Searching for non-B DNA-forming repeats in flanking sequences
Non-B DNA-forming repeats within each flanking sequence were obtained
from the non-B DB database(Cer et al., 2011; Cer et al., 2013) with
custom filters for mirror repeats (Table S1). As shown in Table S1, the
mirror repeats were filtered by triplex-motif that is predicted by non-B
DB as subset=1. In this study, six types of non-B DNA-forming repeat
were considered, specifically direct repeats (DR), inverted repeats
(IR), mirror repeats (MR), G-quartets (GQ), short tandem repeats (STR),
and Z-DNA (Z)(Ghosh & Bansal, 2003; Kondrashov & Rogozin, 2004; Wells,
2007). More detailed information on each type of non-B DNA-forming
repeat is to be found in the Supplementary Material (Table S1). The
frequencies of the non-B DNA-forming repeats in the flanking sequences
of the pathogenic deletions were compared with the frequencies of these
repeats in the simulated data, the control1 dataset. Statistical
significance was assessed by means of the Student’s t-test, and a
Bonferroni correction was applied to allow for multiple testing.