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Clinical Chemistry and Laboratory Medicine (CCLM)

Published in Association with the European Federation of Clinical Chemistry and Laboratory Medicine (EFLM)

Editor-in-Chief: Plebani, Mario

Ed. by Gillery, Philippe / Greaves, Ronda / Lackner, Karl J. / Lippi, Giuseppe / Melichar, Bohuslav / Payne, Deborah A. / Schlattmann, Peter


IMPACT FACTOR 2017: 3.556

CiteScore 2017: 2.34

SCImago Journal Rank (SJR) 2017: 1.114
Source Normalized Impact per Paper (SNIP) 2017: 1.188

Online
ISSN
1437-4331
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Volume 40, Issue 9

Issues

Accurate Microsatellite Typing and Inter-study Comparison: Pitfalls and Solutions Using Interferon-γ (IFNG) and Natural Resistance-associated Mocrophage Protein 2 (NRAMP2) Genes as Examples

Manda Rossouw / Robin Warren / Eileen G. Hoal
Published Online: 2005-06-01 | DOI: https://doi.org/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-γ (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.

About the article

Published Online: 2005-06-01

Published in Print: 2002-09-24


Citation Information: Clinical Chemistry and Laboratory Medicine, Volume 40, Issue 9, Pages 926–929, ISSN (Print) 1434-6621, DOI: https://doi.org/10.1515/CCLM.2002.162.

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