Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data : Article : Nature Reviews Genetics
September 10, 2011
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Gotta love this quote: ” true hypotheses are true, and false hypotheses are false, regardless of how many are tested”
Greg Cooper and Jay Shendure on finding causal variants.
Genetic approaches (a) ??? for example, linkage analysis followed by re-sequencing, genome-wide association studies (GWASs), exome or genome sequencing ??? define both candidate loci (b) and candidate variants within those loci, often in many functional categories (c). Methods to predict the phenotypic relevance of individual variants within these often lengthy lists of candidates (represented by the row of stars) include predictions of deleteriousness based on comparative genomics (d, for coding and non-coding variants), knowledge of protein biochemistry and structure (e, for coding variants) and experimental approaches (f, for coding and non-coding variants). Panel d is an illustration of three aligned nucleotides, showing one that is completely conserved (left column), one that is highly variable (middle column) and one that is moderately conserved (right column). Evaluation of this information depends on the scope and neutral divergence of the phylogeny (left side) relating the aligned sequences.