Typing Method for the QUB11a Locus of Mycobacterium tuberculosis : IS 6110 Insertions and Tandem Repeat Analysis

QUB11a is used as a locus for variable number of tandem repeats (VNTR) analysis of Mycobacterium tuberculosis Beijing lineage. However, amplification of QUB11a occasionally produces large fragments (>1,400 bp) that are not easily measured by capillary electrophoresis because of a lack of the typical stutter peak patterns that are used for counting repeat numbers. IS 6110 insertion may complicate VNTR analysis of large QUB11a fragments in M. tuberculosis . We established a method for determining both tandem repeat numbers and IS 6110 insertion in the QUB11a locus of M. tuberculosis using capillary electrophoresis analysis and Bsm BI digestion. All 29 large QUB11a fragments (>1,200 bp) investigated contained IS 6110 insertions and varied in the number of repeats (18 patterns) and location of IS 6110 insertions. This method allows VNTR analysis with high discrimination.