Fig. 2

Sequence analysis favors the existence of a heterozygous insertion in patient 1205. A, Local alignment of selected sequence reads from patient 1205 in the region containing a single-nucleotide insertion (hg18; chr5:13,754,404–13,754,447). The top line of the alignment represents the NCBI 36 reference sequence at this location. Gaps introduced into the alignment are represented by a “-.” Yellow highlights the stretch of 7 adenine (7A) nucleotides where the insertion should result in 8 adenine (8A) nucleotides. B, The proportion of reads containing 5, 6, 7, 8, 9, or 10 adenine nucleotides reveal a clear difference in patient 1205. Patients 475, 998, and 1072 act as “controls” as they are homozygous for reference 7A alleles. The highest proportions of reads in these samples were 7A, with Gaussian distributions (R² > 0.998) having peaks at approximately 6.75 (6.607, 6.778, and 6.842), consistent with a homozygous 7A genotype at this position. In contrast, the number of adenine residues in the sample from patient 1205 ranged from 5 to 10, with a Gaussian distribution (R² = 0.964) that was broader than the first three patients and had a peak at 7.54. C, When compared with simulated genotypes, the distribution from patient 1205 most closely resembles the heterozygous distribution. The distributions of the three “control” samples were averaged to obtain a simulated homozygous 7A distribution (SIM-7A). This distribution was shifted to the right to generate a simulated homozygous 8A distribution (SIM-8A). The SIM-7A and SIM-8A distributions were averaged to simulate the expected distribution in an individual heterozygous for 7A and 8A (SIM-7A/8A Het).