Massively Parallel Assays and Quantitative Sequence-Function Relationships

Kinney, J. B., McCandlish, D. M. (May 2019) Massively Parallel Assays and Quantitative Sequence-Function Relationships. Annu Rev Genomics Hum Genet, 20. pp. 99-127. ISSN 1527-8204

DOI: 10.1146/annurev-genom-083118-014845


Over the last decade, a rich variety of massively parallel assays have revolutionized our understanding of how biological sequences encode quantitative molecular phenotypes. These assays include deep mutational scanning, high-throughput SELEX, and massively parallel reporter assays. Here, we review these experimental methods and how the data they produce can be used to quantitatively model sequence-function relationships. In doing so, we touch on a diverse range of topics, including the identification of clinically relevant genomic variants, the modeling of transcription factor binding to DNA, the functional and evolutionary landscapes of proteins, and cis-regulatory mechanisms in both transcription and mRNA splicing. We further describe a unified conceptual framework and a core set of mathematical model strategies that studies in these diverse areas can make use of. Finally, we highlight key aspects of experimental design and mathematical modeling that are important for the results of such studies to be interpretable and reproducible. Expected final online publication date for the Annual Review of Genomics and Human Genetics Volume 20 is August 30, 2019. Please see for revised estimates.

Item Type: Paper
Subjects: bioinformatics
CSHL Authors:
Communities: CSHL Cancer Center Program > Cancer Genetics and Genomics Program
CSHL Cancer Center Program > Gene Regulation and Inheritance Program
CSHL labs > Kinney lab
CSHL labs > McCandlish lab
Depositing User: Matthew Dunn
Date: 15 May 2019
Date Deposited: 29 May 2019 18:57
Last Modified: 14 Dec 2020 16:08
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