When doing association analysis one does not always have the genotypes for the control population. In such cases it may be
necessary to fall back on frequency based tests using well known sources for the frequencies in the control population, for instance, from the
1000 Genomes Project. The Allele Frequency Comparison ('AssocAFC') package performs multiple rare variant association analyses in both population and family-based GWAS (Genome-Wide Association Study) designs. It includes
three score tests that are based on the difference of the sum of allele
frequencies between cases and controls. Two of these tests, Wcorrected() and Wqls(), are collapsing-based tests and suffer from having protective and risk variants. The third test, afcSKAT(), is a score test that overcomes the mix of SNP (Single-Nucleotide Polymorphism) effect directions. For more details see
Saad M and Wijsman EM (2017).
Availability: AssocAFC is also available as
Qatar Genome Programme is an initiative that aims to use the latest DNA sequencing technology to establish a genome map of the local population. It uses a collection of samples and data from Qatar Biobank participants to identify genotype-phenotype associations relevant to the Qatari population. This will provide unique insights that would enable the development of personalized healthcare in Qatar.
QCRI Bioinformatics group is part of the QGP consortium and is involved in solving how the Whole Genome Sequencing Reveals the Germline Landscape of Cancer-Susceptibility Genes Variation in Qataris population.