Table 2

Assay optimisation on female and male lymphoblastoid cell lines carrying NL, PM, and/or FM FMR1 (CGG)n alleles

Coriell ID/sexSouthern result (kb/CGG rpt*)Southern classificationNon-Met-PCR result (bp/CGG rpt)†Met-PCR result (bp/CGG rpt)†mTP-PCR resultTriple ms-PCR classificationHUMARA 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/F2.9 and 5.2 kb/30 rptNL female260 bp/30 rpt200 bp/30 rptNL smearNL female⩾85%
GM06907/F2.9 and 5.4 kb/30 and 100 rptPM female (skewed)‡260 & 450 bp/30 & 95 rpt200 & 390 bp/30 & 95 rptPFM smearPM female (skewed)‡⩾95%
GM06896/F2.9 and 5.4 kb/30 and 100 rptPM female (skewed)‡260 bp/30 rpt470 bp/120 rptPFM smearPM female (skewed)‡⩾99%
GM07537/F2.9 and 6.3 kb/30 and 400 rptFM female (skewed)‡270 bp/35 rpt>1000 bp/>295 rptPFM smearFM female (skewed)‡⩾99%
GM06890/M2.9 kb/30 rptNL male270 bp/35 rptNo PCR pdtNo smearNL maleNA
GM06891/M3.3 kb/150 rptPM male640 bp/155 rptNo PCR pdtNo smearPM maleNA
GM06892/M3.1 kb/100 rptPM male410 bp/80 rptNo PCR pdtNo smearPM maleNA
GM06852/M6.3 kb/400 rptFM male640 bp/155 rpt>1000 bp/>295 rptPFM smearMosaic FM maleNA