Evidence map›Paper›PMID 27745836›Full record

ArticleAmerican journal of human genetics2016

Comprehensive Genetic Landscape of Uveal Melanoma by Whole-Genome Sequencing.

Beryl Royer-Bertrand, Matteo Torsello, Donata Rimoldi, Ikram El Zaoui, Katarina Cisarova, Rosanna Pescini-Gobert, Franck Raynaud, Leonidas Zografos, Ann Schalenbourg, Daniel Speiser and 8 more

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

Article in American journal of human genetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 89 papers, 2 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
89citing papers in PubMed, 2 pooled it
17.9field-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

89 citing papers in PubMed, 2 syntheses or guidelines pooled it, 175 citations in OpenAlex.

  1. Pooled it
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29 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

18 authors at 5 institutions in 2 countries.

Beryl Royer-BertrandDepartment of Computational Biology, Unit of Medical Genetics, University of Lausanne, 1011 Lausanne Switzerland; Center for Molecular Diseases, Lausanne University Hospital, 1011 Lausanne, Switzerland.
Matteo TorselloExperimental Pathology, Institute of Pathology, Lausanne University Hospital, 1011 Lausanne, Switzerland.
Donata RimoldiLudwig Cancer Research, Department of Oncology, University of Lausanne, 1066 Epalinges, Switzerland.
Ikram El ZaouiDepartment of Computational Biology, Unit of Medical Genetics, University of Lausanne, 1011 Lausanne Switzerland.
Katarina CisarovaDepartment of Computational Biology, Unit of Medical Genetics, University of Lausanne, 1011 Lausanne Switzerland.
Rosanna Pescini-GobertDepartment of Computational Biology, Unit of Medical Genetics, University of Lausanne, 1011 Lausanne Switzerland.
Franck RaynaudDepartment of Computational Biology, Computational Systems Oncology, University of Lausanne, 1011 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
Leonidas ZografosJules-Gonin Eye Hospital, Department of Ophthalmology, Fondation Asile des Aveugles, University of Lausanne, 1004 Lausanne, Switzerland.
Ann SchalenbourgJules-Gonin Eye Hospital, Department of Ophthalmology, Fondation Asile des Aveugles, University of Lausanne, 1004 Lausanne, Switzerland.
Daniel SpeiserLudwig Cancer Research, Department of Oncology, University of Lausanne, 1066 Epalinges, Switzerland.
Michael NicolasJules-Gonin Eye Hospital, Department of Ophthalmology, Fondation Asile des Aveugles, University of Lausanne, 1004 Lausanne, Switzerland.
Laureen VallatJules-Gonin Eye Hospital, Department of Ophthalmology, Fondation Asile des Aveugles, University of Lausanne, 1004 Lausanne, Switzerland.
Robert KleinFormerly Complete Genomics, Mountain View, CA 94043, USA.
Serge LeyvrazDepartment of Oncology, Lausanne University Hospital, 1011 Lausanne, Switzerland.
Giovanni CirielloDepartment of Computational Biology, Computational Systems Oncology, University of Lausanne, 1011 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
Nicolò RiggiExperimental Pathology, Institute of Pathology, Lausanne University Hospital, 1011 Lausanne, Switzerland.
Alexandre P MoulinJules-Gonin Eye Hospital, Department of Ophthalmology, Fondation Asile des Aveugles, University of Lausanne, 1004 Lausanne, Switzerland.
Carlo RivoltaDepartment of Computational Biology, Unit of Medical Genetics, University of Lausanne, 1011 Lausanne Switzerland. Electronic address: carlo.rivolta@unil.ch.
University of Lausanne · CHFondation Asile des Aveugles · CHComplete Genomics (United States) · USLudwig Cancer Research · CHSIB Swiss Institute of Bioinformatics · CH

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Uveal melanoma (UM) is a rare intraocular tumor that, similar to cutaneous melanoma, originates from melanocytes. To gain insights into its genetics, we performed whole-genome sequencing at very deep coverage of tumor-control pairs in 33 samples (24 primary and 9 metastases). Genome-wide, the number of coding mutations was rather low (only 17 variants per tumor on average; range 7-28), thus radically different from cutaneous melanoma, where hundreds of exonic DNA insults are usually detected. Furthermore, no UV light-induced mutational signature was identified. Recurrent coding mutations were found in the known UM drivers GNAQ, GNA11, BAP1, EIF1AX, and SF3B1. Other genes, i.e., TP53BP1, CSMD1, TTC28, DLK2, and KTN1, were also found to harbor somatic mutations in more than one individual, possibly indicating a previously undescribed association with UM pathogenesis. De novo assembly of unmatched reads from non-coding DNA revealed peculiar copy-number variations defining specific UM subtypes, which in turn could be associated with metastatic transformation. Mutational-driven comparison with other tumor types showed that UM is very similar to pediatric tumors, characterized by very few somatic insults and, possibly, important epigenetic changes. Through the analysis of whole-genome sequencing data, our findings shed new light on the molecular genetics of uveal melanoma, delineating it as an atypical tumor of the adult for which somatic events other than mutations in exonic DNA shape its genetic landscape and define its metastatic potential.

Indexed as

Genome-Wide Association StudyAdultAgedAged, 80 and overCase-Control StudiesCutaneous Malignant MelanomaDNA Copy Number VariationsEukaryotic Initiation Factor-1ExonsFemaleGTP-Binding Protein alpha SubunitsGTP-Binding Protein alpha Subunits, Gq-G11HumansMaleMelanocytesMelanomaBAP1 protein, humanCSMD1 protein, humanEukaryotic Initiation Factor-1eukaryotic peptide initiation factor-1AGNA11 protein, humanGNAQ protein, humanGTP-Binding Protein alpha SubunitsGTP-Binding Protein alpha Subunits, Gq-G11KTN1 protein, humanMembrane ProteinsPhosphoproteinsRNA Splicing FactorsSF3B1 protein, humanTP53BP1 protein, humanTTC3 protein, humanTumor Suppressor p53-Binding Protein 1Tumor Suppressor ProteinsUbiquitin-Protein LigasesUbiquitin Thiolesterase

Identifiers

PMID27745836
PMCPMC5097942
OpenAlexW2530190674

What OpenQuestion holds

Textmetadata
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.