ArticleHuman mutation2017
Ensemble variant interpretation methods to predict enzyme activity and assign pathogenicity in the CAGI4 NAGLU (Human N-acetyl-glucosaminidase) and UBE2I (Human SUMO-ligase) challenges.
Article in Human mutation, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
9 citing papers in PubMed, 15 citations in OpenAlex.
- Meta-EA: a gene-specific combination of available computational tools for predicting missense variant effects.Nature communications · 2025Article
- CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods.Genome biology · 2024Article
- Genome interpretation using in silico predictors of variant impact.Human genetics · 2022Review
- Matching whole genomes to rare genetic disorders: Identification of potential causative variants using phenotype-weighted knowledge in the CAGI SickKids5 clinical genomes challenge.Human mutation · 2020Article
- Assessment of methods for predicting the effects of PTEN and TPMT protein variants.Human mutation · 2019Article
- Assessment of predicted enzymatic activity of α-N-acetylglucosaminidase variants of unknown significance for CAGI 2016.Human mutation · 2019Article
- A novel mutation in the NAGLU gene associated with Sanfilippo syndrome type B (mucopolysaccharidosis III B).Clinical case reports · 2018Article
- Utilizing ExAC to assess the hidden contribution of variants of unknown significance to Sanfilippo Type B incidence.PloS one · 2018Article
- Reports from CAGI: The Critical Assessment of Genome Interpretation.Human mutation · 2017Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
CAGI (Critical Assessment of Genome Interpretation) conducts community experiments to determine the state of the art in relating genotype to phenotype. Here, we report results obtained using newly developed ensemble methods to address two CAGI4 challenges: enzyme activity for population missense variants found in NAGLU (Human N-acetyl-glucosaminidase) and random missense mutations in Human UBE2I (Human SUMO E2 ligase), assayed in a high-throughput competitive yeast complementation procedure. The ensemble methods are effective, ranked second for SUMO-ligase and third for NAGLU, according to the CAGI independent assessors. However, in common with other methods used in CAGI, there are large discrepancies between predicted and experimental activities for a subset of variants. Analysis of the structural context provides some insight into these. Post-challenge analysis shows that the ensemble methods are also effective at assigning pathogenicity for the NAGLU variants. In the clinic, providing an estimate of the reliability of pathogenic assignments is the key. We have also used the NAGLU dataset to show that ensemble methods have considerable potential for this task, and are already reliable enough for use with a subset of mutations.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.