Evidence map›Paper›PMID 39652558›Full record

ArticlePloS one2024

stilPCR increases the effective sequencing length of Illumina targeted next-generation sequencing.

Jason D Limberis, Roland J Nagel, Soumitesh Chakravorty, Dena Block, Scott Dewell, Alina Nalyvayko, Zach Howard, Grant Theron, Rouxjeane Venter, John Z Metcalfe

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in PloS one, 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

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

10 authors.

Jason D LimberisDivision of Pulmonary and Critical Care Medicine, Zuckerberg San Francisco General Hospital and Trauma Centre, University of California, San Francisco, San Francisco, CA, United States of America.ORCID 0000-0002-7893-8416
Roland J NagelCepheid Inc., Sunnyvale, California, United States of America.
Soumitesh ChakravortyCepheid Inc., Sunnyvale, California, United States of America.
Dena BlockCepheid Inc., Sunnyvale, California, United States of America.
Scott DewellCepheid Inc., Sunnyvale, California, United States of America.
Alina NalyvaykoDivision of Pulmonary and Critical Care Medicine, Zuckerberg San Francisco General Hospital and Trauma Centre, University of California, San Francisco, San Francisco, CA, United States of America.
Zach HowardDivision of Experimental Medicine, University of California, San Francisco, San Francisco, CA, United States of America.
Grant TheronDSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Stellenbosch, South Africa.
Rouxjeane VenterDSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Stellenbosch, South Africa.
John Z MetcalfeDivision of Pulmonary and Critical Care Medicine, Zuckerberg San Francisco General Hospital and Trauma Centre, University of California, San Francisco, San Francisco, CA, United States of America.

Funding

A novel cartridge-based sequencing solution for decentralized M. tuberculosis resistance detectionR01AI177637 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI Soumitesh Chakravorty, John Zapata Metcalfe · 2023 to 2026
$2.8M
NIAID NIH HHS R01 AI177637
6 · The paper itself

Abstract

Identifying pathogens, resistance-conferring mutations, and strain types through targeted amplicon sequencing is an important tool. However, due to the limitations of short read sequencing, many applications require the division of limited clinical samples. Here, we present stilPCR (single-tube Illumina long read PCR), which allows the generation of hemi-nested amplicons in a single tube, with Illumina indexes and adapters, effectively increasing the Illumina read length without increasing the input requirements of reagents or sample. We have successfully utilized stilPCR on clinical sputum from tuberculosis patients to detect drug resistance mutations.

Indexed as

High-Throughput Nucleotide SequencingMycobacterium tuberculosisHumansMutationPolymerase Chain ReactionSequence Analysis, DNASputumTuberculosis

Identifiers

PMID39652558
PMCPMC11627403

What OpenQuestion holds

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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.