CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods

Genome biology, 2024 - Springer
Abstract Background The Critical Assessment of Genome Interpretation (CAGI) aims to
advance the state-of-the-art for computational prediction of genetic variant impact …

Genome interpretation using in silico predictors of variant impact

P Katsonis, K Wilhelm, A Williams, O Lichtarge - Human genetics, 2022 - Springer
Estimating the effects of variants found in disease driver genes opens the door to
personalized therapeutic opportunities. Clinical associations and laboratory experiments …

Deep mutational scanning reveals a correlation between degradation and toxicity of thousands of aspartoacylase variants

M Grønbæk-Thygesen, V Voutsinos… - Nature …, 2024 - nature.com
Unstable proteins are prone to form non-native interactions with other proteins and thereby
may become toxic. To mitigate this, destabilized proteins are targeted by the protein quality …

Monogenic causes of non-obstructive azoospermia: challenges, established knowledge, limitations and perspectives

L Kasak, M Laan - Human genetics, 2021 - Springer
It is estimated that one in 100 men have azoospermia, the complete lack of sperm in the
ejaculate. Currently,~ 20% of azoospermia cases remain idiopathic. Non-obstructive …

Crowdsourcing assessment of maternal blood multi-omics for predicting gestational age and preterm birth

AL Tarca, BÁ Pataki, R Romero, M Sirota, Y Guan… - Cell Reports …, 2021 - cell.com
Identification of pregnancies at risk of preterm birth (PTB), the leading cause of newborn
deaths, remains challenging given the syndromic nature of the disease. We report a …

Predicting disease severity in metachromatic leukodystrophy using protein activity and a patient phenotype matrix

M Trinidad, X Hong, S Froelich, J Daiker, J Sacco… - Genome Biology, 2023 - Springer
Background Metachromatic leukodystrophy (MLD) is a lysosomal storage disorder caused
by mutations in the arylsulfatase A gene (ARSA) and categorized into three subtypes …

Reports from the fifth edition of CAGI: The Critical Assessment of Genome Interpretation

G Andreoletti, LR Pal, J Moult, SE Brenner - Human mutation, 2019 - Wiley Online Library
Abstract Interpretation of genomic variation plays an essential role in the analysis of cancer
and monogenic disease, and increasingly also in complex trait disease, with applications …

Novel gene-specific Bayesian Gaussian mixture model to predict the missense variants pathogenicity of Sanfilippo syndrome

EEA Mohammed, AG Fayez, NM Abdelfattah… - Scientific Reports, 2024 - nature.com
MPS III is an autosomal recessive lysosomal storage disease caused mainly by missense
variants in the NAGLU, GNS, HGSNAT, and SGSH genes. The pathogenicity interpretation …

Meta-EA: a gene-specific combination of available computational tools for predicting missense variant effects

P Katsonis, O Lichtarge - Nature Communications, 2025 - nature.com
Computational methods for estimating missense variant impact suffer from inconsistent
performance across genes, which poses a major challenge for their reliable use in clinical …

Functional profiling of the sequence stockpile: a protein pair-based assessment of in silico prediction tools

R Prabakaran, Y Bromberg - Bioinformatics, 2025 - academic.oup.com
Motivation In silico functional annotation of proteins is crucial to narrowing the sequencing-
accelerated gap in our understanding of protein activities. Numerous function annotation …