Evidence map›Paper›PMID 29427260›Full record

ArticleCancer causes & control : CCC2018

Feasibility of analyzing DNA copy number variation in breast cancer tumor specimens from 1950 to 2010: how old is too old?

Nancy Krieger, Sheida Nabavi, Pamela D Waterman, Ninah S Achacoso, Luana Acton, Stuart J Schnitt, Laurel A Habel

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

Article in Cancer causes & control : CCC, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
0.5field-weighted citation impact, top 28% 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

2 citing papers in PubMed, 4 citations in OpenAlex.

  1. Article
  2. 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

7 authors at 4 institutions in 1 country.

Nancy KriegerDept of Social and Behavioral Sciences, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Kresge 717, Boston, MA, 02130, USA. nkrieger@hsph.harvard.edu.ORCID http://orcid.org/0000-0002-4815-5947
Sheida NabaviDept of Computer Science and Engineering, University of Connecticut, 371 Fairfield Way, Storrs, CT, 06269, USA.
Pamela D WatermanDept of Social and Behavioral Sciences, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA, 02130, USA.
Ninah S AchacosoDivision of Research, Kaiser Permanente Northern California, 2000 Broadway, Oakland, CA, 94612, USA.
Luana ActonDivision of Research, Kaiser Permanente Northern California, 2000 Broadway, Oakland, CA, 94612, USA.
Stuart J SchnittDana-Farber Cancer Institute/Brigham and Women's Hospital Breast Oncology Program, Department of Pathology, Brigham and Women's Hospital, 75 Francis Street, Boston, MA, 02115, USA.
Laurel A HabelDivision of Research, Kaiser Permanente Northern California, 2000 Broadway, Oakland, CA, 94612, USA.
Kaiser Permanente · USHarvard University · USBrigham and Women's Hospital · USUniversity of Connecticut · US

Funding

Snap-To-It ProbesR44CA094612 · NCI · SYNTRIX BIOSYSTEMS, INC. · PI MORGAN, JOEL R, ZEBALA, JOHN A · 2007 to 2009
$1.4M
Snap-To-It PNA ArraysR43CA094612 · NCI · SYNTRIX BIOSYSTEMS, INC. · PI ZEBALA, JOHN A · 2002 to 2003
$284k
Long-term trends in breast cancer DNA copy number alterations & disparitiesR03CA193078 · NCI · HARVARD SCHOOL OF PUBLIC HEALTH · PI KRIEGER, NANCY · 2016 to 2017
$171k
NCI NIH HHS R03 CA193078NCI NIH HHS R43 CA094612NCI NIH HHS R44 CA094612
6 · The paper itself

Abstract

purposeThe purpose of the study was to assess the feasibility of quantifying long-term trends in breast tumor DNA copy number variation (CNV) profiles.

methodsWe evaluated CNV profiles in formalin-fixed paraffin-embedded (FFPE) tumor specimens from 30 randomly selected Kaiser Permanente Northern California health plan women members diagnosed with breast cancer from 1950 to 2010. Assays were conducted for five cases per decade who had available tumor blocks and pathology reports.

resultsAs compared to the tumors from the 1970s to 2000s, the older tumors dating back to the 1950s and 1960s were much more likely to (1) fail quality control, and (2) have fewer CNV events (average 23 and 31 vs. 58 to 69), fewer CNV genes (average 5.1 and 3.7k vs. 8.1 to 10.3k), shorter CNV length (average 2,440 and 3,300k vs. 5,740 to 9,280k), fewer high frequency Del genes (37 and 25% vs. 54 to 76%), and fewer high frequency high_Amp genes (20% vs. 56 to 73%). On average, assay interpretation took an extra 60 min/specimen for cases from the 1960s versus 20 min/specimen for the most recent tumors.

conclusionsAssays conducted in the mid-2010s for CNVs may be feasible for FFPE tumor specimens dating back to the 1980s, but less feasible for older specimens.

Indexed as

DNADNA Copy Number VariationsSpecimen HandlingBreast NeoplasmsFemaleFormaldehydeHumansParaffin EmbeddingTime FactorsTissue FixationDNAFormaldehydeArchival specimenBiomarkerBreast cancerDNA copy number variationEpidemiologyHistorical trend

Identifiers

PMID29427260
PMCPMC5835216
OpenAlexW2791843514

What OpenQuestion holds

Textmetadata
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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.