[HTML][HTML] Artificial intelligence (AI) and big data in cancer and precision oncology

Z Dlamini, FZ Francies, R Hull, R Marima - Computational and structural …, 2020 - Elsevier
Artificial intelligence (AI) and machine learning have significantly influenced many facets of
the healthcare sector. Advancement in technology has paved the way for analysis of big …

Using the ACMG/AMP framework to capture evidence related to predicted and observed impact on splicing: Recommendations from the ClinGen SVI Splicing …

LC Walker, M de la Hoya, GAR Wiggins, A Lindy… - The American Journal of …, 2023 - cell.com
Summary The American College of Medical Genetics and Genomics (ACMG)/Association for
Molecular Pathology (AMP) framework for classifying variants uses six evidence categories …

In silico methods for predicting functional synonymous variants

BC Lin, U Katneni, KI Jankowska, D Meyer… - Genome Biology, 2023 - Springer
Single nucleotide variants (SNVs) contribute to human genomic diversity. Synonymous
SNVs are previously considered to be “silent,” but mounting evidence has revealed that …

Transcriptome-directed analysis for Mendelian disease diagnosis overcomes limitations of conventional genomic testing

DR Murdock, H Dai, LC Burrage… - The Journal of …, 2021 - Am Soc Clin Investig
BACKGROUND Transcriptome sequencing (RNA-seq) improves diagnostic rates in
individuals with suspected Mendelian conditions to varying degrees, primarily by directing …

Benchmarking deep learning splice prediction tools using functional splice assays

TV Riepe, M Khan, S Roosing, FPM Cremers… - Human …, 2021 - Wiley Online Library
Hereditary disorders are frequently caused by genetic variants that affect pre‐messenger
RNA splicing. Though genetic variants in the canonical splice motifs are almost always …

Performance Evaluation of SpliceAI for the Prediction of Splicing of NF1 Variants

C Ha, JW Kim, JH Jang - Genes, 2021 - mdpi.com
Neurofibromatosis type 1, characterized by neurofibromas and café-au-lait macules, is one
of the most common genetic disorders caused by pathogenic NF1 variants. Because of the …

Splicing predictions, minigene analyses, and ACMG‐AMP clinical classification of 42 germline PALB2 splice‐site variants

A Valenzuela‐Palomo, E Bueno‐Martínez… - The Journal of …, 2022 - Wiley Online Library
PALB2 loss‐of‐function variants confer high risk of developing breast cancer. Here we
present a systematic functional analysis of PALB2 splice‐site variants detected in …

What has the undiagnosed diseases network taught us about the clinical applications of genomic testing?

DR Murdock, JA Rosenfeld, B Lee - Annual review of medicine, 2022 - annualreviews.org
Genetic testing has undergone a revolution in the last decade, particularly with the advent of
next-generation sequencing and its associated reductions in costs and increases in …

Variant effect on splicing regulatory elements, branchpoint usage, and pseudoexonization: Strategies to enhance bioinformatic prediction using hereditary cancer …

D Canson, D Glubb, AB Spurdle - Human Mutation, 2020 - Wiley Online Library
It is possible to estimate the prior probability of pathogenicity for germline disease gene
variants based on bioinformatic prediction of variant effect/s. However, routinely used …

Large‐scale comparative evaluation of user‐friendly tools for predicting variant‐induced alterations of splicing regulatory elements

H Tubeuf, C Charbonnier, O Soukarieh… - Human …, 2020 - Wiley Online Library
Discriminating which nucleotide variants cause disease or contribute to phenotypic traits
remains a major challenge in human genetics. In theory, any intragenic variant can …