Mutations in COL1A1 Gene Change Dentin Nanostructure: A response.

(Opening paragraph) The mild OI phenotype (commonly referred to as type I OI) displayed by the proband and its mode of inheritance revealed by the pedigree (Figure 3A) are wholly consistent with a causative sequence variant in either one of the genes encoding the constituent chains of type I collagen (COL1A1 or COL1A2). Sequence analysis should reveal a variant for which the proband is heterozygous. However, the upper sequencing trace in Figure 3B is consistent with the proband being homozygous for the two inserted bases. The expectation for a patient who is heterozygous for the inserted bases is a sequencing trace in which the sequences of the two COL1A1 alleles are out of register with one another beginning at the first inserted base. The superimposition of the sequences derived from the normal and mutant alleles should be apparent in the upper trace, but it is not. The trace ought to show three single C peaks at positions 1 to 3 followed by double peaks at positions 4 to 7: C+T, G+C, G+A & G+A respectively. A further anomaly is that the lower trace (CCCCGGA) and the upper trace (CCCTCAGGA), which is two bases longer, appear to be in exact register at their start and finish in spite of the length discrepancy. For that to happen the inserted T and A bases would need to create a rather large electrophoretic compression to compensate for the two inserted bases and that would be unlikely. It is also worth noting that the base caller used to analyse the raw sequence data has not called the T and A peaks in the upper trace and no confidence values are displayed for any of the peak sequence‐calls in either trace.