Evidence map›Paper›PMID 31112502›Full record

ArticleClinical chemistry and laboratory medicine2019

Development and interlaboratory evaluation of a NIST Reference Material RM 8366 for EGFR and MET gene copy number measurements.

Hua-Jun He, Biswajit Das, Megan H Cleveland, Li Chen, Corinne E Camalier, Liang-Chun Liu, Kara L Norman, Andrew P Fellowes, Christopher R McEvoy, Steve P Lund and 5 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Clinical chemistry and laboratory medicine, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.

0numbers the graph read from it
0cells of the map it votes in
6citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

6 citing papers in PubMed.

  1. Article
  2. Review
  3. Article
  4. Review
  5. Article
  6. The NHanceBiomedicines · 2021
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

15 authors.

Hua-Jun HeBiosystems and Biomaterials Division, National Institute of Standards and Technology, 100 Bureau Drive, MS 8312, Gaithersburg, MD 20899, USA, Phone: +301-975-2169, Fax: +301-330-3447.
Biswajit DasMolecular Characterization and Clinical Assay Development Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
Megan H ClevelandBiomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, MD, USA.
Li ChenMolecular Characterization and Clinical Assay Development Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
Corinne E CamalierMolecular Characterization and Clinical Assay Development Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
Liang-Chun LiuThermo Fisher Scientific, Fremont, CA, USA.
Kara L NormanThermo Fisher Scientific, Fremont, CA, USA.
Andrew P FellowesPeter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
Christopher R McEvoyPeter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
Steve P LundStatistical Engineering Division, National Institute of Standards and Technology, Gaithersburg, MD, USA.
Jamie AlmeidaBiosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, USA.
Carolyn R SteffenBiomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, MD, USA.
Chris KarlovichMolecular Characterization and Clinical Assay Development Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
P Mickey WilliamsMolecular Characterization and Clinical Assay Development Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
Kenneth D ColeBiosystems and Biomaterials Division, National Institute of Standards and Technology, 100 Bureau Drive, MS 8312, Gaithersburg, MD 20899, USA, Phone: +301-975-2169, Fax: +301-330-3447.

Funding

Intramural NIST DOC 9999-NIST
6 · The paper itself

Abstract

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.

Indexed as

DNA, NeoplasmErbB ReceptorsGene DosageHigh-Throughput Nucleotide SequencingHumansPolymerase Chain ReactionProto-Oncogene MasProto-Oncogene Proteins c-metReference StandardsTumor Cells, CulturedDNA, NeoplasmEGFR protein, humanErbB ReceptorsMAS1 protein, humanMET protein, humanProto-Oncogene MasProto-Oncogene Proteins c-metcancerdigital PCREGFRMETnext generation sequencingreference material

Identifiers

PMID31112502
PMCPMC6875440

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.