scholarly journals A Pilot Proficiency Testing Study for Assessing Cancer Gene Panel using Patient Samples and Next-generation Sequencing in Japan

2021 ◽  
Author(s):  
Masato Maekawa ◽  
Terumi Taniguchi ◽  
Kazuto Nishio ◽  
Kazuko Sakai ◽  
Kazuyuki Matsushita ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Proficiency Testing ◽  
Dna Integrity ◽  
Cancer Tissue ◽  
Sufficient Information ◽  
Precision Oncology ◽  
Cancer Gene ◽  
Next Generation ◽  
Advantages And Disadvantages ◽  
Generation Sequencing

Abstract To implement precision oncology, analytical validity as well as clinical validity and utility are important. However, proficiency testing (PT) to assess validity has not yet been systematically performed in Japan. To investigate the quality of next-generation sequencing (NGS) platforms and cancer genome testing prevalent in laboratories, we performed pilot PT using patient samples. We prepared 5 samples from patients with lung or colorectal cancer, extracted genomic DNA from the cancer tissue and peripheral blood, and distributed these to 15 laboratories. Most participating laboratories successfully identified the pathogenic variants, except for two closely located KRAS variants, and 25-bp delins in the EGFR exon 19, not identified by the in vitro diagnostics testing. Conversely, the EGFR L858R variant was successfully identified, and the allele frequency was similar for all the laboratories. A high DNA integrity number led to excellent depth and reliable NGS results. All NGS platforms and bioinformatics pipelines have advantages and disadvantages. We propose the use of a PT program using patient samples to ascertain the quality status of cancer gene testing in laboratories and to ensure that laboratories have sufficient information to develop advancements in precision medicine for cancer.

scholarly journals A Window Into Clinical Next-Generation Sequencing–Based Oncology Testing Practices

2017 ◽  
Vol 141 (12) ◽  
pp. 1679-1685 ◽  
Author(s):  
Rakesh Nagarajan ◽  
Angela N. Bartley ◽  
Julia A. Bridge ◽  
Lawrence J. Jennings ◽  
Suzanne Kamel-Reid ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Proficiency Testing ◽  
Clinical Laboratory ◽  
Precision Oncology ◽  
Next Generation ◽  
Single Nucleotide Variants ◽  
Molecular Oncology ◽  
Survey Results ◽  
Testing Practices ◽  
Generation Sequencing

Context.— Detection of acquired variants in cancer is a paradigm of precision medicine, yet little has been reported about clinical laboratory practices across a broad range of laboratories. Objective.— To use College of American Pathologists proficiency testing survey results to report on the results from surveys on next-generation sequencing–based oncology testing practices. Design.— College of American Pathologists proficiency testing survey results from more than 250 laboratories currently performing molecular oncology testing were used to determine laboratory trends in next-generation sequencing–based oncology testing. Results.— These presented data provide key information about the number of laboratories that currently offer or are planning to offer next-generation sequencing–based oncology testing. Furthermore, we present data from 60 laboratories performing next-generation sequencing–based oncology testing regarding specimen requirements and assay characteristics. The findings indicate that most laboratories are performing tumor-only targeted sequencing to detect single-nucleotide variants and small insertions and deletions, using desktop sequencers and predesigned commercial kits. Despite these trends, a diversity of approaches to testing exists. Conclusions.— This information should be useful to further inform a variety of topics, including national discussions involving clinical laboratory quality systems, regulation and oversight of next-generation sequencing–based oncology testing, and precision oncology efforts in a data-driven manner.

scholarly journals Comparison of three commercial decision support platforms for matching of next-generation sequencing results with therapies in patients with cancer

ESMO Open ◽  
2020 ◽  
Vol 5 (5) ◽  
pp. e000872
Author(s):  
Samantha O Perakis ◽  
Sabrina Weber ◽  
Qing Zhou ◽  
Ricarda Graf ◽  
Sabine Hojas ◽  
...  
Keyword(s):  
Decision Support ◽  
Next Generation Sequencing ◽  
Metastatic Breast ◽  
Clinical Decision ◽  
Molecular Data ◽  
Current Status ◽  
Precision Oncology ◽  
Next Generation ◽  
Generation Sequencing ◽  
Tier I

ObjectivePrecision oncology depends on translating molecular data into therapy recommendations. However, with the growing complexity of next-generation sequencing-based tests, clinical interpretation of somatic genomic mutations has evolved into a formidable task. Here, we compared the performance of three commercial clinical decision support tools, that is, NAVIFY Mutation Profiler (NAVIFY; Roche), QIAGEN Clinical Insight (QCI) Interpret (QIAGEN) and CureMatch Bionov (CureMatch).MethodsIn order to obtain the current status of the respective tumour genome, we analysed cell-free DNA from patients with metastatic breast, colorectal or non-small cell lung cancer. We evaluated somatic copy number alterations and in parallel applied a 77-gene panel (AVENIO ctDNA Expanded Panel). We then assessed the concordance of tier classification approaches between NAVIFY and QCI and compared the strategies to determine actionability among all three platforms. Finally, we quantified the alignment of treatment suggestions across all decision tools.ResultsEach platform varied in its mode of variant classification and strategy for identifying druggable targets and clinical trials, which resulted in major discrepancies. Even the frequency of concordant actionable events for tier I-A or tier I-B classifications was only 4.3%, 9.5% and 28.4% when comparing NAVIFY with QCI, NAVIFY with CureMatch and CureMatch with QCI, respectively, and the obtained treatment recommendations differed drastically.ConclusionsTreatment decisions based on molecular markers appear at present to be arbitrary and dependent on the chosen strategy. As a consequence, tumours with identical molecular profiles would be differently treated, which challenges the promising concepts of genome-informed medicine.

scholarly journals Precision Oncology in Sarcomas: Divide and Conquer

2019 ◽  
pp. 1-16 ◽  
Author(s):  
Roberto Carmagnani Pestana ◽  
Roman Groisberg ◽  
Jason Roszik ◽  
Vivek Subbiah
Keyword(s):  
Next Generation Sequencing ◽  
Soft Tissue Sarcomas ◽  
Genetic Alterations ◽  
Divide And Conquer ◽  
Precision Oncology ◽  
Next Generation ◽  
Mesenchymal Tumors ◽  
Next Generation Sequencing Technology ◽  
Molecular Abnormalities ◽  
Generation Sequencing

Sarcomas are a heterogeneous group of rare malignancies that exhibit remarkable heterogeneity, with more than 50 subtypes recognized. Advances in next-generation sequencing technology have resulted in the discovery of genetic events in these mesenchymal tumors, which in addition to enhancing understanding of the biology, have opened up avenues for molecularly targeted therapy and immunotherapy. This review focuses on how incorporation of next-generation sequencing has affected drug development in sarcomas and strategies for optimizing precision oncology for these rare cancers. In a significant percentage of soft tissue sarcomas, which represent up to 40% of all sarcomas, specific driver molecular abnormalities have been identified. The challenge to evaluate these mutations across rare cancer subtypes requires the careful characterization of these genetic alterations to further define compelling drivers with therapeutic implications. Novel models of clinical trial design also are needed. This shift would entail sustained efforts by the sarcoma community to move from one-size-fits-all trials, in which all sarcomas are treated similarly, to divide-and-conquer subtype-specific strategies.

scholarly journals A Model Study of In Silico Proficiency Testing for Clinical Next-Generation Sequencing

2016 ◽  
Vol 140 (10) ◽  
pp. 1085-1091 ◽  
Author(s):  
Eric J. Duncavage ◽  
Haley J. Abel ◽  
Jason D. Merker ◽  
John B. Bodner ◽  
Qin Zhao ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Proficiency Testing ◽  
In Silico ◽  
Absolute Difference ◽  
Ion Torrent ◽  
Next Generation ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Clinical Laboratories ◽  
Generation Sequencing

Context.—Most current proficiency testing challenges for next-generation sequencing assays are methods-based proficiency testing surveys that use DNA from characterized reference samples to test both the wet-bench and bioinformatics/dry-bench aspects of the tests. Methods-based proficiency testing surveys are limited by the number and types of mutations that either are naturally present or can be introduced into a single DNA sample. Objective.—To address these limitations by exploring a model of in silico proficiency testing in which sequence data from a single well-characterized specimen are manipulated electronically. Design.—DNA from the College of American Pathologists reference genome was enriched using the Illumina TruSeq and Life Technologies AmpliSeq panels and sequenced on the MiSeq and Ion Torrent platforms, respectively. The resulting data were mutagenized in silico and 26 variants, including single-nucleotide variants, deletions, and dinucleotide substitutions, were added at variant allele fractions (VAFs) from 10% to 50%. Participating clinical laboratories downloaded these files and analyzed them using their clinical bioinformatics pipelines. Results.—Laboratories using the AmpliSeq/Ion Torrent and/or the TruSeq/MiSeq participated in the 2 surveys. On average, laboratories identified 24.6 of 26 variants (95%) overall and 21.4 of 22 variants (97%) with VAFs greater than 15%. No false-positive calls were reported. The most frequently missed variants were single-nucleotide variants with VAFs less than 15%. Across both challenges, reported VAF concordance was excellent, with less than 1% median absolute difference between the simulated VAF and mean reported VAF. Conclusions.—The results indicate that in silico proficiency testing is a feasible approach for methods-based proficiency testing, and demonstrate that the sensitivity and specificity of current next-generation sequencing bioinformatics across clinical laboratories are high.

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