Evidence map›Paper›PMID 24823667›Full record

ArticleGenome research2014

Somatic retrotransposition in human cancer revealed by whole-genome and exome sequencing.

Elena Helman, Michael S Lawrence, Chip Stewart, Carrie Sougnez, Gad Getz, Matthew Meyerson

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

Article in Genome research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 160 papers.

0numbers the graph read from it
0cells of the map it votes in
160citing 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

160 citing papers in PubMed, 247 citations in OpenAlex.

  1. Review
  2. Review
  3. Article
  4. Review
  5. LINE-1 retrotransposition is a recurrent cause ofbioRxiv : the preprint server for biology · 2026
    Article
  6. Article
  7. Review
  8. Review
  9. Revisiting Clonal Evolution Through the Light of Retrotransposons.BioEssays : news and reviews in molecular, cellular and developmental biology · 2025
    Review
  10. Article
  11. Review
  12. Article
  13. Review
  14. Article
  15. Enhancer activation from transposable elements in extrachromosomal DNA.bioRxiv : the preprint server for biology · 2025
    Article
  16. Article
  17. Review
  18. Review
  19. Article
  20. Review

100 more citing papers are in PubMed but not listed here.

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

6 authors at 1 institution in 1 country.

Elena HelmanHarvard-MIT Division of Health Sciences & Technology, Cambridge, Massachusetts 02139, USA; Broad Institute of MIT and Harvard, Cambridge, Masachusetts 02142, USA;
Michael S LawrenceBroad Institute of MIT and Harvard, Cambridge, Masachusetts 02142, USA;
Chip StewartBroad Institute of MIT and Harvard, Cambridge, Masachusetts 02142, USA;
Carrie SougnezBroad Institute of MIT and Harvard, Cambridge, Masachusetts 02142, USA;
Gad GetzBroad Institute of MIT and Harvard, Cambridge, Masachusetts 02142, USA; Massachusetts General Hospital, Boston, Massachusetts 02114, USA;
Matthew MeyersonHarvard-MIT Division of Health Sciences & Technology, Cambridge, Massachusetts 02139, USA; Broad Institute of MIT and Harvard, Cambridge, Masachusetts 02142, USA; Center for Cancer Genome Discovery and Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA; Department of Pathology, Brigham & Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA.
Broad Institute · US

Funding

Genome Characterization Center (GCC)U24CA143867 · NCI · BROAD INSTITUTE, INC. · PI GABRIEL, STACEY, MEYERSON, MATTHEW L. · 2009 to 2016
$17.0M
Center for Cancer Genome CharacterizationU24CA126546 · NCI · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI MEYERSON, MATTHEW L. · 2006 to 2009
$7.7M
NCI NIH HHS U24 CA126546NCI NIH HHS U24CA126546NCI NIH HHS U24 CA143867NCI NIH HHS U24CA143867
6 · The paper itself

Abstract

Retrotransposons constitute a major source of genetic variation, and somatic retrotransposon insertions have been reported in cancer. Here, we applied TranspoSeq, a computational framework that identifies retrotransposon insertions from sequencing data, to whole genomes from 200 tumor/normal pairs across 11 tumor types as part of The Cancer Genome Atlas (TCGA) Pan-Cancer Project. In addition to novel germline polymorphisms, we find 810 somatic retrotransposon insertions primarily in lung squamous, head and neck, colorectal, and endometrial carcinomas. Many somatic retrotransposon insertions occur in known cancer genes. We find that high somatic retrotransposition rates in tumors are associated with high rates of genomic rearrangement and somatic mutation. Finally, we developed TranspoSeq-Exome to interrogate an additional 767 tumor samples with hybrid-capture exome data and discovered 35 novel somatic retrotransposon insertions into exonic regions, including an insertion into an exon of the PTEN tumor suppressor gene. The results of this large-scale, comprehensive analysis of retrotransposon movement across tumor types suggest that somatic retrotransposon insertions may represent an important class of structural variation in cancer.

Indexed as

ExomeGenome, HumanBase SequenceComputational BiologyDatabases, Nucleic AcidDNA Transposable ElementsHigh-Throughput Nucleotide SequencingHumansMutagenesis, InsertionalNeoplasmsRetroelementsSequence Analysis, DNADNA Transposable ElementsRetroelements

Identifiers

PMID24823667
PMCPMC4079962
OpenAlexW2115520939

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC
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.