Evidence map›Paper›PMID 42774951›Full record

ArticleAcademic pathology

Landscape of approaches for streamlining pre-analytical and early analytical variables for solid tumor next-generation sequencing: A Genomics Organization for Academic Laboratories consortium report.

Marjorie P David, Jennifer J D Morrissette, Noah Brown, Georgios Deftereos, Fei Dong, Karin E Finberg, Yulong Fu, Jeffrey Gagan, Christopher D Gocke, Audrey N Jajosky and 17 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Academic pathology. 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

27 authors.

Marjorie P DavidDepartment of Pathology and Laboratory Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.
Jennifer J D MorrissetteDivision of Precision and Computational Diagnostics, Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
Noah BrownDepartment of Pathology, University of Michigan, Ann Arbor, MI, USA.
Georgios DeftereosDepartment of Pathology, University of California at San Francisco, San Francisco, CA, USA.
Fei DongDepartment of Pathology, Brigham and Women's Hospital, Boston, MA, USA.
Karin E FinbergDepartment of Pathology, Yale School of Medicine, New Haven, CT, USA.
Yulong FuDepartment of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA.
Jeffrey GaganLaboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
Christopher D GockeDepartment of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
Audrey N JajoskyDepartment of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY, USA.
Eric KonnickDepartment of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.
Thomas D LeeDepartment of Pathology and Laboratory Medicine, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, CA, USA.
David B LiebermanDivision of Precision and Computational Diagnostics, Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
Deqin MaDepartment of Pathology, University of Iowa, Iowa City, IA, USA.
Laura MacConaillDepartment of Pathology, Brigham and Women's Hospital, Boston, MA, USA.
Christopher MignognaDivision of Precision and Computational Diagnostics, Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
Andrew C NelsonDepartment of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA.
Erik NohrDepartment of Pathology and Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada.
Megan ParillaDepartment of Pathology, NorthShore Hospital, Evanston, IL, USA.
Adam D PfefferleDepartment of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, USA.
Somak RoyDepartment of Pathology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
Pamela SnyderThe Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.
Eric VailDepartment of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
Peng WangDepartment of Pathology, University of Chicago, Chicago, IL, USA.
Liqiang XiLaboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.
Daniel JonesThe Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.
Dara L AisnerDepartment of Pathology, University of Colorado, Denver, CO, USA.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

The scope of pre-analytical and early analytical methods used in clinical molecular laboratories can have vast effects on the quality and turnaround time for solid tumor next-generation sequencing assays. To learn more about various approaches, a survey of 24 academic laboratories within the Genomics Organization for Academic Laboratories consortium was administered, focusing on pre-analytical and early analytical issues in next-generation sequencing clinical assays that may affect patient care. The survey revealed the landscape of clinical laboratory practices for use of cytopathology smears, block selection, histology practices and protocols, sample transport, slide imaging, sample adequacy assessment, tumor cell enrichment, and deparaffinization methods. Most laboratories reported that they either accepted cytopathology smears for next-generation sequencing testing or had a plan to accept them soon. All laboratories surveyed performed micro- or macro-dissection on unstained formalin-fixed, paraffin-embedded slides for tumor cell enrichment. Several laboratories reported sectioning blocks within the molecular laboratory. While most respondents used an organic solvent for deparaffinization, several laboratories used mineral oil as an alternative. The approaches of other laboratories reported here are expected to be an impactful resource to address pre-analytical issues that may improve assay quality and turnaround time.

Indexed as

Academic laboratoryClinical laboratoryMolecular pathologyNext-generation sequencingPre-analyticalSolid tumor

Identifiers

PMID42774951
PMCPMC13594886

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.