Evidence map›Paper›PMID 38826386›Full record

ArticleResearch square2024

Sequencing by Binding rivals error-corrected Sequencing by Synthesis technology for accurate detection and quantification of minor (<0.1%) subpopulation variants.

Christopher J Allender, Candice Wike, Dean Ellis, Darrin Lemmer, Tanner Porter, Stephanie J K Pond, David M Engelthaler

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in Research square, 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

5 · Who and what money

Authors and funding

7 authors.

Christopher J AllenderTranslational Genomics Research Institute.
Candice WikeTranslational Genomics Research Institute.
Dean EllisTranslational Genomics Research Institute.
Darrin LemmerTranslational Genomics Research Institute.
Tanner PorterTranslational Genomics Research Institute.
Stephanie J K PondTranslational Genomics Research Institute.
David M EngelthalerTranslational Genomics Research Institute.

Funding

Novel next-generation sequencing assay for monitoring multidrug resistant tuberculosis treatment in the setting of HIV infectionR01AI131939 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI ENGELTHALER, DAVID M, METCALFE, JOHN ZAPATA · 2018 to 2023
$3.9M
Handheld and population-based sequencing for rapid detection of new and repurposed drug resistance in M. tuberculosisR01AI153213 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI David M Engelthaler, John Zapata Metcalfe · 2021 to 2026
$3.7M
NIAID NIH HHS R01 AI131939NIAID NIH HHS R01 AI153213
6 · The paper itself

Abstract

Detecting very minor (< 1%) subpopulations using next-generation sequencing is a critical need for multiple applications including detection of drug resistant pathogens and somatic variant detection in oncology. To enable these applications, wet lab enhancements and bioinformatic error correction methods have been developed for 'sequencing by synthesis' technology to reduce its inherent sequencing error rate. A recently available sequencing approach termed 'sequencing by binding' claims to have higher base calling accuracy data "out of the box." This paper evaluates the utility of using 'sequencing by binding' for the detection of ultra-rare subpopulations down to 0.001%.

Indexed as

heteroresistanceNGS benchmarkingsequencing by binding (SBB)sequencing by synthesis (SBS)single molecule overlapping reads (SMOR)tuberculosis (TB)ultra-rare mutation detection

Identifiers

PMID38826386
PMCPMC11142358

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.