Evidence map›Paper›PMID 32293247›Full record

ArticleBMC bioinformatics2020

TarPan: an easily adaptable targeted sequencing panel viewer for research and clinical use.

Cody Ashby, Michael Rutherford, Michael A Bauer, Erich A Peterson, Yan Wang, Eileen M Boyle, Christopher P Wardell, Brian A Walker

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

Article in BMC bioinformatics, 2020. 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
0.4field-weighted citation impact, top 34% 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. Myeloma Genome Project Panel is a Comprehensive Targeted Genomics Panel for Molecular Profiling of Patients with Multiple Myeloma.Clinical cancer research : an official journal of the American Association for Cancer Research · 2022
    Article
  3. Article
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

8 authors at 3 institutions in 1 country.

Cody AshbyDepartment of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA. tcashby@uams.edu.ORCID http://orcid.org/0000-0002-9361-0283
Michael RutherfordDepartment of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
Michael A BauerDepartment of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
Erich A PetersonDepartment of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
Yan WangCancer Institute: Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
Eileen M BoyleCancer Institute: Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
Christopher P WardellDepartment of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
Brian A WalkerDivision of Hematology Oncology, Indiana University, Indianapolis, IN, USA.
University of Arkansas for Medical Sciences · USIndiana University – Purdue University Indianapolis · USUniversity of Arkansas Medical Center · US

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundThe study of cancer genomics continually matures as the number of patient samples sequenced increases. As more data is generated, oncogenic drivers for specific cancer types are discovered along with their associated risks. This in turn leads to potential treatment strategies that pave the way to precision medicine. However, significant financial and analytical barriers make it infeasible to sequence the entire genome of every patient. In contrast, targeted sequencing panels give reliable information on relevant portions of the genome at a fiscally responsible cost. Therefore, we have created the Targeted Panel (TarPan) Viewer, a software tool, to investigate this type of data.

resultsTarPan Viewer helps investigators understand data from targeted sequencing data by displaying the information through a web browser interface. Through this interface, investigators can easily observe copy number changes, mutations, and structural events in cancer samples. The viewer runs in R Shiny with a robust SQLite backend and its input is generated from bioinformatic algorithms reliably described in the literature. Here we show the results from using TarPan Viewer on publicly available follicular lymphoma, breast cancer, and multiple myeloma data. In addition, we have tested and utilized the viewer internally, and this data has been used in high-impact peer-reviewed publications.

conclusionsWe have designed a flexible, simple to setup viewer that is easily adaptable to any type of cancer targeted sequencing, and has already proven its use in a research laboratory environment. Further, we believe with deeper sequencing and/or more targeted application it could be of use in the clinic in conjunction with an appropriate targeted sequencing panel as a cost-effective diagnostic test, especially in cancers such as acute leukemia or diffuse large B-cell lymphoma that require rapid interventions.

Indexed as

SoftwareAlgorithmsBreast NeoplasmsFemaleGene DosageGenome, HumanGenomicsHigh-Throughput Nucleotide SequencingHumansLymphoma, FollicularMultiple MyelomaMutationNeoplasmsPrecision MedicineWeb BrowserCancerCopy numberSomatic mutationsStructural variantsVisualization

Identifiers

PMID32293247
PMCPMC7158102
OpenAlexW3016144503

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.