Emile CHIMUSA                   
Department of Integrative Biomedical Sciences
Institute of Infectious Disease and Molecular Medicine
Anzio Rd, Observatory 7925.
Cape Town, South Africa.
Tel: +27 21 406 6058/6176.
Fax: +27 21 406 6068.



Software

 

 

PROXYANC

 

  • PROXYANC implements an approach to select the best proxy ancestral populations for admixed populations. It searches for the best combination of reference populations that can minimize the genetic distance between the admixed population and all possible synthetic populations, consisting of a linear combination from reference populations. PROXYANC also computes a proxy-ancestry score by regressing a statistic for LD (at short distance < 0.25 Morgan) between a pair of SNPs in the admixed population against a weighted ancestral allele frequency differentiation. Download PROXYANC.
  • PROXYANANC can select AIMs based on the relationship between the observed local multi-locus linkage disequilibrium in a recently admixed population and ancestral population difference in allele frequency and based on the Kernel principal component analysis (Kernel-PCA), which is the extension of the linear PCA.
  • PROXYANC can identify possible unusual difference in allele frequency between pair-wise popualtions, as signal of natural selection.
  • PROXYANC compute the expected maximun admixture LD from proxy ancestral populations of the admixed population.
  • PROXYANC compute population pair-wise Fst (Genetic distance).
  • Download PROXYANC.
  • Download AIMs panels for the South African Coloured population.
  • Download Affymetrix.dat .
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      ancGWAS

       

  • ancGWAS is an algebraic graph-based method to identify the most significant sub-network underlying ethnic difference in complex diseases risk in a recently admixed population.
  • This approach integrates the association signal from a GWAS data set, the local ancestry, and SNP pair-wise linkage disequilibrium from the admixed population into the PPI network.
  • Download curent version of ancGWAS.
  • Old version.
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      ancMETA

       

  • ancMETA is an application for leveraging cross-population Gene/Sub-network Meta-analysis to recover Disease Association Signal (DAS) risk in a homogenous or recently admixed population.
  • This approach integrates the association signal from a GWAS data set, the local ancestry, and SNP pair-wise linkage disequilibrium into both the PPI and Protein-functional network.
  • Link to ancMETA.
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      FractalSIM

       

  • FractalSIM is a Python based software package, a multi-scenario whole genome-based medical population genetics simulation framework. FractalSIM, designed under the whole genome resampling simulation approach, to mimic various scenarios of population genetic diversity, genomic variation affecting diseases and DNA sequence patterns of admixed and/or homogeneous populations, particularly those under natural selection models.
  • Link to FractalSIM.
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      TagMix

       

  • TagMix is an integrated cross-populations LD-based, haplotype-based and principal component analysis genome-wide tag SNPs selection algorithm to efficiently identify informative variants, prioritized across multi-populations of low LD and high diversity populations for custom chip array.
  • This approach improves the efficiency of variants and optimizing the discovery of disease-associated genetic variations.
  • Link to TagMix.
  • Link to JOHN Essay data.
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