Evidence map›Paper›PMID 37712171›Full record

ArticleCytopathology : official journal of the British Society for Clinical Cytology2023

Pre-analytical effects on whole transcriptome and targeted RNA sequencing analysis in cytology: The effects of prolonged time in storage of effusion specimens prior to preservation.

Gloria H Sura, Kevin Tran, Chunxiao Fu, Lili Du, Michał Marczyk, Rebekah E Gould, Eveline Chen, Amy M Tasto, Agata A Tinnirello, W Fraser Symmans

Open access · bronzeAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cytopathology : official journal of the British Society for Clinical Cytology, 2023. 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
0.8field-weighted citation impact, top 27% of its field
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, 5 citations in OpenAlex.

  1. Review
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 at 3 institutions in 2 countries.

Gloria H SuraDepartment of Pathology and Genomic Medicine, Houston Methodist, Houston, Texas, USA.ORCID 0000-0003-4817-458X
Kevin TranDepartment of Pathology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
Chunxiao FuDepartment of Pathology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
Lili DuDepartment of Pathology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
Michał MarczykDepartment of Data Science and Engineering, Silesian University of Technology, Gliwice, Poland.ORCID 0000-0003-2508-5736
Rebekah E GouldDepartment of Pathology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
Eveline ChenDepartment of Pathology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
Amy M TastoDepartment of Pathology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
Agata A TinnirelloDepartment of Pathology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.ORCID 0000-0002-2172-7263
W Fraser SymmansDepartment of Pathology and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
The University of Texas MD Anderson Cancer Center · USHouston Methodist · USSilesian University of Technology · PL

Funding

Integrating Biospecimen Science Into The Development Of RNA-Based Clinical Assays For Patients With Metastatic Breast CancerU01CA215547 · NCI · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI SYMMANS, WILLIAM F · 2017 to 2021
$1.6M
NCI NIH HHSNCI NIH HHS U01 CA215547
6 · The paper itself

Abstract

objectivesTo investigate the pre-analytics of the molecular testing of cytology specimens, we studied the effects of time in refrigerator storage (4°C) of malignant effusions on RNA sequencing (RNAseq) results.

methodsTen effusion specimens were stored in a refrigerator (4°C) for different durations (day 0, 1, 4, and 7). All specimens were prepared as cytospins fixed in either Carnoy's solution or 95% ethanol (EtOH) and in an RNA preservative for a fresh frozen (FF) high-quality reference. Whole transcriptome (wt) and targeted (t)RNAseq of two multigene expression signatures were performed. We then compared transcript expression levels (including mutant allele fraction) according to pre-analytical variables using a concordance correlation coefficient (CCC) and a mixed effect model.

resultsSequencing results were mostly stable over increasing time in storage. Cytospins fixed in Carnoy's solution were more concordant with FF samples than cytospins fixed in 95% EtOH at all timepoints. This finding was consistent for both wtRNAseq (averages: day 0 CCC = 0.98 vs 0.91; day 7 CCC = 0.88 vs 0.78) and tRNAseq methods (averages: day 0 CCC = 0.98 vs 0.81; day 7 CCC = 0.98 vs 0.90). Cytospins fixed in Carnoy's solution did not show significant changes in expression over timepoints or between expression signatures, whereas 95% EtOH did.

conclusionRNAseq can be accurately performed on effusion specimens after prolonged refrigerator storage. RNA extracted from scraped cytospin slides fixed in Carnoy's solution was marginally superior to 95% EtOH fixation, but either method had comparable analytic performance to high-quality FF RNA samples.

Indexed as

Sequence Analysis, RNASpecimen HandlingTranscriptomeCytodiagnosisHumansPleural Effusion, MalignantPreservation, BiologicalTime Factorscytology processingcytopathologyeffusionfixativeliquidmolecularRNA sequencing

Identifiers

PMID37712171
PMCPMC10592006
OpenAlexW4386757567

What OpenQuestion holds

Textmetadata
LicenceTDM
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.