Evidence map›Paper›PMID 38328152›Full record

ArticlebioRxiv : the preprint server for biology2024

Genome-wide profiling of genetic variation at tandem repeat from long reads.

Helyaneh Ziaei Jam, Justin M Zook, Sara Javadzadeh, Jonghun Park, Aarushi Sehgal, Melissa Gymrek

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing 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

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

6 authors.

Helyaneh Ziaei JamDepartment of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.ORCID 0009-0002-9832-1437
Justin M ZookMaterial Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Dr., Gaithersburg, MD, USA.ORCID 0000-0003-2309-8402
Sara JavadzadehDepartment of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
Jonghun ParkDepartment of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
Aarushi SehgalDepartment of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.
Melissa GymrekDepartment of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA.

Funding

Refining Mendelian disease analysis via detection of clinically relevant repeat variantsR01HG010149 · NHGRI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Vineet Bafna, Vikas Bansal · 2018 to 2026
$4.5M
The role of structural variants and tandem repeats in substance abuse-related behavioral traitsU01DA051234 · NIDA · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI GYMREK, MELISSA, PALMER, ABRAHAM A · 2021 to 2025
$3.5M
NHGRI NIH HHS R01 HG010149NIDA NIH HHS U01 DA051234
6 · The paper itself

Abstract

Tandem repeats are frequent across the human genome, and variation in repeat length has been linked to a variety of traits. Recent improvements in long read sequencing technologies have the potential to greatly improve TR analysis, especially for long or complex repeats. Here we introduce LongTR, which accurately genotypes tandem repeats from high fidelity long reads available from both PacBio and Oxford Nanopore Technologies. LongTR is freely available at https://github.com/gymrek-lab/longtr.

Identifiers

PMID38328152
PMCPMC10849534

What OpenQuestion holds

Textmetadata
LicenceCC BY-ND
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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.