Evidence map›Paper›PMID 27807467›Full record

ArticleMobile DNA2016

A map of mobile DNA insertions in the NCI-60 human cancer cell panel.

John G Zampella, Nemanja Rodić, Wan Rou Yang, Cheng Ran Lisa Huang, Jane Welch, Veena P Gnanakkan, Toby C Cornish, Jef D Boeke, Kathleen H Burns

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

Article in Mobile DNA, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
0.3field-weighted citation impact, top 37% 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

3 citing papers in PubMed, 5 citations in OpenAlex.

  1. Article
  2. Article
  3. 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

9 authors at 3 institutions in 1 country.

John G ZampellaDepartment of Dermatology, Johns Hopkins University School of Medicine, 733 North Broadway, Miller Research Building Room 469, Baltimore, MD 21205 USA.
Nemanja RodićDepartment of Pathology, Johns Hopkins University School of Medicine, 733 North Broadway, Miller Research Building Room 469, Baltimore, MD 21205 USA.
Wan Rou YangDepartment of Pathology, Johns Hopkins University School of Medicine, 733 North Broadway, Miller Research Building Room 469, Baltimore, MD 21205 USA.
Cheng Ran Lisa HuangMcKusick-Nathans Institute of Genetic Medicine, 733 North Broadway, Miller Research Building Room 469, Baltimore, MD 21205 USA.
Jane WelchMcKusick-Nathans Institute of Genetic Medicine, 733 North Broadway, Miller Research Building Room 469, Baltimore, MD 21205 USA.
Veena P GnanakkanMcKusick-Nathans Institute of Genetic Medicine, 733 North Broadway, Miller Research Building Room 469, Baltimore, MD 21205 USA.
Toby C CornishDepartment of Pathology, Johns Hopkins University School of Medicine, 733 North Broadway, Miller Research Building Room 469, Baltimore, MD 21205 USA.
Jef D BoekeMcKusick-Nathans Institute of Genetic Medicine, 733 North Broadway, Miller Research Building Room 469, Baltimore, MD 21205 USA ; High Throughput (HiT) Biology Center, 733 North Broadway, Miller Research Building Room 469, Baltimore, MD 21205 USA ; Present address: Institute for Systems Genetics, NYU Langone University School of Medicine, New York, NY 10016 USA.
Kathleen H BurnsDepartment of Pathology, Johns Hopkins University School of Medicine, 733 North Broadway, Miller Research Building Room 469, Baltimore, MD 21205 USA ; McKusick-Nathans Institute of Genetic Medicine, 733 North Broadway, Miller Research Building Room 469, Baltimore, MD 21205 USA ; High Throughput (HiT) Biology Center, 733 North Broadway, Miller Research Building Room 469, Baltimore, MD 21205 USA ; The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, 733 North Broadway, Miller Research Building Room 469, Baltimore, MD 21205 USA.
Johns Hopkins Medicine · USJohns Hopkins University · USHigh Throughput Biology (United States) · US

Funding

Vaccine FacilityP30CA016087 · NCI · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · PI ADRIANA HEGUY · 1985 to 2026
$83.1M
Tumor Antigens for Individual Signatures and TherapyP50CA062924 · NCI · JOHNS HOPKINS UNIVERSITY · PI LENNON, ANNE MARIE · 1993 to 2022
$54.6M
Somatic Activation of Retrotransposition: A New Molecular Mechanism of Aging?P01AG051449 · NIA · BROWN UNIVERSITY · PI Jef D BOEKE · 2016 to 2026
$30.4M
Predoctoral Training Program in Human GeneticsT32GM007814 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI VALLE, DAVID · 1985 to 2021
$10.6M
Training CoreP50GM107632 · NIGMS · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · PI BOEKE, JEF D · 2013 to 2017
$10.0M
Transposon Insertion Polymorphisms in Predispositions to Hematopoietic NeoplasiaR01CA163705 · NCI · JOHNS HOPKINS UNIVERSITY · PI BURNS, KATHLEEN H · 2013 to 2017
$1.7M
Mouse Models of Functional Insertion PolymorphismsR01GM103999 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI BURNS, KATHLEEN H · 2013 to 2016
$1.2M
NCI NIH HHS P30 CA016087NCI NIH HHS P50 CA062924NCI NIH HHS R01 CA163705NIA NIH HHS P01 AG051449NIGMS NIH HHS P50 GM107632NIGMS NIH HHS R01 GM103999NIGMS NIH HHS T32 GM007814
6 · The paper itself

Abstract

backgroundThe National Cancer Institute-60 (NCI-60) cell lines are among the most widely used models of human cancer. They provide a platform to integrate DNA sequence information, epigenetic data, RNA and protein expression, and pharmacologic susceptibilities in studies of cancer cell biology. Genome-wide studies of the complete panel have included exome sequencing, karyotyping, and copy number analyses but have not targeted repetitive sequences. Interspersed repeats derived from mobile DNAs are a significant source of heritable genetic variation, and insertions of active elements can occur somatically in malignancy.

methodWe used Transposon Insertion Profiling by microarray (TIP-chip) to map Long INterspersed Element-1 (LINE-1, L1) and

resultsWe catalogued a total of 749 and 2,100 loci corresponding to candidate LINE-1 and

conclusionsThese data provide a resource for investigators with interests in specific cancer gene loci or mobile element insertion effects more broadly. Our data underscore that significant genetic variation in cancer genomes is owed to LINE-1 and

Identifiers

PMID27807467
PMCPMC5087121
OpenAlexW2541492538

What OpenQuestion holds

Textmetadata
LicenceCC BY
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.