Format

Send to:

Choose Destination
See comment in PubMed Commons below
Genomics. 2011 Apr;97(4):193-9. doi: 10.1016/j.ygeno.2011.01.001. Epub 2011 Jan 9.

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

Author information

  • 1Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061-0477, USA.

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.

Copyright © 2011 Elsevier Inc. All rights reserved.

PMID:
21223998
[PubMed - indexed for MEDLINE]
PMCID:
PMC3065957
Free PMC Article
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for Elsevier Science Icon for PubMed Central
    Loading ...
    Write to the Help Desk