Evidence map›Paper›PMID 40799530›Full record

ArticlebioRxiv : the preprint server for biology2025

Defining and cataloging variants in pangenome graphs.

Pouria Salehi Nowbandegani, Shenghan Zhang, Haoyang Hu, Heng Li, Luke J O'Connor

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2025. 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

5 authors.

Pouria Salehi NowbandeganiDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.ORCID 0000-0002-3659-0765
Shenghan ZhangDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
Haoyang HuDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
Heng LiDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
Luke J O'ConnorDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.

Funding

The WashU-UCSC-EBI Human Genome Reference Center."U41HG010972 · NHGRI · WASHINGTON UNIVERSITY · PI Ira M Hall, Heng Li · 2019 to 2026
$24.9M
Advanced computational methods in analyzing high-throughput sequencing dataR01HG010040 · NHGRI · DANA-FARBER CANCER INST · PI Heng Li · 2018 to 2026
$3.7M
Tools for comprehensive variant characterization using the pangenomeU01HG013748 · NHGRI · UNIVERSITY OF CALIFORNIA SANTA CRUZ · PI LI, HENG, MARSCHALL, TOBIAS · 2024 to 2024
$1.7M
The functional and phenotypic effects of protein coding genetic variationR35GM155278 · NIGMS · HARVARD MEDICAL SCHOOL · PI Luke Jen O'Connor · 2024 to 2026
$1.3M
NHGRI NIH HHS R01 HG010040NHGRI NIH HHS U01 HG013748NHGRI NIH HHS U41 HG010972NIGMS NIH HHS R35 GM155278
6 · The paper itself

Abstract

Structural variation causes some human haplotypes to align poorly with the linear reference genome, leading to 'reference bias'. A pangenome reference graph could ameliorate this bias by relating a sample to multiple reference assemblies. However, this approach requires a new definition of a 'genetic variant.' We introduce a definition of pangenome variants and a method,

Identifiers

PMID40799530
PMCPMC12340789

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Registered trials

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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.