Evidence map›Paper›PMID 39350042›Full record

ArticleBMC genomics2024

Performance of somatic structural variant calling in lung cancer using Oxford Nanopore sequencing technology.

Lingchen Liu, Jia Zhang, Scott Wood, Felicity Newell, Conrad Leonard, Lambros T Koufariotis, Katia Nones, Andrew J Dalley, Haarika Chittoory, Farzad Bashirzadeh and 13 more

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PubMed Full text at PMC Publisher
In one paragraph

Article in BMC genomics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing 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

5 citing papers in PubMed.

  1. Review
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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

23 authors.

Lingchen LiuQIMR Berghofer Medical Research Institute, Brisbane, Australia.
Jia ZhangQIMR Berghofer Medical Research Institute, Brisbane, Australia.
Scott WoodQIMR Berghofer Medical Research Institute, Brisbane, Australia.
Felicity NewellQIMR Berghofer Medical Research Institute, Brisbane, Australia.
Conrad LeonardQIMR Berghofer Medical Research Institute, Brisbane, Australia.
Lambros T KoufariotisQIMR Berghofer Medical Research Institute, Brisbane, Australia.
Katia NonesQIMR Berghofer Medical Research Institute, Brisbane, Australia.
Andrew J DalleyFaculty of Medicine, The University of Queensland, Brisbane, Australia.
Haarika ChittooryFaculty of Medicine, The University of Queensland, Brisbane, Australia.
Farzad BashirzadehDepartment of Thoracic Medicine, The Royal Brisbane & Women's Hospital, Brisbane, Australia.
Jung Hwa SonDepartment of Thoracic Medicine, The Royal Brisbane & Women's Hospital, Brisbane, Australia.
Daniel SteinfortDepartment of Thoracic Medicine, Royal Melbourne Hospital, Melbourne, Australia.
Jonathan P WilliamsonDepartment of Thoracic Medicine, Liverpool Hospital Sydney, Sydney, Australia.
Michael BintDepartment of Thoracic Medicine, Sunshine Coast University Hospital, Birtinya, Australia.
Carl PahoffDepartment of Thoracic Medicine, Gold Coast University Hospital, Southport, Australia.
Phan T NguyenDepartment of Thoracic Medicine, Royal Adelaide Hospital, Adelaide, Australia.
Scott TwaddellDepartment of Respiratory and Sleep Medicine, John Hunter Hospital, Newcastle, Australia.
David ArnoldDepartment of Respiratory and Sleep Medicine, John Hunter Hospital, Newcastle, Australia.
Christopher GraingeDepartment of Respiratory and Sleep Medicine, John Hunter Hospital, Newcastle, Australia.
Peter T SimpsonFaculty of Medicine, The University of Queensland, Brisbane, Australia.
David FieldingFaculty of Medicine, The University of Queensland, Brisbane, Australia.
Nicola Waddell *QIMR Berghofer Medical Research Institute, Brisbane, Australia. nic.waddell@qimrberghofer.edu.au.
John V Pearson *QIMR Berghofer Medical Research Institute, Brisbane, Australia.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundLung cancer is a heterogeneous disease and the primary cause of cancer-related mortality worldwide. Somatic mutations, including large structural variants, are important biomarkers in lung cancer for selecting targeted therapy. Genomic studies in lung cancer have been conducted using short-read sequencing. Emerging long-read sequencing technologies are a promising alternative to study somatic structural variants, however there is no current consensus on how to process data and call somatic events. In this study, we preformed whole genome sequencing of lung cancer and matched non-tumour samples using long and short read sequencing to comprehensively benchmark three sequence aligners and seven structural variant callers comprised of generic callers (SVIM, Sniffles2, DELLY in generic mode and cuteSV) and somatic callers (Severus, SAVANA, nanomonsv and DELLY in somatic modes).

resultsDifferent combinations of aligners and variant callers influenced somatic structural variant detection. The choice of caller had a significant influence on somatic structural variant detection in terms of variant type, size, sensitivity, and accuracy. The performance of each variant caller was assessed by comparing to somatic structural variants identified by short-read sequencing. When compared to somatic structural variants detected with short-read sequencing, more events were detected with long-read sequencing. The mean recall of somatic variant events identified by long-read sequencing was higher for the somatic callers (72%) than generic callers (53%). Among the somatic callers when using the minimap2 aligner, SAVANA and Severus achieved the highest recall at 79.5% and 79.25% respectively, followed by nanomonsv with a recall of 72.5%.

conclusionLong-read sequencing can identify somatic structural variants in clincal samples. The longer reads have the potential to improve our understanding of cancer development and inform personalized cancer treatment.

Indexed as

Lung NeoplasmsNanopore SequencingHigh-Throughput Nucleotide SequencingHumansMutationWhole Genome SequencingBenchmarking long read approachesLong read sequencingSmall cell lung cancerSomatic structural variants detection

Identifiers

PMID39350042
PMCPMC11441263

What Socratic holds

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LicenceCC BY-NC-ND
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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 Socratic graph.