Evidence map›Paper›PMID 41010007›Full record

ArticleGenes2025

CREPE (CREate Primers and Evaluate): A Computational Tool for Large-Scale Primer Design and Specificity Analysis.

Jonathan W Pitsch, Sara A Wirth, Nicole T Costantino, Josh Mejia, Rose M Doss, Ava V A Warren, Jack Ustanik, Xiaoxu Yang, Martin W Breuss

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genes, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

9 authors.

Jonathan W PitschDepartment of Pediatrics, Section of Genetics and Metabolism, University of Colorado School of Medicine, Aurora, CO 80045, USA.
Sara A WirthDepartment of Pediatrics, Section of Genetics and Metabolism, University of Colorado School of Medicine, Aurora, CO 80045, USA.
Nicole T CostantinoDepartment of Pediatrics, Section of Genetics and Metabolism, University of Colorado School of Medicine, Aurora, CO 80045, USA.ORCID 0009-0004-5312-0759
Josh MejiaDepartment of Pediatrics, Section of Genetics and Metabolism, University of Colorado School of Medicine, Aurora, CO 80045, USA.
Rose M DossDepartment of Pediatrics, Section of Genetics and Metabolism, University of Colorado School of Medicine, Aurora, CO 80045, USA.
Ava V A WarrenDepartment of Pediatrics, Section of Genetics and Metabolism, University of Colorado School of Medicine, Aurora, CO 80045, USA.
Jack UstanikDepartment of Pediatrics, Section of Genetics and Metabolism, University of Colorado School of Medicine, Aurora, CO 80045, USA.
Xiaoxu YangDepartment of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA.ORCID 0000-0003-0219-0023
Martin W BreussDepartment of Pediatrics, Section of Genetics and Metabolism, University of Colorado School of Medicine, Aurora, CO 80045, USA.ORCID 0000-0003-2200-8604

Funding

Genome-wide assessment of transcriptional state historyR01HG013472 · NHGRI · UNIVERSITY OF COLORADO DENVER · PI Martin Werner Breuss · 2024 to 2026
$1.2M
Understanding genomic stability between generations by assessing mutational burdens in single spermsR00HD111686 · NICHD · UTAH STATE HIGHER EDUCATION SYSTEM--UNIVERSITY OF UTAH · PI Xiaoxu Yang · 2025 to 2026
$498k
Mechanisms controlling HIV latency and pathogenesis in microgliaR21MH134401 · NIMH · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI SCHLACHETZKI, JOHANNES CAROLUS MAGNUS, YANG, XIAOXU · 2023 to 2023
$435k
Boettcher Foundation 2022 InvestigatorEunice Kennedy Shriver National Institute of Child Health and Human Development R00HD111686NHGRI NIH HHS R01 HG013472NHGRI NIH HHS R01HG013472NICHD NIH HHS R00 HD111686NIMH NIH HHS R21 MH134401NIMH NIH HHS R21MH134401
6 · The paper itself

Abstract

BACKGROUND/

objectivesPolymerase chain reaction (PCR) is ubiquitous in biological research labs, as it is a fast, flexible, and cost-effective technique to amplify a DNA region of interest. However, manual primer design can be an error-prone and time-consuming process depending on the number and composition of target sites. While Primer3 has emerged as an accessible tool to solve some of these issues, additional computational pipelines are required for appropriate scaling. Moreover, this does not replace the manual confirmation of primer specificity (i.e., the assessment of off-targets).

methodsTo overcome the challenges of large-scale primer design, we fused the functionality of Primer3 and In-Silico PCR (ISPCR); this integrated pipeline, CREPE (CREate Primers and Evaluate), performs primer design and specificity analysis through a custom evaluation script for any given number of target sites at scale.

resultsCREPE's final output summarizes the lead forward and reverse primer pair for each target site, a measure of the likelihood of binding to off-targets, and additional information to aid decision-making. We provide this through a customized workflow for targeted amplicon sequencing (TAS) on a 150 bp paired-end Illumina platform. Experimental testing showed successful amplification for more than 90% of primers deemed acceptable by CREPE.

conclusionsWe here provide CREPE, a software platform that allows for parallelized primer design for PCR applications and that is optimized for targeted amplicon sequencing.

Indexed as

Computational BiologyDNA PrimersPolymerase Chain ReactionSoftwareDNA Primersbioinformatic toolpolymerase chain reactionprimer designtargeted amplicon sequencing

Identifiers

PMID41010007
PMCPMC12469620

What OpenQuestion holds

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LicenceCC BY
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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.