BMC Genetics (Feb 2008)

Analysis of genetic variation in Ashkenazi Jews by high density SNP genotyping

  • Ellis Nathan A,
  • Norton Larry,
  • Friedman Eitan,
  • Klein Robert J,
  • Lautenberger James A,
  • Kirchhoff Tomas,
  • Eskin Eleazar,
  • Stefanov Stefan A,
  • Satagopan Jaya,
  • Struewing Jeffery P,
  • Lohmueller Kirk E,
  • Gold Bert,
  • Olshen Adam B,
  • Viale Agnes,
  • Lee Catherine S,
  • Borgen Patrick I,
  • Clark Andrew G,
  • Offit Kenneth,
  • Boyd Jeff

DOI
https://doi.org/10.1186/1471-2156-9-14
Journal volume & issue
Vol. 9, no. 1
p. 14

Abstract

Read online

Abstract Background Genetic isolates such as the Ashkenazi Jews (AJ) potentially offer advantages in mapping novel loci in whole genome disease association studies. To analyze patterns of genetic variation in AJ, genotypes of 101 healthy individuals were determined using the Affymetrix EAv3 500 K SNP array and compared to 60 CEPH-derived HapMap (CEU) individuals. 435,632 SNPs overlapped and met annotation criteria in the two groups. Results A small but significant global difference in allele frequencies between AJ and CEU was demonstrated by a mean FST of 0.009 (P Conclusion LD in the AJ versus was lower than expected by some measures and higher by others. Any putative advantage in whole genome association mapping using the AJ population will be highly dependent on regional LD structure.