scholarly journals Oncomine™ Comprehensive Assay v3 vs. Oncomine™ Comprehensive Assay Plus

Cancers ◽  
2021 ◽  
Vol 13 (20) ◽  
pp. 5230
Author(s):  
Lau K. Vestergaard ◽  
Douglas N. P. Oliveira ◽  
Tim S. Poulsen ◽  
Claus K. Høgdall ◽  
Estrid V. Høgdall
Keyword(s):  
Clinical Decision Making ◽  
Gene Mutations ◽  
Clinical Decision ◽  
Overlapping Genes ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Tumor Mutational Burden ◽  
Gene Panels ◽  
Multiple Samples ◽  
Formalin Fixed

The usage of next generation sequencing in combination with targeted gene panels has enforced a better understanding of tumor compositions. The identification of key genomic biomarkers underlying a disease are crucial for diagnosis, prognosis, treatment and therapeutic responses. The Oncomine™ Comprehensive Assay v3 (OCAv3) covers 161 cancer-associated genes and is routinely employed to support clinical decision making for a therapeutic course. An improved version, Oncomine™ Comprehensive Assay Plus (OCA-Plus), has been recently developed, covering 501 genes (144 overlapping with OCAv3) in addition to microsatellite instability (MSI) and tumor mutational burden (TMB) assays in one workflow. The validation of MSI and TMB was not addressed in the present study. However, the implementation of new assays must be validated and confirmed across multiple samples before it can be introduced into a clinical setting. Here, we report the comparison of DNA sequencing results from 50 ovarian cancer formalin-fixed, paraffin-embedded samples subjected to OCAv3 and OCA-Plus. A validation assessment of gene mutations identified using OCA-Plus was performed on the 144 overlapping genes and 313,769 intersecting nucleotide positions of the OCAv3 and the OCA-Plus. Our results showed a 91% concordance within variants classified as likely-pathogenic or pathogenic. Moreover, results showed that a region of PTEN is poorly covered by the OCA-Plus assay, hence, we implemented rescue filters for those variants. In conclusion, the OCA-Plus can reflect the mutational profile of genomic variants compared with OCAv3 of 144 overlapping genes, without compromising performance.

scholarly journals Large scale, robust, and accurate whole transcriptome profiling from clinical formalin-fixed paraffin-embedded samples

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Yulia Newton ◽  
Andrew J. Sedgewick ◽  
Luis Cisneros ◽  
Justin Golovato ◽  
Mark Johnson ◽  
...  
Keyword(s):  
Large Scale ◽  
Clinical Decision Making ◽  
Rna Extraction ◽  
Transcriptome Profiling ◽  
Clinical Decision ◽  
Extraction Methods ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Whole Transcriptome ◽  
Formalin Fixed

Abstract Transcriptome profiling can provide information of great value in clinical decision-making, yet RNA from readily available formalin-fixed paraffin-embedded (FFPE) tissue is often too degraded for quality sequencing. To assess the clinical utility of FFPE-derived RNA, we performed ribo-deplete RNA extractions on > 3200 FFPE slide samples; 25 of these had direct FFPE vs. fresh frozen (FF) replicates, 57 were sequenced in 2 different labs, 87 underwent multiple library analyses, and 16 had direct microdissected vs. macrodissected replicates. Poly-A versus ribo-depletion RNA extraction methods were compared using transcriptomes of TCGA cohort and 3116 FFPE samples. Compared to FF, FFPE transcripts coding for nuclear/cytoplasmic proteins involved in DNA packaging, replication, and protein synthesis were detected at lower rates and zinc finger family transcripts were of poorer quality. The greatest difference in extraction methods was in histone transcripts which typically lack poly-A tails. Encouragingly, the overall sequencing success rate was 81%. Exome coverage was highly concordant in direct FFPE and FF replicates, with 98% agreement in coding exon coverage and a median correlation of whole transcriptome profiles of 0.95. We provide strong rationale for clinical use of FFPE-derived RNA based on the robustness, reproducibility, and consistency of whole transcriptome profiling.

Comparison of whole-exome sequencing of matched fresh and formalin fixed paraffin embedded melanoma tumours: implications for clinical decision making

Pathology ◽  
2016 ◽  
Vol 48 (3) ◽  
pp. 261-266 ◽  
Author(s):  
Ricardo De Paoli-Iseppi ◽  
Peter A. Johansson ◽  
Alexander M. Menzies ◽  
Kerith-Rae Dias ◽  
Gulietta M. Pupo ◽  
...  
Keyword(s):  
Decision Making ◽  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Clinical Decision Making ◽  
Clinical Decision ◽  
Whole Exome ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Formalin Fixed

scholarly journals Formalin-fixed paraffin-embedded renal biopsy tissues: an underexploited biospecimen resource for gene expression profiling in IgA nephropathy

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Sharon Natasha Cox ◽  
Samantha Chiurlia ◽  
Chiara Divella ◽  
Michele Rossini ◽  
Grazia Serino ◽  
...  
Keyword(s):  
Gene Expression ◽  
Iga Nephropathy ◽  
Clinical Decision Making ◽  
Expression Profiles ◽  
Specific Gene ◽  
Renal Lesions ◽  
Formalin Fixed Paraffin ◽  
Renal Biopsies ◽  
Formalin Fixed Paraffin Embedded ◽  
Formalin Fixed

Abstract Primary IgA nephropathy (IgAN) diagnosis is based on IgA-dominant glomerular deposits and histological scoring is done on formalin-fixed paraffin embedded tissue (FFPE) sections using the Oxford classification. Our aim was to use this underexploited resource to extract RNA and identify genes that characterize active (endocapillary–extracapillary proliferations) and chronic (tubulo-interstitial) renal lesions in total renal cortex. RNA was extracted from archival FFPE renal biopsies of 52 IgAN patients, 22 non-IgAN and normal renal tissue of 7 kidney living donors (KLD) as controls. Genome-wide gene expression profiles were obtained and biomarker identification was carried out comparing gene expression signatures a subset of IgAN patients with active (N = 8), and chronic (N = 12) renal lesions versus non-IgAN and KLD. Bioinformatic analysis identified transcripts for active (DEFA4,TNFAIP6,FAR2) and chronic (LTB,CXCL6, ITGAX) renal lesions that were validated by RT-PCR and IHC. Finally, two of them (TNFAIP6 for active and CXCL6 for chronic) were confirmed in the urine of an independent cohort of IgAN patients compared with non-IgAN patients and controls. We have integrated transcriptomics with histomorphological scores, identified specific gene expression changes using the invaluable repository of archival renal biopsies and discovered two urinary biomarkers that may be used for specific clinical decision making.

scholarly journals A scalable solution for tumor mutational burden from formalin-fixed, paraffin-embedded samples using the Oncomine Tumor Mutation Load Assay

2018 ◽  
Vol 7 (5) ◽  
pp. 616-630 ◽  
Author(s):  
Ruchi Chaudhary ◽  
Luca Quagliata ◽  
Jermann Philip Martin ◽  
Ilaria Alborelli ◽  
Dinesh Cyanam ◽  
...  
Keyword(s):  
Mutation Load ◽  
Mutational Burden ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Tumor Mutational Burden ◽  
Formalin Fixed

Justification of direct Sanger sequencing application for detection of KIT and PDGFRα gene mutations in formalin-fixed, paraffin-embedded samples from gastrointestinal stromal tumours

2019 ◽  
Vol 73 (4) ◽  
pp. 213-219
Author(s):  
Katarzyna Kiwerska ◽  
Joanna Wroblewska ◽  
Apolonia Kaluzna ◽  
Andrzej Marszalek
Keyword(s):  
Sanger Sequencing ◽  
Mutational Analysis ◽  
Gene Mutations ◽  
Disease Diagnosis ◽  
Gastrointestinal Stromal Tumours ◽  
Coding Regions ◽  
Hrm Analysis ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Formalin Fixed

AimsThe knowledge concerning genetic background of gastrointestinal stromal tumours (GISTs) is well recognised, and the accurate detection of KIT and PDGFRα mutations is of great importance for the process of disease diagnosis and patient’s treatment. In this study, we compare the usefulness of real-time PCR-based techniques and Sanger sequencing to detect mutations of both genes in 41 formalin-fixed, paraffin-embedded GIST samples.MethodsThe analysis encompassed most frequently mutated coding regions of KIT (exons 9, 11, 13 and 17) and PDGFRα (exons 12, 14 and 18) genes. The GIST Mutation Detection Kit (EntroGen), direct Sanger sequencing and high-resolution melting (HRM) analysis were applied to conduct the study.ResultsWith the application of EntroGen kit, we found alterations in 22/38 samples, with Sanger sequencing variants were found in 36/41 samples. The concordant results for both methods were observed in 19/38 samples. With subsequently applied HRM analysis, we have confirmed that all samples, except one, harboured alterations in the regions indicated by Sanger sequencing.ConclusionsOur results show that in GIST samples, carrying a broad spectrum of deletions, Sanger sequencing is a better, more sensitive method for mutational analysis of KIT and PDGFRα genes.

scholarly journals Characteristics of genomic alterations in Chinese cholangiocarcinoma patients

2020 ◽  
Vol 50 (10) ◽  
pp. 1117-1125
Author(s):  
Guoping Jiang ◽  
Wu Zhang ◽  
Ting Wang ◽  
Songming Ding ◽  
Xiaoliang Shi ◽  
...  
Keyword(s):  
Genomic Alteration ◽  
Molecular Evidence ◽  
Cancer Genes ◽  
Primary Malignancy ◽  
Exact Test ◽  
Mutational Burden ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Tumor Mutational Burden ◽  
Formalin Fixed

Abstract Objective Cholangiocarcinoma (CCA) is a primary malignancy, which is often diagnosed as advanced and inoperable due to the lack of effective biomarkers and poor sensitivity of clinical diagnosis. Here, we aimed to identify the genomic profile of CCA and provided molecular evidence for further biomarker development. Methods The formalin-fixed paraffin-embedded and matching blood samples were sequenced by deep sequencing targeting 450 cancer genes and genomic alteration analysis was performed. Tumor mutational burden (TMB) was measured by an algorithm developed in-house. Correlation analysis was performed by Fisher’s exact test. Results The most commonly altered genes in this cohort were TP53 (41.27%, 26/63), KRAS (31.75%, 20/63), ARID1A and IDH1 (15.87%, 10/63, for both), SMAD4 (14.29%, 9/63), FGFR2 and BAP1 (12.70%, 8/63, for both), and CDKN2A (11.11%, 7/63). BAP1 mutations were significantly correlated with the CCA subtype. LRP2 mutations were significantly associated with the younger intrahepatic CCA (iCCA) patients, while BAP1 was associated with iCCA patients aged 55–65 years old. BAP1 and LRP2 mutations were associated with TMB. Conclusions Most Chinese CCA patients were 50–70 years old. BAP1 and LRP2 mutations were associated with the age of iCCA patients.

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