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Update browser/help/topics/constraint.md
Co-authored-by: jkgoodrich <33063077+jkgoodrich@users.noreply.github.com>
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#### <a id="loeuf"></a>Observed / expected (`oe`) and the Loss-of-function Observed / expected upper bound fraction (`LOEUF`) score
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We have calculated the ratio of the observed / expected (`oe`) number of loss-of-function variants for all bases with median AN percent ≥ 20 in the MANE Select (v4 on GRCh38) or canonical (ExAC and v2 on GRCh37) and other non-Select/canonical transcript for each gene. The expected counts are based on a mutational model that takes sequence context and methylation into account.
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We have calculated the ratio of the observed / expected (`oe`) number of loss-of-function variants for all bases with AN percent ≥ 20 in the MANE Select (v4 on GRCh38) or canonical (ExAC and v2 on GRCh37) and other non-Select/canonical transcript for each gene. The expected counts are based on a mutational model that takes sequence context and methylation into account.
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In its original formulation, LOEUF was computed using a frequentist approach: the observed and expected LoF counts were modeled as Poisson-distributed, and the score was defined as the upper bound of a central 90% Poisson confidence interval around the observed count, divided by the neutral expectation. While intuitive, this approach treats the true underlying number of LoF variants as a fixed but unknown parameter, and the confidence interval it produces has a strictly frequentist interpretation — one that does not directly quantify uncertainty about it given the data at hand.
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