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A periodic pattern of SNPs in the human genome.

Authors
  • Madsen, Bo Eskerod
  • Villesen, Palle
  • Wiuf, Carsten
Type
Published Article
Journal
Genome Research
Publisher
Cold Spring Harbor Laboratory
Publication Date
Oct 01, 2007
Volume
17
Issue
10
Pages
1414–1419
Identifiers
PMID: 17673700
Source
Medline
License
Unknown

Abstract

By surveying a filtered, high-quality set of SNPs in the human genome, we have found that SNPs positioned 1, 2, 4, 6, or 8 bp apart are more frequent than SNPs positioned 3, 5, 7, or 9 bp apart. The observed pattern is not restricted to genomic regions that are known to cause sequencing or alignment errors, for example, transposable elements (SINE, LINE, and LTR), tandem repeats, and large duplicated regions. However, we found that the pattern is almost entirely confined to what we define as "periodic DNA." Periodic DNA is a genomic region with a high degree of periodicity in nucleotide usage. It turned out that periodic DNA is mainly small regions (average length 16.9 bp), widely distributed in the genome. Furthermore, periodic DNA has a 1.8 times higher SNP density than the rest of the genome and SNPs inside periodic DNA have a significantly higher genotyping error rate than SNPs outside periodic DNA. Our results suggest that not all SNPs in the human genome are created by independent single nucleotide mutations, and that care should be taken in analysis of SNPs from periodic DNA. The latter may have important consequences for SNP and association studies.

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