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Taking into account phenotype frequencies #114

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julesjacobsen opened this issue Feb 26, 2016 · 1 comment
Open

Taking into account phenotype frequencies #114

julesjacobsen opened this issue Feb 26, 2016 · 1 comment
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@julesjacobsen
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For example in Decipher ARID1B

Code    Phenotype   Affected patients with Sequence Variants in ARID1B  Percentage of phenotyped patients with Sequence Variants in ARID1B  Affected patients in DECIPHER   Percentage of 12981 phenotyped patients in DECIPHER p value Odds ratio
HP:0001601  Laryngomalacia  4   12.90%  29  0.22%   6.00 × 10-07   76.59 ( 24.97 - 234.98 )
HP:0012718  Morphological abnormality of the gastrointestinal tract     8   25.81%  363     2.80%   1.44 × 10-06   12.34 ( 5.48 - 27.78 )
HP:0002307  Drooling    4   12.90%  36  0.28%   1.47 × 10-06   59.81 ( 19.79 - 180.73 )

HP:0001601 and HP:0002307 are highly significant phenotypic markers of ARID1B pathology.
@julesjacobsen julesjacobsen changed the title Fisher exact on phenotypes in OMIM/Orphanet diseases to create p-values for marher phenotypes of particular disease Fisher exact on phenotypes in OMIM/Orphanet diseases to create p-values for marker phenotypes of particular disease Feb 26, 2016
@damiansm
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Is this related to phenotype annotation frequency data as provided by Orphanet to weight our scores. Need to wait until the Bayesian implementation to do properly

@damiansm damiansm added this to New variant scores in Issues triage Oct 30, 2018
@damiansm damiansm changed the title Fisher exact on phenotypes in OMIM/Orphanet diseases to create p-values for marker phenotypes of particular disease Taking into account phenotype frequencies Oct 30, 2018
@damiansm damiansm moved this from New variant scores to New algs in Issues triage Oct 30, 2018
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@julesjacobsen @damiansm