A periodic pattern of SNPs in the human genome

By surveying all validated SNPs in the human genome we have found that SNPs positioned 1, 2, 4, 6 or 8 bp apart are more frequent than SNPs 3, 5, 7 or 9 bp apart. This holds even when we correct for nucleotide frequencies and site dependencies in nucleotide usage in the genome. The observed pattern is not restricted to any of the genomic regions that might give sequencing or alignment errors; i.e. transposable elements (SINE, LINE and LTR), tandem repeats and large duplicated regions. However we can define periodic DNA, which virtually capture the entire pattern. Periodic DNA is defined as small DNA sequences (16.9 bp average length) with a high degree of periodicity in nucleotide usage. Periodic DNA is widely distributed in the genome, underrepresented in exons, widespread in transcripts and slightly overrepresented in tandem repeats. Furthermore periodic DNA has a 1.8 times higher SNP density than the rest of the genome.A possible biological explanation of these observations is that during DNA replication small fragments of (periodic) DNA is copied to nearby positions, substituting the original sequence. If the copied fragment differs from the original sequence a new SNP is created. In conclusion these observations suggest that not all SNPs in the human genome are created by independent single nucleotide mutations.