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
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Manda Rossouw
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.
Copyright © 2002 by Walter de Gruyter GmbH & Co. KG
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Articles in the same Issue
- Addressing Diseases in Africa
- Tuberculosis: The Struggle Continues
- Genetic Susceptibility to Tuberculosis
- Protein Expression in Mycobacterium tuberculosis Differs with Growth Stage and Strain Type
- Molecular Detection of Early Appearance of Drug Resistance during Mycobacterium tuberculosis Infection
- Prevalence of Anti-mycolic Acid Antibodies in Patients with Pulmonary Tuberculosis Co-infected with HIV
- Reduction of the Rate of False-Positive Cultures of Mycobacterium tuberculosis in a Laboratory with a High Culture Positivity Rate
- Enhanced Immune Response in Mycobacterium bovis Bacille Calmette Guerin (BCG)-Infected IL-10-Deficient Mice
- The ELISPOT Assay: An Easily Transferable Method for Measuring Cellular Responses and Identifying T Cell Epitopes
- Coreceptor Usage and Biological Phenotypes of HIV-1 Isolates
- Overcoming Multidrug Resistance in Taxane Chemotherapy
- 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
- Synergism between Urinary Prothrombin Fragment 1 and Urine: A Comparison of Inhibitory Activities in Stone-Prone and Stone-Free Population Groups
- Immunoglobulin G and Subclass Responses to Plasmodium falciparum Antigens: A Study in Highly Exposed Cameroonians
- Infrequent Somatic Deletion of the 5' Region of the COL1A2 Gene in Oesophageal Squamous Cell Cancer Patients
- The Quantitative Analysis of Zearalenone and Its Derivatives in Plasma of Patients with Breast and Cervical Cancer
- Genetic Polymorphism of Cytochrome P450 1A1 (CYP1A1) and Glutathione Transferases (M1, T1 and P1) among Africans
- Meetings and Awards
