Evidence map›Paper›PMID 36712073›Full record

ArticlebioRxiv : the preprint server for biology2023

LRphase: an efficient method for assigning haplotype identity to long reads.

Monica J Holmes, Babak Mahjour, Christopher P Castro, Gregory A Farnum, Adam G Diehl, Alan P Boyle

Open access · greenAbstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2023. 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, 1 citations in OpenAlex.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

6 authors at 1 institution in 1 country.

Monica J HolmesDepartment of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA 48109.
Babak MahjourDepartment of Medicinal Chemistry, University of Michigan, Ann Arbor, MI, USA 48109.
Christopher P CastroDepartment of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA 48109.
Gregory A FarnumDepartment of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA 48109.
Adam G DiehlDepartment of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA 48109.
Alan P BoyleDepartment of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA 48109.
University of Michigan · US

Funding

Training Program in BioinformaticsT32GM070449 · NIGMS · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI ATHEY, BRIAN DAVID, BURMEISTER, MARGIT · 2005 to 2020
$3.6M
Mobile element derived chromatin looping variability in human populationsR01GM144484 · NIGMS · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI BOYLE, ALAN P · 2022 to 2025
$1.6M
New technologies for accurate capture and sequencing of repeat-associated regionsR21HG011493 · NHGRI · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI BOYLE, ALAN P, MILLS, RYAN E · 2021 to 2022
$643k
NHGRI NIH HHS R21 HG011493NIGMS NIH HHS R01 GM144484NIGMS NIH HHS T32 GM070449
6 · The paper itself

Abstract

Understanding the functional effects of sequence variation is among the primary goals of contemporary genomics. Individual human genomes contain millions of variants which are thought to contribute to phenotypic variability and differential disease risks at the population level. However, because variants rarely act in isolation, we cannot accurately predict functional effects without first considering the potential effects of other interacting variants on the same chromosome. This information can be obtained by phasing the read data from sequencing experiments. However, no standalone tools are available to simply phase reads based on known haplotypes. Here we present LRphase: a user-friendly utility for simple phasing of long sequencing reads.

Identifiers

PMID36712073
PMCPMC9882277
OpenAlexW4317611403

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC
Read underepoch 390

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.