Assay optimisation on female and male lymphoblastoid cell lines carrying NL, PM, and/or FM FMR1 (CGG)n alleles
| Coriell ID/sex | Southern result (kb/CGG rpt*) | Southern classification | Non-Met-PCR result (bp/CGG rpt)† | Met-PCR result (bp/CGG rpt)† | mTP-PCR result | Triple ms-PCR classification | HUMARA assay (% skewing) |
|---|---|---|---|---|---|---|---|
| *Repeat sizes are based on EcoRI/NruI double digests hybridised with probe StB12.3, where a 2.9 kb non-methylated or a 5.2 kb methylated fragment indicates a 30 repeat normal allele. Larger fragments are rounded off to the nearest 50 repeats. | |||||||
| †Rounded off to the nearest 10 bp and five CGG repeats. | |||||||
| ‡Majority of cells carry the NL FMR1 allele on the active X and the PM or FM allele on the inactive X. | |||||||
| F, female; M, male; NA, not applicable; pdt, product; rpt, repeats. | |||||||
| GM07175/F | 2.9 and 5.2 kb/30 rpt | NL female | 260 bp/30 rpt | 200 bp/30 rpt | NL smear | NL female | ⩾85% |
| GM06907/F | 2.9 and 5.4 kb/30 and 100 rpt | PM female (skewed)‡ | 260 & 450 bp/30 & 95 rpt | 200 & 390 bp/30 & 95 rpt | PFM smear | PM female (skewed)‡ | ⩾95% |
| GM06896/F | 2.9 and 5.4 kb/30 and 100 rpt | PM female (skewed)‡ | 260 bp/30 rpt | 470 bp/120 rpt | PFM smear | PM female (skewed)‡ | ⩾99% |
| GM07537/F | 2.9 and 6.3 kb/30 and 400 rpt | FM female (skewed)‡ | 270 bp/35 rpt | >1000 bp/>295 rpt | PFM smear | FM female (skewed)‡ | ⩾99% |
| GM06890/M | 2.9 kb/30 rpt | NL male | 270 bp/35 rpt | No PCR pdt | No smear | NL male | NA |
| GM06891/M | 3.3 kb/150 rpt | PM male | 640 bp/155 rpt | No PCR pdt | No smear | PM male | NA |
| GM06892/M | 3.1 kb/100 rpt | PM male | 410 bp/80 rpt | No PCR pdt | No smear | PM male | NA |
| GM06852/M | 6.3 kb/400 rpt | FM male | 640 bp/155 rpt | >1000 bp/>295 rpt | PFM smear | Mosaic FM male | NA |