Accurate microsatellite typing and inter-study comparison: pitfalls and solutions using interferon-gamma (IFNG) and natural resistance-associated macrophage protein 2 (NRAMP2) genes as examples. Rossouw, M., Warren, R., & Hoal, E. G. Clinical chemistry and laboratory medicine: CCLM / FESCC, 40(9):926–929, September, 2002. 00000 doi abstract bibtex Microsatellite typing is frequently used in disease diagnosis and in genetic association studies. Inter-study consistency and comparability is essential in both applications. In this study, we show that the interlaboratory comparison of microsatellite sizes is often discrepant and misleading. This is a matter of great concern in the recent literature. However, accurate allele designation is easily attainable by the simple procedures we report, which are applicable to all gel-based genotyping methods. These involve: 1) the creation of dedicated standards for a specific microsatellite by PCR-amplifying representative alleles to generate an allelic ladder with comparable electrophoretic characteristics; 2) including both internal and external standards during electrophoresis to facilitate alignment. In addition, we recommend procedures that will improve inter-study comparability of all microsatellite analyses regardless of genotyping method. These involve: 1) cloning and sequencing representative microsatellite alleles to obtain accurate size designation; 2) sharing alleles of known sequence between laboratories to use as standards. We report on the typing of natural resistance-associated macrophage protein (NRAMP2) and interferon-y (IFNG) gene microsatellites as examples, the latter of which is crucial to many pathogenic processes. We describe in detail the varying allele sizes obtained by different methods, which prevent meaningful inter-study comparisons.
@article{rossouw_accurate_2002,
title = {Accurate microsatellite typing and inter-study comparison: pitfalls and solutions using interferon-gamma ({IFNG}) and natural resistance-associated macrophage protein 2 ({NRAMP2}) genes as examples},
volume = {40},
issn = {1434-6621},
shorttitle = {Accurate microsatellite typing and inter-study comparison},
doi = {10.1515/CCLM.2002.162},
abstract = {Microsatellite typing is frequently used in disease diagnosis and in genetic association studies. Inter-study consistency and comparability is essential in both applications. In this study, we show that the interlaboratory comparison of microsatellite sizes is often discrepant and misleading. This is a matter of great concern in the recent literature. However, accurate allele designation is easily attainable by the simple procedures we report, which are applicable to all gel-based genotyping methods. These involve: 1) the creation of dedicated standards for a specific microsatellite by PCR-amplifying representative alleles to generate an allelic ladder with comparable electrophoretic characteristics; 2) including both internal and external standards during electrophoresis to facilitate alignment. In addition, we recommend procedures that will improve inter-study comparability of all microsatellite analyses regardless of genotyping method. These involve: 1) cloning and sequencing representative microsatellite alleles to obtain accurate size designation; 2) sharing alleles of known sequence between laboratories to use as standards. We report on the typing of natural resistance-associated macrophage protein (NRAMP2) and interferon-y (IFNG) gene microsatellites as examples, the latter of which is crucial to many pathogenic processes. We describe in detail the varying allele sizes obtained by different methods, which prevent meaningful inter-study comparisons.},
language = {eng},
number = {9},
journal = {Clinical chemistry and laboratory medicine: CCLM / FESCC},
author = {Rossouw, Manda and Warren, Robin and Hoal, Eileen G.},
month = sep,
year = {2002},
pmid = {12435110},
note = {00000 },
keywords = {Alleles, Cation Transport Proteins, Clinical Laboratory Techniques, Cloning, Molecular, Databases, Nucleic Acid, Electrophoresis, Polyacrylamide Gel, Genotype, Humans, Interferon-gamma, Iron-Binding Proteins, Microsatellite Repeats, Polymerase Chain Reaction, Reproducibility of Results, Sequence Analysis, DNA},
pages = {926--929},
}
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