Development and interlaboratory evaluation of a NIST Reference Material RM 8366 for EGFR and MET gene copy number measurements
| Autor: | Kenneth D. Cole, Biswajit Das, Li Chen, P. Mickey Williams, Steve Lund, Megan H. Cleveland, Christopher R McEvoy, Jamie L. Almeida, Carolyn R. Steffen, Corinne Camalier, Liang-Chun Liu, Kara L. Norman, Chris Karlovich, Hua-Jun He, Andrew Fellowes |
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| Rok vydání: | 2019 |
| Předmět: |
0301 basic medicine
EGFR Clinical Biochemistry Gene Dosage Computational biology Biology Polymerase Chain Reaction Proto-Oncogene Mas Article DNA sequencing 03 medical and health sciences 0302 clinical medicine Reference genes Tumor Cells Cultured Humans cancer Digital polymerase chain reaction Copy-number variation Gene reference material Exome sequencing next generation sequencing Whole genome sequencing digital PCR Biochemistry (medical) High-Throughput Nucleotide Sequencing DNA Neoplasm General Medicine Proto-Oncogene Proteins c-met Reference Standards ErbB Receptors genomic DNA 030104 developmental biology 030220 oncology & carcinogenesis MET |
| Zdroj: | Clinical chemistry and laboratory medicine |
| ISSN: | 1437-4331 1434-6621 |
| DOI: | 10.1515/cclm-2018-1306 |
| Popis: | Background The National Institute of Standards and Technology (NIST) Reference Material RM 8366 was developed to improve the quality of gene copy measurements of EGFR (epidermal growth factor receptor) and MET (proto-oncogene, receptor tyrosine kinase), important targets for cancer diagnostics and treatment. The reference material is composed of genomic DNA prepared from six human cancer cell lines with different levels of amplification of the target genes. Methods The reference values for the ratios of the EGFR and MET gene copy numbers to the copy numbers of reference genes were measured using digital PCR. The digital PCR measurements were confirmed by two additional laboratories. The samples were also characterized using Next Generation Sequencing (NGS) methods including whole genome sequencing (WGS) at three levels of coverage (approximately 1 ×, 5 × and greater than 30 ×), whole exome sequencing (WES), and two different pan-cancer gene panels. The WES data were analyzed using three different bioinformatic algorithms. Results The certified values (digital PCR) for EGFR and MET were in good agreement (within 20%) with the values obtained from the different NGS methods and algorithms for five of the six components; one component had lower NGS values. Conclusions This study shows that NIST RM 8366 is a valuable reference material to evaluate the performance of assays that assess EGFR and MET gene copy number measurements. |
| Databáze: | OpenAIRE |
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