Evidence map›Paper›PMID 39420419›Full record

ArticleGenome biology2024

MHConstructor: a high-throughput, haplotype-informed solution to the MHC assembly challenge.

Kristen J Wade, Rayo Suseno, Kerry Kizer, Jacqueline Williams, Juliano Boquett, Stacy Caillier, Nicholas R Pollock, Adam Renschen, Adam Santaniello, Jorge R Oksenberg and 3 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genome biology, 2024. 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

13 authors.

Kristen J WadeDepartment of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA.
Rayo SusenoDepartment of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA.
Kerry KizerDepartment of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA.
Jacqueline WilliamsDepartment of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA.
Juliano BoquettDepartment of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA.
Stacy CaillierDepartment of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA.
Nicholas R PollockDepartment of Biomedical Informatics, Anschutz Medical Campus, University of Colorado, Aurora, CO, USA.
Adam RenschenDepartment of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA.
Adam SantanielloDepartment of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA.
Jorge R OksenbergDepartment of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA.
Paul J NormanDepartment of Biomedical Informatics, Anschutz Medical Campus, University of Colorado, Aurora, CO, USA.
Danillo G AugustoDepartment of Biological Sciences, University of North Carolina Charlotte, Charlotte, NC, USA.
Jill A HollenbachDepartment of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA, USA. jill.hollenbach@ucsf.edu.ORCID http://orcid.org/0000-0001-6572-7962

Funding

Insights Into Immune-Related Diseases Born from Population GenomicsU01AI090905 · NIAID · UNIVERSITY OF COLORADO DENVER · PI Paul John Norman · 2010 to 2026
$10.9M
The Role of B cells in the Origin and Progression of Multiple SclerosisR35NS111644 · NINDS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI STEPHEN L HAUSER · 2019 to 2026
$9.1M
NIAID NIH HHS U01 AI090905NINDS NIH HHS R35 NS111644
6 · The paper itself

Abstract

The extremely high levels of genetic polymorphism within the human major histocompatibility complex (MHC) limit the usefulness of reference-based alignment methods for sequence assembly. We incorporate a short-read, de novo assembly algorithm into a workflow for novel application to the MHC. MHConstructor is a containerized pipeline designed for high-throughput, haplotype-informed, reproducible assembly of both whole genome sequencing and target capture short-read data in large, population cohorts. To-date, no other self-contained tool exists for the generation of de novo MHC assemblies from short-read data. MHConstructor facilitates wide-spread access to high-quality, alignment-free MHC sequence analysis.

Indexed as

HaplotypesMajor Histocompatibility ComplexAlgorithmsHigh-Throughput Nucleotide SequencingHumansSoftwareDe novo assemblyHaplotypeHuman leukocyte antigen genesMajor histocompatibility complexShort-read sequencing

Identifiers

PMID39420419
PMCPMC11484429

What OpenQuestion holds

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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.