Background: Microsatellite instability (MSI) is associated with Lynch syndrome and hence is a surrogate marker for defective mismatch repair genes. The aim of this study was to investigate the degree of instability associated with each of the 5 microsatellite (MS) loci recommended by the National Cancer Institute (NCI), USA within an Indian population of mixed ethnicity and suffering from Lynch syndrome. Methods: DNA from clinical samples originating from the study population (n = 130) were subjected to automated fragment analysis for all 5 MS loci, and data generated were analyzed to determine the frequency of variation of each of the MS in the resource population. Results: Out of 130, 116 samples responded to polymerase chain reaction (PCR) for all 5 MS loci. 21 (16.15%) were MSI-high (MSI-H) while 27 (20.76%) and 68 (52.30%) were MSI-low (MSI-L) and microsatellite stable (MSS), respectively. D5S346 exhibited the highest instability (27 out of a total of 82 cases of instability recorded for all 5 MS in all 116 patients tested) followed by D2S123 (23/82), BAT26 (14/82), BAT25 (11/82), and D17S250 (7/82). Conclusion: MS D17S250 and BAT25 of the 5 MS panel recommended by the NCI are not informative enough and hence should be avoided for diagnosing Lynch syndrome in the Indian population.

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