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High-throughput functional analysis of regulatory variants using a massively parallel reporter assay.

ABSTRACT: Association studies describe genetic associations between noncoding variants and disease susceptibility; however, they do not provide functional insight into the underlying molecular mechanisms of these variants. We present a protocol to assay the regulatory potential of thousands of noncoding variants using massively parallel reporter assays. We describe steps for oligo design, generating a plasmid pool, and extracting tag-seq libraries from cells to quantify the tested sequences. For complete details on the use and execution of this protocol, please refer to Oliveros and Delfosse et al.¹.

SUBMITTER: Delfosse K

PROVIDER: S-EPMC10694570 | biostudies-literature | 2023 Nov

REPOSITORIES: biostudies-literature

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High-throughput functional analysis of regulatory variants using a massively parallel reporter assay.

Delfosse Kate K Gerhardinger Chiara C Rinn John L JL Maass Philipp G PG

STAR protocols 20231118 4

Association studies describe genetic associations between noncoding variants and disease susceptibility; however, they do not provide functional insight into the underlying molecular mechanisms of these variants. We present a protocol to assay the regulatory potential of thousands of noncoding variants using massively parallel reporter assays. We describe steps for oligo design, generating a plasmid pool, and extracting tag-seq libraries from cells to quantify the tested sequences. For complete ...[more]

PMID: 37980569

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