scholarly journals Towards standardization of next-generation sequencing of FFPE samples for clinical oncology: intrinsic obstacles and possible solutions

2017 ◽  
Vol 15 (1) ◽  
Author(s):  
Maxim Ivanov ◽  
Konstantin Laktionov ◽  
Valery Breder ◽  
Polina Chernenko ◽  
Ekaterina Novikova ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Clinical Oncology ◽  
Next Generation ◽  
Ffpe Samples ◽  
Generation Sequencing

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.

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.

Targeted next generation sequencing in FFPE samples of NSCLC

Pathology ◽  
2016 ◽  
Vol 48 ◽  
pp. S121
Author(s):  
W.A. Cooper ◽  
S. Kraitsek ◽  
C.I. Selinger ◽  
T. Tran ◽  
M. Kohonen-Corish ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Next Generation ◽  
Targeted Next Generation Sequencing ◽  
Ffpe Samples ◽  
Generation Sequencing

scholarly journals Gastrointestinal manifestations of Talaromyces marneffei infection in an HIV-infected patient rapidly verified by metagenomic next-generation sequencing: a case report

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Ying Zhou ◽  
Yongfeng Liu ◽  
Ying Wen
Keyword(s):  
Abdominal Pain ◽  
Next Generation Sequencing ◽  
Next Generation ◽  
Talaromyces Marneffei ◽  
Clinical Presentations ◽  
Omentum Majus ◽  
Ffpe Samples ◽  
Important Diagnostic Tool ◽  
Living With Hiv ◽  
Generation Sequencing

Abstract Background The manifestation of Talaromyces marneffei infection in some HIV-infected patients may be atypical. Cases with gastrointestinal involvement have rarely been reported. It is hard to make a diagnosis when patients are lacking the characteristic rash and positive blood culture. Case presentation Here, we described a patient living with HIV who complained of fever and abdominal pain, and was rapidly diagnosed with Talaromyces marneffei infection by metagenomic next-generation sequencing (mNGS) using formalin-fixation and paraffin-embedded (FFPE) samples of omentum majus tissue. We also reviewed reported related cases. Conclusions Talaromyces marneffei is an unusual cause of clinical presentations involving obvious abdominal pain and lower gastrointestinal bleeding, but can be included in the differential diagnosis. As an important diagnostic tool, the significance of mNGS using FFPE samples of lesions provides a more targeted diagnosis.

scholarly journals Analysis of Copy Number Variations in Solid Tumors Using a Next Generation Sequencing Custom Panel

2021 ◽  
Vol 2 (2) ◽  
pp. 123-134
Author(s):  
Marta Vives-Usano ◽  
Beatriz García Pelaez ◽  
Ruth Román Lladó ◽  
Mónica Garzón Ibañez ◽  
Erika Aldeguer ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Copy Number ◽  
Copy Number Variations ◽  
Next Generation ◽  
Ffpe Samples ◽  
Custom Panel ◽  
Next Generation Sequencing Ngs ◽  
Generation Sequencing ◽  
Approach Time ◽  
Selection Of

Somatic copy number variations (CNV; i.e., amplifications and deletions) have been implicated in the origin and development of multiple cancers and some of these aberrations are designated targets for therapies. Although FISH is still considered the gold standard for CNV detection, the increasing number of potentially druggable amplifications to be assessed makes a gene-by-gene approach time- and tissue-consuming. Here we investigated the potential of next generation sequencing (NGS) custom panels to simultaneously determine CNVs across FFPE solid tumor samples. DNA was purified from cell lines and FFPE samples and analyzed by NGS sequencing using a 20-gene custom panel in the GeneReader Platform®. CNVs were identified using an in-house algorithm based on the UMI read coverage. Retrospective validation of in-house algorithm to identify CNVs showed 97.1% concordance rate with the NGS custom panel. The prospective analysis was performed in a cohort of 243 FFPE samples from patients arriving at our hospital, which included 74 NSCLC tumors, 148 CRC tumors, and 21 other tumors. Of them, 33% presented CNVs by NGS and in 14 cases (5.9%) the CNV was the only alteration detected. We have identified CNV alterations in about one-third of our cohort, including FGFR1, CDK6, CDK4, EGFR, MET, ERBB2, BRAF, or KRAS. Our work highlights the need to include CNV testing as a part of routine NGS analysis in order to uncover clinically relevant gene amplifications that can guide the selection of therapies.

scholarly journals A cross comparison of technologies for the detection of microRNAs in clinical FFPE samples of hepatoblastoma patients

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Aniruddha Chatterjee ◽  
Anna L Leichter ◽  
Vicky Fan ◽  
Peter Tsai ◽  
Rachel V Purcell ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Mirna Expression ◽  
Expression Profiles ◽  
Next Generation ◽  
Quality Of Data ◽  
Sequencing Platform ◽  
Biological Source ◽  
Two Samples ◽  
Ffpe Samples ◽  
Generation Sequencing

Abstract Although formalin fixed paraffin embedded (FFPE) tissue is a major biological source in cancer research, it is challenging to work with due to macromolecular fragmentation and nucleic acid crosslinking. Therefore, it is important to characterise the quality of data that can be obtained from FFPE samples. We have compared three independent platforms (next generation sequencing, microarray and NanoString) for profiling microRNAs (miRNAs) using clinical FFPE samples from hepatoblastoma (HB) patients. The number of detected miRNAs ranged from 228 to 345 (median=294) using the next generation sequencing platform, whereas 79 to 125 (median=112) miRNAs were identified using microarrays in three HB samples, including technical replicates. NanoString identified 299 to 372 miRNAs in two samples. Between the platforms, we observed high reproducibility and significant levels of shared detection. However, for commonly detected miRNAs, a strong correlation between platforms was not observed. Analysis of 10 additional HB samples with NanoString identified significantly overlapping miRNA expression profiles and an alternative pattern was identified in a poorly differentiated HB with an aggressive phenotype. This investigation serves as a roadmap for future studies investigating miRNA expression in clinical FFPE samples and as a guideline for the selection of an appropriate platform.

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