Validation of WGS telomeric DNA content predictions. (a) Quantitative PCR for a subset of samples, including 16 medulloblastoma and 11 neuroblastoma samples, showing changes in telomeric DNA content between normal and diagnosis log2(Absolute telomere length D/Absolute telomere length N. (b) FISH using probes for telomeric DNA confirms the 'normal' and 'abnormal' (ultra-bright spots, white arrowheads) telomere patterns in SJMB028 and SJMB004, respectively. (c) Telomere restriction fragment (TRF) analysis by southern blotting in 2 osteosarcoma samples, SJOS002 and SJOS004 predicted to have telomere gain and loss by WGS, respectively. (N = matched normal DNA, D = diagnosis tumor DNA). Inlay is the 100ng of genomic DNA on a 0.5% ethidium bromide gel which shows that the DNA quality is acceptable. (d) WGS normalized telomeric read counts for SJOS002 and SJOS004. (e) qPCR measurement of absolute telomeric DNA in SJOS002 and SJOS004 (error bars represent standard deviation of three technical repeats).
Parker et al. Genome Biology 2012 13:R113 doi:10.1186/gb-2012-13-12-r113