298 research outputs found
A New Framework for the Use of Variant Interpretation Tools in Clinical Practice
Current ACMG/AMP guidelines for the use of sequence variants for genetic diagnosis
and treatment permit the use of in silico predictors as Supporting evidence (PP3 and
BP4 criteria). These criteria, however, lack quantitative support and leave clinicians and
scientists without standards for applying these criteria, leading to large interpretation
variability. To address this challenge, our team built upon previous work and introduced
a novel criterion that can be used to calibrate any computational model or any other
continuous-scale evidence on any variant type. We used it to estimate score intervals
corresponding to the four strengths of evidence for pathogenicity and benignity for
fourteen missense variant interpretation tools on a carefully assembled data sets of
known pathogenic and benign variants. We found that most tools achieved the Supporting
evidence level for both pathogenic and benign classification using newly established datadriven
thresholds. Importantly, at appropriate score thresholds, several in silico methods
can also provide Moderate and Strong evidence levels for a limited number of variants.
Based on these findings, we provided recommendations for quantitative revisions of the
PP3 and BP4 criteria within ACMG/AMP guidelines and the future assessment of in silico
methods for clinical interpretation.Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 202
Evaluating purifying selection in the mitochondrial DNA of various mammalian species
Mitochondrial DNA (mtDNA), the circular DNA molecule inside the mitochondria of all eukaryotic cells, has been shown to be under the effect of purifying selection in several species. Traditional testing of purifying selection has been based simply on ratios of nonsynonymous to synonymous mutations, without considering the relative age of each mutation, which can be determined by phylogenetic analysis of this non-recombining molecule. The incorporation of a mutation time-ordering from phylogeny and of predicted pathogenicity scores for nonsynonymous mutations allow a quantitative evaluation of the effects of purifying selection in human mtDNA. Here, by using this additional information, we show that purifying selection undoubtedly acts upon the mtDNA of other mammalian species/genera, namely Bos sp., Canis lupus, Mus musculus, Orcinus orca, Pan sp. and Sus scrofa. The effects of purifying selection were comparable in all species, leading to a significant major proportion of nonsynonymous variants with higher pathogenicity scores in the younger branches of the tree. We also derive recalibrated mutation rates for age estimates of ancestors of these various species and proposed a correction curve in order to take into account the effects of selection. Understanding this selection is fundamental to evolutionary studies and to the identification of deleterious mutations
Uncovering protein interaction in abstracts and text using a novel linear model and word proximity networks
We participated in three of the protein-protein interaction subtasks of the
Second BioCreative Challenge: classification of abstracts relevant for
protein-protein interaction (IAS), discovery of protein pairs (IPS) and text
passages characterizing protein interaction (ISS) in full text documents. We
approached the abstract classification task with a novel, lightweight linear
model inspired by spam-detection techniques, as well as an uncertainty-based
integration scheme. We also used a Support Vector Machine and the Singular
Value Decomposition on the same features for comparison purposes. Our approach
to the full text subtasks (protein pair and passage identification) includes a
feature expansion method based on word-proximity networks. Our approach to the
abstract classification task (IAS) was among the top submissions for this task
in terms of the measures of performance used in the challenge evaluation
(accuracy, F-score and AUC). We also report on a web-tool we produced using our
approach: the Protein Interaction Abstract Relevance Evaluator (PIARE). Our
approach to the full text tasks resulted in one of the highest recall rates as
well as mean reciprocal rank of correct passages. Our approach to abstract
classification shows that a simple linear model, using relatively few features,
is capable of generalizing and uncovering the conceptual nature of
protein-protein interaction from the bibliome. Since the novel approach is
based on a very lightweight linear model, it can be easily ported and applied
to similar problems. In full text problems, the expansion of word features with
word-proximity networks is shown to be useful, though the need for some
improvements is discussed
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