Comparison between two different next generation sequencing platforms for clinical relevant gene mutation test in solid tumours

2020 ◽  
Vol 73 (9) ◽  
pp. 602-604
Author(s):  
Silvia Bessi ◽  
Francesco Pepe ◽  
Marco Ottaviantonio ◽  
Pasquale Pisapia ◽  
Umberto Malapelle ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
High Performance ◽  
Solid Tumours ◽  
Next Generation ◽  
Formalin Fixed Paraffin ◽  
Ffpe Samples ◽  
Thermo Fisher Scientific ◽  
Formalin Fixed Paraffin Embedded ◽  
Sequencing Platforms ◽  
Generation Sequencing

In the present study, we analysed 44 formalin fixed paraffin embedded (FFPE) from different solid tumours by adopting two different next generation sequencing platforms: GeneReader (QIAGEN, Hilden, Germany) and Ion Torrent (Thermo Fisher Scientific, Waltham, Massachusetts, USA). We highlighted a 100% concordance between the platforms. In addition, focusing on variant detection, we evaluated a very good agreement between the two tests (Cohen’s kappa=0.84) and, when taking into account variant allele fraction value for each variant, a very high concordance was obtained (Pearson’s r=0.94). Our results underlined the high performance rate of GeneReader on FFPE samples and its suitability in routine molecular predictive practice.

scholarly journals Robustness of Next Generation Sequencing on Older Formalin-Fixed Paraffin-Embedded Tissue

PLoS ONE ◽  
2015 ◽  
Vol 10 (7) ◽  
pp. e0127353 ◽  
Author(s):  
Danielle Mercatante Carrick ◽  
Michele G. Mehaffey ◽  
Michael C. Sachs ◽  
Sean Altekruse ◽  
Corinne Camalier ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Next Generation ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Generation Sequencing ◽  
Formalin Fixed

scholarly journals Improved next-generation sequencing pre-capture library yields and sequencing parameters using on-bead PCR

BioTechniques ◽  
2020 ◽  
Vol 68 (1) ◽  
pp. 48-51 ◽  
Author(s):  
Christopher R McEvoy ◽  
Timothy Semple ◽  
Bhargavi Yellapu ◽  
David Y Choong ◽  
Huiling Xu ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Variant Calling ◽  
Limiting Factor ◽  
Next Generation ◽  
Tumor Biopsy ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Next Generation Sequencing Ngs ◽  
Tumor Dna ◽  
Generation Sequencing

Tumor DNA sequencing results can have important clinical implications. However, its use is often limited by low DNA input, owing to small tumor biopsy size. To help overcome this limitation we have developed a simple improvement to a commonly used next-generation sequencing (NGS) capture-based library preparation method using formalin-fixed paraffin-embedded-derived tumor DNA. By using on-bead PCR for pre-capture library generation we show that library yields are dramatically increased, resulting in decreased sample failure rates. Improved yields allowed for a reduction in PCR cycles, which translated into improved sequencing parameters without affecting variant calling. This methodology should be applicable to any NGS system in which input DNA is a limiting factor.

scholarly journals Differences in Mutational Profile between Follicular Thyroid Carcinoma and Follicular Thyroid Adenoma Identified Using Next Generation Sequencing

2019 ◽  
Vol 20 (13) ◽  
pp. 3126 ◽  
Author(s):  
Martyna Borowczyk ◽  
Ewelina Szczepanek-Parulska ◽  
Szymon Dębicki ◽  
Bartłomiej Budny ◽  
Frederik A. Verburg ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
P Value ◽  
Thyroid Adenoma ◽  
Next Generation ◽  
Mutational Status ◽  
Follicular Thyroid Adenoma ◽  
Ffpe Samples ◽  
Formalin Fixed Paraffin Embedded ◽  
Follicular Lesions ◽  
Generation Sequencing

We aimed to identify differences in mutational status between follicular thyroid adenoma (FTA) and follicular thyroid cancer (FTC). The study included 35 patients with FTA and 35 with FTC. DNA was extracted from formalin-fixed paraffin-embedded (FFPE) samples from thyroidectomy. Next-generation sequencing (NGS) was performed with the 50-gene Ion AmpliSeq Cancer Hotspot Panel v2. Potentially pathogenic mutations were found in 14 (40%) FTA and 24 (69%) FTC patients (OR (95%CI) = 3.27 (1.22−8.75)). The number of mutations was higher in patients with FTC than FTA (p-value = 0.03). SMAD4 and STK11 mutations were present only in patients with FTA, while defects in FBXW7, JAK3, KIT, NRAS, PIK3CA, SMARCB1, and TP53 were detected exclusively in FTC patients. TP53 mutations increased the risk of FTC; OR (95%CI) = 29.24 (1.64–522.00); p-value = 0.001. FLT3-positivity was higher in FTC than in the FTA group (51.4% vs. 28.6%; p-value = 0.051). The presence of FLT3 and TP53 with no RET mutations increased FTC detectability by 17.1%, whereas the absence of FLT3 and TP53 with a presence of RET mutations increased FTA detectability by 5.7%. TP53 and FLT3 are candidate markers for detecting malignancy in follicular lesions. The best model to predict FTA and FTC may consist of FLT3, TP53, and RET mutations considered together.

scholarly journals Amplicon-Based Next-Generation Sequencing for Detection of Fungi in Formalin-Fixed, Paraffin-Embedded Tissues

2020 ◽  
Vol 22 (10) ◽  
pp. 1287-1293
Author(s):  
Paige M.K. Larkin ◽  
Katy L. Lawson ◽  
Deisy A. Contreras ◽  
Catherine Q. Le ◽  
Marisol Trejo ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Next Generation ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Generation Sequencing ◽  
Formalin Fixed
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