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The human retrotransposon with the highest copy number is the  Alu  element. The human genome contains over one million  Alu  elements that collectively account for over ten percent of our DNA. Full-length  Alu  elements are randomly distributed throughout the genome in both forward and reverse orientations. However, full-length widely spaced  Alu  pairs having two  Alus  in the same (direct) orientation are statistically more prevalent than  Alu  pairs having two  Alus  in the opposite (inverted) orientation. The cause of this phenomenon is unknown. It has been hypothesized that this imbalance is the consequence of anomalous inverted  Alu  pair interactions. One proposed mechanism suggests that inverted  Alu  pairs can ectopically interact, exposing both ends of each  Alu  element making up the pair to a potential double-strand break, or “hit”. This hypothesized “two-hit” (two double-strand breaks) potential per  Alu  element was used to develop a model for comparing the relative instabilities of human genes. The model incorporates both 1) the two-hit double-strand break potential of  Alu  elements and 2) the probability of exon-damaging deletions extending from these double-strand breaks. This model was used to compare the relative instabilities of 50 deletion-prone cancer genes and 50 randomly selected genes from the human genome. The output of the  Alu  element-based genomic instability model developed here is shown to coincide with the observed instability of deletion-prone cancer genes. The 50 cancer genes are collectively estimated to be 58% more unstable than the randomly chosen genes using this model. Seven of the deletion-prone cancer genes,  ATM, BRCA1, FANCA, FANCD2, MSH2, NCOR1 and PBRM1 , were among the most unstable 10% of the 100 genes analyzed. This algorithm may lay the foundation for comparing genetic risks posed by structural variations that are unique to specific individuals, families and people groups.

A Comparison of 100 Human Genes Using an Alu Element-Based Instability Model