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. 2005 Oct;43(10):5034–5043. doi: 10.1128/JCM.43.10.5034-5043.2005

TABLE 2.

PICs of the 48 potential VNTR locia

Tandem repeat locus Designation by other researchers No. of alleles Copy number PIC for:
All isolates Beijing isolates Few-banded (2-5) isolates Heterogeneous (≥6) isolates Single-banded isolates
DR0272 MIRU3 1 1 0 0 0 0 0
DR0642 MIRU6 1 1 0 0 0 0 0
DR2068 1 1 0 0 0 0 0
DR3074 1 1 0 0 0 0 0
DR3319 MIRU33 1 1 0 0 0 0 0
DR3991 MIRU37 1 1 0 0 0 0 0
DR4110 1 1 0 0 0 0 0
ETR4087 1 2 0 0 0 0 0
VNTR2059 MIRU20 1 2 0 0 0 0 0
VNTR0154 MIRU2 3 1-3 0.041 0 0.074 0 0.133
VNTR0569 6 1-6 0.666 0.100 0.764 0.604 0.180
VNTR0577 ETR-C 3 1-3 0.118 0 0 0.269 0.245
VNTR0580 ETR-D, MIRU4 9 1*, 2*, 3, 4*, 5*, 6*, 7*, 9*, 10* 0.795 0.172 0.681 0.753 0.724
VNTR0595 msx.4 9 1, 3-4, 6-7, 9-12 0.728 0 0.743 0.570 0.722
VNTR0917 2 2-3 0.061 0 0.077 0 0.245
VNTR0960 MIRU10 7 0-5, 7 0.619 0.177 0.334 0.461 0.449
VNTR1281 QUB-1281 2 2-3 0.020 0 0 0 0.133
VNTR1305 4 0-3 0.100 0 0.074 0.074 0.133
VNTR1451 QUB-1451 3 1-3 0.410 0 0.142 0.074 0.133
VNTR1644 MIRU16 4 1-4 0.491 0 0.269 0.260 0.521
VNTR1895 QUB-1895 6 2-7 0.419 0.529 0.351 0.346 0.545
VNTR1907 2 1-2 0.021 0 0 0 0.133
VNTR1955 Mtub21 8 0-6, 9 0.688 0.694 0.589 0.747 0.459
VNTR2074 Mtub24 4 1-4 0.291 0.308 0.210 0.342 0.245
VNTR2347 Mtub29 3 1-3 0.495 0.172 0.071 0.370 0.337
VNTR2372 4 1-4 0.464 0.463 0.074 0.423 0.133
VNTR2401 Mtub30 5 0-3, 7 0.387 0.100 0 0.074 0.272
VNTR2461 ETR-B 6 1-6 0.689 0 0.611 0.717 0.314
VNTR2531 MIRU23 4 0-1, 4-5 0.236 0 0.254 0.091 0.142
VNTR2687 MIRU24 3 0-2 0.481 0 0.074 0.426 0.449
VNTR2703 2 2-3 0.041 0.091 0.074 0 0
VNTR2990 Mtub31 4 2-4, 17 0.511 0 0.077 0.448 0.439
VNTR2996 MIRU26 7 1-7 0.460 0.188 0 0.334 0.272
VNTR3007 MIRU27, QUB-5 2 2-3 0.020 0 0 0 0.133
VNTR3155 QUB-15 4 1-3, 6 0.159 0.188 0.150 0.083 0.219
VNTR3171 Mtub34 3 1-3 0.119 0.095 0.260 0 0.142
VNTR3192 ETR-E, MIRU31 5 1-5 0.450 0.180 0.434 0.603 0.417
VNTR3232 QUB-3232 11 0, 3, 6, 9-15, 17 0.425 0.844 0 0.310 0.180
VNTR3239 ETR-F 5 1+1, 2+1, 1+2, 2+2, 3+2 0.247 0.331 0 0.150 0.520
VNTR3336 QUB-3336 8 3-8, 10-11 0.407 0.283 0.480 0.345 0.403
VNTR3594 3 2-4 0.041 0 0 0.074 0.133
VNTR3690 Mtub39 9 1-9 0.758 0 0.723 0.785 0.198
VNTR3820 16 3-10, 12-15, 17-18, 31-32 0.889 0.642 0.781 0.720 0.786
VNTR4052 QUB-26 10 1-8, 10, 4* 0.684 0.449 0.503 0.633 0.367
VNTR4120 9 1-5, 7, 10-12 0.755 0.580 0.556 0.396 0.531
VNTR4155 mpp.8 10 2-3, 10-11, 14, 16-19, 21 0.440 0 0.701 0.350 0.656
VNTR4156 QUB-4156 4 1-4 0.441 0.472 0 0.145 0.255
VNTR4348 MIRU39 3 1-3 0.265 0.346 0.083 0.226 0.444
a

ETR-B to F are tandem repeats previously identified by Frothingham and Meeker-O'Connell (6). MIRU, QUB, and Mtub prefixes are designations of tandem repeats by Supply et al. (31), Roring et al. (23), and Le Flèche et al. (17), respectively. msx.4 and mpp.8 are terms used by Namwat et al. (20). Allelic diversity indices (PICs) were calculated for all M. tuberculosis isolates and for each IS6110 RFLP type: Beijing, few-banded (two to five bands), heterogeneous (at least six bands), and single-banded strains. The PICs of the 10 most polymorphic loci in each IS6110 type are in bold. Asterisks denote the allelic variants found to contain internal deletions of the VNTR sequence. A zero in the copy number column indicates the allelic variants possessing only the incomplete sequence. VNTR3239 is a complex locus composed of 55-bp and 79-bp repeat units of tandem repeats.