Evidence map›Paper›PMID 39713404›Full record

ArticlebioRxiv : the preprint server for biology2024

StarPhase: Comprehensive Phase-Aware Pharmacogenomic Diplotyper for Long-Read Sequencing Data.

James M Holt, John Harting, Xiao Chen, Daniel Baker, Christopher T Saunders, Zev Kronenberg, Nina Gonzaludo, Byunggil Yoo, Georgi Hudjashov, Maarja Jõeloo and 8 more

Abstract readPreprint
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. 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

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

18 authors.

James M HoltPacBio, 1305 O'Brien Drive, Menlo Park, CA 94025, USA.ORCID 0000-0001-6411-9236
John HartingPacBio, 1305 O'Brien Drive, Menlo Park, CA 94025, USA.ORCID 0009-0002-0126-5257
Xiao ChenPacBio, 1305 O'Brien Drive, Menlo Park, CA 94025, USA.ORCID 0000-0002-1432-268X
Daniel BakerPacBio, 1305 O'Brien Drive, Menlo Park, CA 94025, USA.ORCID 0000-0002-0513-6893
Christopher T SaundersPacBio, 1305 O'Brien Drive, Menlo Park, CA 94025, USA.ORCID 0000-0002-0726-7600
Zev KronenbergPacBio, 1305 O'Brien Drive, Menlo Park, CA 94025, USA.ORCID 0000-0002-7627-9808
Nina GonzaludoPacBio, 1305 O'Brien Drive, Menlo Park, CA 94025, USA.ORCID 0000-0002-1256-4685
Byunggil YooChildren's Mercy Kansas City, 2401 Gillham Road, Kansas City, MO 64108, USA.ORCID 0000-0002-7912-1862
Georgi HudjashovEstonian Genome Centre, Institute of Genomics, University of Tartu, Estonia.ORCID 0000-0002-7536-9086
Maarja JõelooEstonian Genome Centre, Institute of Genomics, University of Tartu, Estonia.ORCID 0000-0002-4619-3229
James M J LawlorHudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806, USA.ORCID 0000-0003-1735-1766
Weng Khong LimSingHealth Duke-NUS Institute of Precision Medicine, 5 Hospital Drive, Singapore 169609, Singapore.ORCID 0000-0003-4391-1130
Estonian Biobank Research Team
Saumya S JamuarSingHealth Duke-NUS Institute of Precision Medicine, 5 Hospital Drive, Singapore 169609, Singapore.ORCID 0000-0003-2341-8349
Gregory M CooperHudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL 35806, USA.ORCID 0000-0001-5509-9923
Lili MilaniEstonian Genome Centre, Institute of Genomics, University of Tartu, Estonia.ORCID 0000-0002-5323-3102
Tomi PastinenChildren's Mercy Kansas City, 2401 Gillham Road, Kansas City, MO 64108, USA.ORCID 0000-0003-4016-5021
Michael A EberlePacBio, 1305 O'Brien Drive, Menlo Park, CA 94025, USA.ORCID 0000-0001-8965-1253

Funding

South-seq: DNA sequencing for newborn nurseries in the SouthU01HG007301 · NHGRI · HUDSON-ALPHA INSTITUTE FOR BIOTECHNOLOGY · PI BARSH, GREGORY STEFAN, COOPER, GREGORY MICHAEL · 2017 to 2021
$11.9M
Genomic Diagnosis in Children with Developmental DelayUM1HG007301 · NHGRI · HUDSON-ALPHA INSTITUTE FOR BIOTECHNOLOGY · PI COOPER, GREGORY MICHAEL, MYERS, RICHARD M · 2013 to 2016
$7.5M
Utility of Genomic Sequencing in Community Care ContextsR01HG011598 · NHGRI · UNIVERSITY OF LOUISVILLE · PI BROTHERS, KYLE BERTRAM, COOPER, GREGORY MICHAEL · 2021 to 2024
$3.0M
Long-read genome sequencing for the discovery of highly penetrant variation in rare diseasesR01HD112437 · NICHD · HUDSON-ALPHA INSTITUTE FOR BIOTECHNOLOGY · PI Gregory Michael Cooper, Jane Grimwood · 2024 to 2026
$1.8M
NHGRI NIH HHS R01 HG011598NHGRI NIH HHS U01 HG007301NHGRI NIH HHS UM1 HG007301NICHD NIH HHS R01 HD112437
6 · The paper itself

Abstract

Pharmacogenomics is central to precision medicine, informing medication safety and efficacy. Pharmacogenomic diplotyping of complex genes requires full-length DNA sequences and detection of structural rearrangements. We introduce StarPhase, a tool that leverages PacBio HiFi sequence data to diplotype 21 CPIC Level A pharmacogenes and provides detailed haplotypes and supporting visualizations for

Identifiers

PMID39713404
PMCPMC11661245

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
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.