Evidence map›Paper›PMID 36169416›Full record

ArticleBiopreservation and biobanking2023

Formalin Fixation, Delay to Fixation, and Time in Fixative Adversely Impact Copy Number Variation Analysis by aCGH.

James Li, Sarah R Greytak, Ping Guan, Kelly B Engel, David S Goerlitz, Md Islam, Rency S Varghese, Helen M Moore, Habtom W Ressom

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

Article in Biopreservation and biobanking, 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
0.2field-weighted citation impact, top 54% 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, 2 citations in OpenAlex.

  1. Article
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

9 authors at 4 institutions in 3 countries.

James LiDepartment of Biostatistics, Bioinformatics, and Biomathematics, Georgetown University, Washington, District of Columbia, USA.
Sarah R GreytakKelly Government Solutions, Rockville, Maryland, USA.ORCID 0000-0002-2823-7136
Ping GuanBiorepositories & Biospecimen Research Branch, National Cancer Institute, Bethesda, Maryland, USA.
Kelly B EngelPreferred Staffing Group, Arlington, Virginia, USA.
David S GoerlitzDepartment of Biostatistics, Bioinformatics, and Biomathematics, Georgetown University, Washington, District of Columbia, USA.
Md IslamDepartment of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia, USA.
Rency S VargheseDepartment of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia, USA.
Helen M MooreBiorepositories & Biospecimen Research Branch, National Cancer Institute, Bethesda, Maryland, USA.
Habtom W RessomDepartment of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia, USA.
Georgetown University · USSpecim (Finland) · FIKelly Services (United States) · USPreferred Networks (Japan) · JP

Funding

Systems Metabolomics for Biomarker DiscoveryR35GM141944 · NIGMS · GEORGETOWN UNIVERSITY · PI RESSOM, HABTOM W · 2021 to 2025
$2.4M
NIGMS NIH HHS R35 GM141944
6 · The paper itself

Abstract

Although molecular profiling of DNA isolated from formalin-fixed, paraffin-embedded (FFPE) tumor specimens has become more common in recent years, it remains unclear how discrete FFPE processing variables may affect detection of copy number variation (CNV). To better understand such effects, array comparative genomic hybridization (aCGH) profiles of FFPE renal cell carcinoma specimens that experienced different delays to fixation (DTFs; 1, 2, 3, and 12 hours) and times in fixative (TIFs; 6, 12, 23, and 72 hours) were compared to snap-frozen tumor and blood specimens from the same patients. A greater number of regions containing CNVs relative to commercial reference DNA were detected in DNA from FFPE tumor specimens than snap-frozen tumor specimens even though they originated from the same tumor blocks. Extended DTF and TIF affected the number of DNA segments with a copy number status that differed between FFPE and frozen tumor specimens; a DTF ≥3 hours led to more segments, while a TIF of 72 hours led to fewer segments. Importantly, effects were not random as a higher guanine-cytosine (GC) content and/or a higher percentage of repeats were observed among stable regions. While limiting aCGH analysis to FFPE specimens with a DTF <3 hours and a TIF <72 hours may circumvent some effects, results from FFPE specimens should be validated against fresh or frozen specimens whenever possible.

Indexed as

DNA Copy Number VariationsFormaldehydeComparative Genomic HybridizationDNAFixativesHumansParaffin EmbeddingTissue FixationDNAFixativesFormaldehydearray comparative genomic hybridizationcopy number variationdelay to fixationformalinpre-analytic variablestime in fixative

Identifiers

PMID36169416
PMCPMC10460690
OpenAlexW4297461543

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.