Evaluation of microsatellite variation in the 1000 Genomes Project pilot studies is indicative of the quality and utility of the raw data and alignments

L. J. McIver, J. W. Fondon, M. A. Skinner, H. R. Garner

Research output: Contribution to journalArticle

34 Scopus citations

Abstract

We performed an analysis of global microsatellite variation on the two kindreds sequenced at high depth (~20×-60×) in the 1000 Genomes Project pilot studies because alterations in these highly mutable repetitive sequences have been linked with many phenotypes and disease risks. The standard alignment technique performs poorly in microsatellite regions as a consequence of low effective coverage (~1×-5×) resulting in 79% of the informative loci exhibiting non-Mendelian inheritance patterns. We used a more stringent approach in computing robust allelotypes resulting in 94.4% of the 1095 informative repeats conforming to traditional inheritance. The high-confidence allelotypes were analyzed to obtain an estimate of the minimum polymorphism rate as a function of motif length, motif sequence, and distribution within the genome.

Original languageEnglish (US)
Pages (from-to)193-199
Number of pages7
JournalGenomics
Volume97
Issue number4
DOIs
StatePublished - Apr 2011

Keywords

  • 1000 Genomes Project
  • Genomics
  • Microsatellites
  • Repetitive DNA

ASJC Scopus subject areas

  • Genetics

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