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SHR Neuro Cancer Cardio Lipid Metab Microb
Kimbacher, C; Paar, C; Freystetter, A; Berg, J.
Cell Line Controls for the Genotyping of a Spectrum of Human Single Nucleotide Polymorphisms in the Clinical Laboratory.
Clin Lab. 2018; 64(5):823-834
Doi: 10.7754/Clin.Lab.2018.171212
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- Leading authors Med Uni Graz
- Berg Jörg
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- Abstract:
- Genotyping for clinically important single nucleotide polymorphisms (SNPs) is performed by many clinical routine laboratories. To support testing, quality controls and reference materials are needed. Those may be derived from residual patient samples, left over samples of external quality assurance schemes, plasmid DNA or DNA from cell lines. DNAs from cell lines are commutable and available in large amounts. DNA from 38 cell lines were examined for suitability as controls in 11 SNP assays that are frequently used in a clinical routine laboratory: FV (1691G>A), FII (20210G>A), PAI-1 4G/5G polymorphism, MTHFR (677C>T, 1298A>C), HFE (H63D, S65C, C282Y), APOE (E2, E3, E4), LPH (-13910C>T), UGT1A1 (*28, *36, *37), TPMT (*2, *3A, *3B, *3C), VKORC1 (-1639G>A, 1173C>T), CYP2C9 (*2, *3, *5). Genotyping was performed by real-time PCR with melting curve analysis and confirmed by bi-directional sequencing. We find an almost complete spectrum of genotypic constellations within these 38 cell lines. About 12 cell lines appear sufficient as genotypic controls for the 11 SNP assays by covering almost all of the genotypes. However, hetero- and homozygous genotypes for FII and the alleles TPMT*2, UGT1A1*37 and CYP2C9*5 were not detected in any of the cell lines. DNA from most of the examined cell lines appear suitable as quality controls for these SNP assays in the laboratory routine, as to the implementation of those assays or to prepare samples for quality assurance schemes. Our study may serve as a pilot to further characterize these cell lines to arrive at the status of reference materials.
- Find related publications in this database (using NLM MeSH Indexing)
- Cell Line -
- Cell Line, Tumor -
- Clinical Laboratory Services - standards
- Clinical Laboratory Techniques - methods
- Clinical Laboratory Techniques - standards
- Genotype -
- Genotyping Techniques - methods
- HL-60 Cells -
- Humans -
- K562 Cells -
- Polymorphism, Single Nucleotide -
- Quality Control -
- Reproducibility of Results -
- Find related publications in this database (Keywords)
- single nucleotide polymorphism
- SNP
- genotyping
- cell line control
- FV
- PAI-1
- HFE
- MTHFR
- VKORC1