Evidence map›Paper›PMID 38036971›Full record

ArticleBMC bioinformatics2023

Completing a genomic characterisation of microscopic tumour samples with copy number.

Joel Nulsen, Nosheen Hussain, Aws Al-Deka, Jason Yap, Khalil Uddin, Christopher Yau, Ahmed Ashour Ahmed

Erratum issuedAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC bioinformatics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing 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

2 citing papers in PubMed.

  1. Article
  2. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

7 authors.

Joel NulsenWeatherall Institute for Molecular Medicine, University of Oxford, Oxford, UK.
Nosheen HussainWeatherall Institute for Molecular Medicine, University of Oxford, Oxford, UK.
Aws Al-DekaWeatherall Institute for Molecular Medicine, University of Oxford, Oxford, UK.
Jason YapUniversity of Birmingham, Birmingham, UK.
Khalil UddinUniversity of Birmingham, Birmingham, UK.
Christopher YauNuffield Department for Women's and Reproductive Health, University of Oxford, Oxford, UK.
Ahmed Ashour AhmedWeatherall Institute for Molecular Medicine, University of Oxford, Oxford, UK. ahmed.ahmed@wrh.ox.ac.uk.

Funding

Ovarian Cancer Action HER00760
6 · The paper itself

Abstract

backgroundGenomic insights in settings where tumour sample sizes are limited to just hundreds or even tens of cells hold great clinical potential, but also present significant technical challenges. We previously developed the DigiPico sequencing platform to accurately identify somatic mutations from such samples.

resultsHere, we complete this genomic characterisation with copy number. We present a novel protocol, PicoCNV, to call allele-specific somatic copy number alterations from picogram quantities of tumour DNA. We find that PicoCNV provides exactly accurate copy number in 84% of the genome for even the smallest samples, and demonstrate its clinical potential in maintenance therapy.

conclusionsPicoCNV complements our existing platform, allowing for accurate and comprehensive genomic characterisations of cancers in settings where only microscopic samples are available.

Indexed as

DNA Copy Number VariationsNeoplasmsDNA, NeoplasmGenomeGenomicsHumansDNA, NeoplasmCancer genomicsCopy numberMicroscopic samples

Identifiers

PMID38036971
PMCPMC10688092

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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.