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Author Notes:

Corresponding Author: Karen Friderici, frideric@msu.edu, Telephone 517-884-5347, Fax 517-353-8957.

Subjects:

Research Funding:

This research was supported by RO1MH070004 (KHF) and MSU Office of the Vice President for Research (JTN)

Keywords:

  • Base Sequence
  • Chromosome Mapping
  • Gene Duplication
  • Genetic Techniques
  • Haplotypes
  • Humans
  • Molecular Sequence Data
  • Open Reading Frames
  • Polymorphism, Single Nucleotide
  • Pseudogenes
  • Receptors, Dopamine D5
  • Triplets

SNP discovery and haplotype analysis in the segmentally duplicated DRD5 coding region

Tools:

Journal Title:

Annals of Human Genetics

Volume:

Volume 73, Number 3

Publisher:

, Pages 274-282

Type of Work:

Article | Post-print: After Peer Review

Abstract:

The dopamine receptor 5 gene (DRD5) holds much promise as a candidate locus for contributing to neuropsychiatric disorders and other diseases influenced by the dopaminergic system, as well as having potential to affect normal behavioral variation. However, detailed analyses of this gene have been complicated by its location within a segmentally duplicated chromosomal region. Microsatellites and SNPs upstream from the coding region have been used for association studies, but we find, using bioinformatics resources, that these markers all lie within a previously unrecognized second segmental duplication (SD). In order to accurately analyze the DRD5 locus for polymorphisms in the absence of contaminating pseudogene sequences, we developed a fast and reliable method for sequence analysis and genotyping within the DRD5 coding region. We employed restriction enzyme digestion of genomic DNA to eliminate the pseudogenes prior to PCR amplification of the functional gene. This approach allowed us to determine the DRD5 haplotype structure using 31 trios and to reveal additional rare variants in 171 unrelated individuals. We clarify the inconsistencies and errors of the recorded SNPs in dbSNP and HapMap and illustrate the importance of using caution when choosing SNPs in regions of suspected duplications. The simple and relatively inexpensive method presented herein allows for convenient analysis of sequence variation in DRD5 and can be easily adapted to other duplicated genomic regions in order to obtain good quality sequence data. © 2009 The Authors Journal compilation

Copyright information:

© 2009 Blackwell Publishing Ltd/University College London.

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