certain referral sites were identified.ConclusionsA tNGS panel approach is practically achievable, with acceptable success rates and turnaround times, in the context of a routine clinical service. Furthermore, it provides additional clinically and analytically relevant information, which is not available from single gene testing alone.

scholarly journals Improving hearing loss gene testing: a systematic review of gene evidence toward more efficient next-generation sequencing–based diagnostic testing and interpretation

2015 ◽  
Vol 18 (6) ◽  
pp. 545-553 ◽  
Author(s):  
Ahmad N. Abou Tayoun ◽  
Saeed H. Al Turki ◽  
Andrea M. Oza ◽  
Mark J. Bowser ◽  
Amy L. Hernandez ◽  
...  
Keyword(s):  
Systematic Review ◽  
Hearing Loss ◽  
Next Generation Sequencing ◽  
Diagnostic Testing ◽  
Next Generation ◽  
Gene Testing ◽  
Generation Sequencing

scholarly journals Next-Generation Sequencing in Clinical Practice: Is It a Cost-Saving Alternative to a Single-Gene Testing Approach?

2021 ◽  
Author(s):  
Giancarlo Pruneri ◽  
Filippo De Braud ◽  
Anna Sapino ◽  
Massimo Aglietta ◽  
Andrea Vecchione ◽  
...  
Keyword(s):  
Clinical Practice ◽  
Next Generation Sequencing ◽  
Cost Saving ◽  
Single Gene ◽  
Next Generation ◽  
Gene Testing ◽  
Testing Approach ◽  
Generation Sequencing

Next generation sequencing for detection of EGFR alterations in NSCLC: is more better?

2020 ◽  
pp. jclinpath-2020-207212
Author(s):  
Ullas Batra ◽  
Shrinidhi Nathany ◽  
Mansi Sharma ◽  
Parveen Jain ◽  
Anurag Mehta
Keyword(s):  
Next Generation Sequencing ◽  
Kinase Inhibitor ◽  
Single Gene ◽  
Next Generation ◽  
Cell Lung Carcinoma ◽  
Molecular Features ◽  
Gene Testing ◽  
Clinical Records ◽  
Egfr Mutated ◽  
Generation Sequencing

AimsThe emergence of sophisticated next generation sequencing (NGS) based technologies in routine molecular diagnostics has paved the way for robust and accurate detection of variants which may otherwise be missed on single gene testing. This study aims at highlighting the same premise in EGFR mutated non-small cell lung carcinoma (NSCLC).Methods1350 cases of NSCLC were screened, of which 490 EGFR mutated cases were taken. The clinical records and molecular features were evaluated retrospectively to determine those cases which were missed on single gene testing.ResultsAmong these 490 cases, there were 11 (2.2%) cases which tested negative on single gene testing using polymerase chain reaction (therascreen). These were then subjected to NGS based testing and were positive for 13 different EGFR mutations. Five out of the 11 cases received EGFR tyrosine kinase inhibitor (TKI) based on the NGS test outcome. Four cases with exon 20 insertion mutations were not offered TKI as these mutations are known to be intrinsically resistant to TKI therapy. The five patients who have been treated with TKI have shown fair response and have not progressed to date.ConclusionsWe demonstrated a potentially preferable way to profile treatment-naïve patients with NSCLC by NGS and from our early experience in EGFR mutant cases, the advantages of NGS over single gene testing is clearly evident.

scholarly journals Paroxysmal Movement Disorders

2021 ◽  
Vol 12 ◽  
Author(s):  
Susan Harvey ◽  
Mary D. King ◽  
Kathleen M. Gorman
Keyword(s):  
Next Generation Sequencing ◽  
Movement Disorders ◽  
Clinical Phenotype ◽  
Single Gene ◽  
Copy Number Variant ◽  
Genomic Research ◽  
Next Generation ◽  
Causative Gene ◽  
Gene Testing ◽  
Generation Sequencing

Paroxysmal movement disorders (PxMDs) are a clinical and genetically heterogeneous group of movement disorders characterized by episodic involuntary movements (dystonia, dyskinesia, chorea and/or ataxia). Historically, PxMDs were classified clinically (triggers and characteristics of the movements) and this directed single-gene testing. With the advent of next-generation sequencing (NGS), how we classify and investigate PxMDs has been transformed. Next-generation sequencing has enabled new gene discovery (RHOBTB2, TBC1D24), expansion of phenotypes in known PxMDs genes and a better understanding of disease mechanisms. However, PxMDs exhibit phenotypic pleiotropy and genetic heterogeneity, making it challenging to predict genotype based on the clinical phenotype. For example, paroxysmal kinesigenic dyskinesia is most commonly associated with variants in PRRT2 but also variants identified in PNKD, SCN8A, and SCL2A1. There are no radiological or biochemical biomarkers to differentiate genetic causes. Even with NGS, diagnosis rates are variable, ranging from 11 to 51% depending on the cohort studied and technology employed. Thus, a large proportion of patients remain undiagnosed compared to other neurological disorders such as epilepsy, highlighting the need for further genomic research in PxMDs. Whole-genome sequencing, deep-sequencing, copy number variant analysis, detection of deep-intronic variants, mosaicism and repeat expansions, will improve diagnostic rates. Identifying the underlying genetic cause has a significant impact on patient care, modification of treatment, long-term prognostication and genetic counseling. This paper provides an update on the genetics of PxMDs, description of PxMDs classified according to causative gene rather than clinical phenotype, highlighting key clinical features and providing an algorithm for genetic testing of PxMDs.

Analysis of germline mutations in Chinese colorectal cancer patients with next-generation sequencing.

2020 ◽  
Vol 38 (15_suppl) ◽  
pp. e13651-e13651
Author(s):  
Jing Gao ◽  
Hua Ren ◽  
Haiyan Liao ◽  
Luo Hai ◽  
Yuwei Cong ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Next Generation Sequencing ◽  
Lynch Syndrome ◽  
Genetic Susceptibility ◽  
Susceptibility Gene ◽  
Germline Mutations ◽  
Next Generation ◽  
Pathogenic Variants ◽  
Gene Testing ◽  
Generation Sequencing

e13651 Background: Colorectal cancer (CRC) remains one of the leading causes of morbidity and mortality around the world. Familial cancer syndromes are common in CRC, inherited syndromes including Lynch syndrome (LS), familial adenomatous polyposis (FAP), and MutY human homolog (MUTYH)-associated polyposis (MAP) were well defined. But still, there are not well-established evidence between other several genes and CRC risk. Expanded multi-gene testing may be an alternative to find out the underlying mechanism for genetic susceptibility. Our study aims to assess the germline alternation landscape of Chinese CRC patients. Methods: We performed hybrid capture-based next-generation sequencing (NGS) of 381 genes on tissues from patients with CRC between January 01, 2017 and December 02, 2019 in 3D Medicines database. Genomic alterations including single nucleotide variation (SNV), insertions/deletions, copy number variations, gene rearrangement and fusions were assessed. Results: 1360 CRC patients were included for analysis, in which 95 (7.0%) patients harbored pathogenic (80/95) and likely pathogenic (15/95) germline mutations in 28 cancer predisposition genes. 33 subjects had pathogenic variants associated with Lynch syndrome (15 mutations in MLH1, 9 mutations in MSH2, 6 mutations in MSH6, 3 mutations in PMS2, respectively). 8 subjects had pathogenic variants associated with FAP (3 APC), MAP (3 MUTYH) and Li-Fraumeni syndrome (2 TP53). In addition, 14 pathogenic mutations in moderate penetrance genes (5 ATM, 3 BLM and 6 CHEK2) were found. The frequency of pathogenic BRCA mutations were 1 alternation in BRCA1 and 3 alternations in BRCA2. Conclusions: 7.0 % of patients with Chinese CRC carried germline cancer susceptibility gene mutations. Multi-gene testing would provide references for assessing genetic susceptibility and managing increased surveillance.

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