Multiplexed assays of variant effects contribute to a growing genotype–phenotype atlas

J Weile, FP Roth - Human genetics, 2018 - Springer
Given the constantly improving cost and speed of genome sequencing, it is reasonable to
expect that personal genomes will soon be known for many millions of humans. This stands …

An Atlas of Variant Effects to understand the genome at nucleotide resolution

DM Fowler, DJ Adams, AL Gloyn, WC Hahn, DS Marks… - Genome Biology, 2023 - Springer
Sequencing has revealed hundreds of millions of human genetic variants, and continued
efforts will only add to this variant avalanche. Insufficient information exists to interpret the …

Variant interpretation: functional assays to the rescue

LM Starita, N Ahituv, MJ Dunham, JO Kitzman… - The American Journal of …, 2017 - cell.com
Classical genetic approaches for interpreting variants, such as case-control or co-
segregation studies, require finding many individuals with each variant. Because the …

From variant to function in human disease genetics

T Lappalainen, DG MacArthur - Science, 2021 - science.org
Over the next decade, the primary challenge in human genetics will be to understand the
biological mechanisms by which genetic variants influence phenotypes, including disease …

The power of multiplexed functional analysis of genetic variants

M Gasperini, L Starita, J Shendure - Nature protocols, 2016 - nature.com
New technologies have recently enabled saturation mutagenesis and functional analysis of
nearly all possible variants of regulatory elements or proteins of interest in single …

Recommendations for the collection and use of multiplexed functional data for clinical variant interpretation

H Gelman, JN Dines, J Berg, AH Berger, S Brnich… - Genome Medicine, 2019 - Springer
Variants of uncertain significance represent a massive challenge to medical genetics.
Multiplexed functional assays, in which the functional effects of thousands of genomic …

Variant effect prediction tools assessed using independent, functional assay-based datasets: implications for discovery and diagnostics

K Mahmood, C Jung, G Philip, P Georgeson, J Chung… - Human genomics, 2017 - Springer
Background Genetic variant effect prediction algorithms are used extensively in clinical
genomics and research to determine the likely consequences of amino acid substitutions on …

Scalable functional assays for the interpretation of human genetic variation

D Tabet, V Parikh, P Mali, FP Roth… - Annual Review of …, 2022 - annualreviews.org
Scalable sequence–function studies have enabled the systematic analysis and cataloging of
hundreds of thousands of coding and noncoding genetic variants in the human genome …

MaveDB: an open-source platform to distribute and interpret data from multiplexed assays of variant effect

D Esposito, J Weile, J Shendure, LM Starita… - Genome biology, 2019 - Springer
Multiplex assays of variant effect (MAVEs), such as deep mutational scans and massively
parallel reporter assays, test thousands of sequence variants in a single experiment. Despite …

Integration of multiple epigenomic marks improves prediction of variant impact in saturation mutagenesis reporter assay

D Shigaki, O Adato, AN Adhikari, S Dong… - Human …, 2019 - Wiley Online Library
The integrative analysis of high‐throughput reporter assays, machine learning, and profiles
of epigenomic chromatin state in a broad array of cells and tissues has the potential to …