Variant annotation and ranking for whole genome sequence data

PCA informative markers and PCA-based genotype imputation

  • Paschou et al. Genome Research 2007. Inter- and intrapopulation genotype reconstruction from tagging SNPs.(MATLAB code)
  • Paschou et al. PLoS Genetics 2007. PCA-correlated SNPs for structure identification in worldwide human populations. (supplementary results and MATLAB code)
  • Paschou et al. PLoS Genetics 2008. Tracing sub-structure in the European American population with PCA-informative markers. (supplementary results and MATLAB code)
  • Drineas et al. PLoS ONE 2010. Inferring Geographic Coordinates of Origin for Europeans using Small Panels of Ancestry Informative Markers.  (supplementary results and MATLAB code)
  • Paschou et al. Journal of Medical Genetics 2010.  Ancestry informative markers for fine-scale individual assignment to worldwide populations. (supplementary results and MATLAB code)
  • Lewis et al. PLoS ONE 2011.  Tracing Cattle Breeds With PCA-based Ancestry Informative SNPs. (supplementary results and MATLAB code)
  • Javed et al. submitted. Efficient genomewide selection of PCA-correlated tSNPs for genotype imputation. (TRIMMER will be released shortly).