Evidence map›Paper›PMID 24448499›Full record

ArticleNature communications2014

Integrated analysis of germline and somatic variants in ovarian cancer.

Krishna L Kanchi, Kimberly J Johnson, Charles Lu, Michael D McLellan, Mark D M Leiserson, Michael C Wendl, Qunyuan Zhang, Daniel C Koboldt, Mingchao Xie, Cyriac Kandoth and 14 more

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

Article in Nature communications, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 189 papers, 3 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
189citing papers in PubMed, 3 pooled it
10.1field-weighted citation impact, top 1% 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

189 citing papers in PubMed, 3 syntheses or guidelines pooled it, 298 citations in OpenAlex.

  1. A Systematic Literature Review of Whole Exome and Genome Sequencing Population Studies of Genetic Susceptibility to Cancer.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2020
    Pooled it
  2. Germline and Somatic Tumor Testing in Epithelial Ovarian Cancer: ASCO Guideline.Journal of clinical oncology : official journal of the American Society of Clinical Oncology · 2020
    Pooled it
  3. Pooled it
  4. Article
  5. Breast cancer prevention in patients with gBRCA-mutated ovarian cancer.Journal of cancer research and clinical oncology · 2026
    Article
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  8. Tissue-Specific Prevalence and Clonal Architecture ofbioRxiv : the preprint server for biology · 2026
    Article
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  10. Article
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  12. Functional Profiling ofCirculation. Genomic and precision medicine · 2025
    Article
  13. Homologous Recombination Deficiency and Survival in Ovarian High-Grade Serous Carcinoma by Self-Reported Race.Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology · 2025
    Article
  14. Article
  15. Review
  16. Review
  17. Article
  18. Article
  19. Review
  20. Genomics of ovarian cancers and the potential of precision medicine.Therapeutic advances in medical oncology · 2025
    Review

129 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

24 authors at 4 institutions in 1 country.

Krishna L Kanchi1] The Genome Institute, Washington University, St. Louis, Missouri 63108, USA [2].
Kimberly J Johnson1] The Genome Institute, Washington University, St. Louis, Missouri 63108, USA [2] Brown School, Washington University, St. Louis, Missouri 63130, USA [3] Oregon Health and Science University, Portland, Oregon 97239, USA [4].
Charles Lu1] The Genome Institute, Washington University, St. Louis, Missouri 63108, USA [2].
Michael D McLellanThe Genome Institute, Washington University, St. Louis, Missouri 63108, USA.
Mark D M LeisersonDepartment of Computer Science, Brown University, Providence, Rhode Island 02912, USA.
Michael C Wendl1] The Genome Institute, Washington University, St. Louis, Missouri 63108, USA [2] Department of Genetics, Washington University, St. Louis, Missouri 63108, USA [3] Department of Mathematics, Washington University, St. Louis, Missouri 63108, USA.
Qunyuan Zhang1] The Genome Institute, Washington University, St. Louis, Missouri 63108, USA [2] Department of Genetics, Washington University, St. Louis, Missouri 63108, USA.
Daniel C KoboldtThe Genome Institute, Washington University, St. Louis, Missouri 63108, USA.
Mingchao XieThe Genome Institute, Washington University, St. Louis, Missouri 63108, USA.
Cyriac KandothThe Genome Institute, Washington University, St. Louis, Missouri 63108, USA.
Joshua F McMichaelThe Genome Institute, Washington University, St. Louis, Missouri 63108, USA.
Matthew A WyczalkowskiThe Genome Institute, Washington University, St. Louis, Missouri 63108, USA.
David E Larson1] The Genome Institute, Washington University, St. Louis, Missouri 63108, USA [2] Department of Genetics, Washington University, St. Louis, Missouri 63108, USA.
Heather K SchmidtThe Genome Institute, Washington University, St. Louis, Missouri 63108, USA.
Christopher A MillerThe Genome Institute, Washington University, St. Louis, Missouri 63108, USA.
Robert S Fulton1] The Genome Institute, Washington University, St. Louis, Missouri 63108, USA [2] Department of Genetics, Washington University, St. Louis, Missouri 63108, USA.
Paul T SpellmanOregon Health and Science University, Portland, Oregon 97239, USA.
Elaine R Mardis1] The Genome Institute, Washington University, St. Louis, Missouri 63108, USA [2] Department of Genetics, Washington University, St. Louis, Missouri 63108, USA [3] Siteman Cancer Center, Washington University, St. Louis, Missouri 63108, USA.
Todd E Druley1] Department of Genetics, Washington University, St. Louis, Missouri 63108, USA [2] Department of Pediatrics, Washington University, St. Louis, Missouri 63108, USA.
Timothy A Graubert1] Siteman Cancer Center, Washington University, St. Louis, Missouri 63108, USA [2] Department of Medicine, Washington University, St. Louis, Missouri 63108, USA.
Paul J GoodfellowThe Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA.
Benjamin J RaphaelDepartment of Computer Science, Brown University, Providence, Rhode Island 02912, USA.
Richard K Wilson1] The Genome Institute, Washington University, St. Louis, Missouri 63108, USA [2] Department of Genetics, Washington University, St. Louis, Missouri 63108, USA [3] Siteman Cancer Center, Washington University, St. Louis, Missouri 63108, USA.
Li Ding1] The Genome Institute, Washington University, St. Louis, Missouri 63108, USA [2] Department of Genetics, Washington University, St. Louis, Missouri 63108, USA [3] Siteman Cancer Center, Washington University, St. Louis, Missouri 63108, USA [4] Department of Medicine, Washington University, St. Louis, Missouri 63108, USA.
Washington University in St. Louis · USBrown University · USOregon Health & Science University · USThe Ohio State University · US

Funding

Large Scale Genome SequencingU54HG003079 · NHGRI · WASHINGTON UNIVERSITY · PI DUTCHER, SUSAN K · 2004 to 2016
$445.7M
A Turnkey System for High-throughput Variant Discovery and InterpretationU01HG006517 · NHGRI · WASHINGTON UNIVERSITY · PI DING, LI · 2012 to 2015
$3.0M
Computational Approaches for Structural Variation Studies in GenomesR01HG005690 · NHGRI · BROWN UNIVERSITY · PI RAPHAEL, BENJAMIN · 2011 to 2015
$2.4M
CANCER SUSCEPTIBILITY VARIANT DISCOVERY IN HIGH THROUGHPUT SEQUENCING DATAR01CA180006 · NCI · WASHINGTON UNIVERSITY · PI DING, LI · 2013 to 2016
$1.1M
NCI NIH HHS R01 CA180006NCI NIH HHS R01CA180006NHGRI NIH HHS R01 HG005690NHGRI NIH HHS R01HG005690NHGRI NIH HHS U01 HG006517NHGRI NIH HHS U54 HG003079NHGRI NIH HHS U54HG003079
6 · The paper itself

Abstract

We report the first large-scale exome-wide analysis of the combined germline-somatic landscape in ovarian cancer. Here we analyse germline and somatic alterations in 429 ovarian carcinoma cases and 557 controls. We identify 3,635 high confidence, rare truncation and 22,953 missense variants with predicted functional impact. We find germline truncation variants and large deletions across Fanconi pathway genes in 20% of cases. Enrichment of rare truncations is shown in BRCA1, BRCA2 and PALB2. In addition, we observe germline truncation variants in genes not previously associated with ovarian cancer susceptibility (NF1, MAP3K4, CDKN2B and MLL3). Evidence for loss of heterozygosity was found in 100 and 76% of cases with germline BRCA1 and BRCA2 truncations, respectively. Germline-somatic interaction analysis combined with extensive bioinformatics annotation identifies 222 candidate functional germline truncation and missense variants, including two pathogenic BRCA1 and 1 TP53 deleterious variants. Finally, integrated analyses of germline and somatic variants identify significantly altered pathways, including the Fanconi, MAPK and MLL pathways.

Indexed as

Germ CellsAgedFemaleHumansLoss of HeterozygosityMiddle AgedOncogenesOvarian Neoplasms

Identifiers

PMID24448499
PMCPMC4025965
OpenAlexW2126633009

What OpenQuestion holds

Textmetadata
LicenceTDM
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.