Evidence map›Paper›PMID 38795236›Full record

ArticleInternational journal of clinical oncology2024

Genomic landscape of comprehensive genomic profiling in patients with malignant solid tumors in Japan.

Tatsuro Yamaguchi, Masachika Ikegami, Tomoyuki Aruga, Yusuke Kanemasa, Shin-Ichiro Horiguchi, Kazushige Kawai, Misato Takao, Takeshi Yamada, Hideyuki Ishida

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Article in International journal of clinical oncology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 10 papers.

0numbers the graph read from it
0cells of the map it votes in
10citing 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

10 citing papers in PubMed.

  1. Observational
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  4. Article
  5. Review
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4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

9 authors.

Tatsuro YamaguchiDepartment of Clinical Genetics, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo, Japan. tatsuro@yamaguchi.email.ne.jp.ORCID http://orcid.org/0000-0001-8454-1995
Masachika IkegamiDepartment of Clinical Genetics, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo, Japan.
Tomoyuki ArugaDepartment of Clinical Genetics, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo, Japan.
Yusuke KanemasaDepartment of Clinical Genetics, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo, Japan.
Shin-Ichiro HoriguchiDepartment of Pathology, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo, Japan.
Kazushige KawaiDepartment of Surgery, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo, Japan.
Misato TakaoDepartment of Surgery, Tokyo Metropolitan Cancer and Infectious Diseases Center Komagome Hospital, Tokyo, Japan.
Takeshi YamadaDepartment of Surgery, Nihon Medical University, Tokyo, Japan.
Hideyuki IshidaDepartment of Digestive Tract and General Surgery, Saitama Medical Center, Saitama Medical University, Kawagoe, Japan.

Funding

Japan Society for the Promotion of Science 18K07314Japan Society for the Promotion of Science 21K07187Japan Society for the Promotion of Science 21K16437
6 · The paper itself

Abstract

backgroundComprehensive genomic profiling (CGP) can aid the discovery of clinically useful, candidate antitumor agents; however, the variant annotations sometimes differ among the various types of CGP tests as well as the public database. The aim of this study is to clarify the genomic landscape of evaluating detected variants in patients with a malignant solid tumor.

methodsThe present, cross-sectional study used data from 57,084 patients with a malignant solid tumor who underwent CGP at the Center for Cancer Genomics and Advanced Therapeutics (C-CAT) between June 1, 2019 and August 18, 2023. The pathogenicity of the variants was annotated using public databases.

resultsAs a result of re-annotation of the detected variants, 20.1% were pathogenic and 1.4% were benign. The mean number of pathogenic variants was 4.30 (95% confidence interval: 4.27-4.32) per patient. Of the entire cohort, 5.7% had no pathogenic variant. The co-occurrence of the genes depended on the tumor type. Germline findings were detected in 6.2%, 8.8%, and 15.8% of the patients using a tumor/normal panel, tumor-only panel, and liquid panel, respectively, with the most common gene being BRCA2 followed by TP53 and BRCA1.

conclusionsThe detected variants should be re-annotated because several benign variants or variants of unknown significance were included in the CGP, and the genomic landscape derived from these results will help researchers and physicians interpret the results of CGP tests. The method of extracting presumptive, germline, pathogenic variants from patients using a tumor-only panel or circulating tumor DNA panel requires improvement.

Indexed as

GenomicsNeoplasmsAdolescentAdultAgedAged, 80 and overBRCA1 ProteinBRCA2 ProteinCross-Sectional StudiesFemaleGerm-Line MutationHumansJapanMaleMiddle AgedTumor Suppressor Protein p53BRCA1 ProteinBRCA1 protein, humanBRCA2 ProteinBRCA2 protein, humanTP53 protein, humanTumor Suppressor Protein p53AnnotationCancer genomicsComprehensive genomic profiling testGermline findingsMalignant solid tumor

Identifiers

PMID38795236

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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.