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Thread: Introduction of new ancestry tool

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    Introduction of new ancestry tool

    It's called SUGIBS. Also, they claim to be able to pick up "appearance" snps. They examine both the ancients and the samples from 1000 Genomes. Other than the different eyes of the samples from the far eas"t and the African samples, they basically all look alike to me. :)

    See:Jairui Li

    "Abstract24 Accurate inference of genomic ancestry is critically important in human genetics, epidemiology, and25 related fields. Geneticists today have access to multiple heterogeneous population-based datasets26 from studies collected under different protocols. Therefore, joint analyses of these datasets require27 robust and consistent inference of ancestry, where a common strategy is to yield an ancestry space28 generated by a reference dataset. However, such a strategy is sensitive to batch artefacts introduced29 by different protocols. In this work, we propose a novel robust genome-wide ancestry inference30 method; referred to as SUGIBS, based on an unnormalized genomic (UG) relationship matrix whose31 spectral (S) decomposition is generalized by an Identity-by-State (IBS) similarity degree matrix. SUGIBS32 robustly constructs an ancestry space from a single reference dataset, and provides a robust33 projection of new samples, from different studies. In experiments and simulations, we show that,34 SUGIBS is robust against individual outliers and batch artifacts introduced by different genotyping35 protocols. The performance of SUGIBS is equivalent to the widely used principal component analysis36 (PCA) on normalized genotype data in revealing the underlying structure of an admixed population37 and in adjusting for false positive findings in a case-control admixed GWAS. We applied SUGIBS on the38 1000 Genome project, as a reference, in combination with a large heterogeneous dataset containing39 auxiliary 3D facial images, to predict population stratified average or ancestry faces. In addition, we40 projected eight ancient DNA profiles into the 1000 Genome ancestry space and reconstructed their41 ancestry face. Based on the visually strong and recognizable human facial phenotype, comprehensive42 facial illustrations of the populations embedded in the 1000 Genome project are provided.43 Furthermore, ancestry facial imaging has important applications in personalized and precision44 medicine along with forensic and archeological DNA phenotyping."
    Last edited by Angela; 15-02-19 at 21:18.

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