Evidence map›Paper›PMID 28254357›Full record

ArticleDNA repair2017

RAD-ADAPT: Software for modelling clonogenic assay data in radiation biology.

Yaping Zhang, Kaiqiang Hu, Jan H Beumer, Christopher J Bakkenist, David Z D'Argenio

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in DNA repair, 2017. 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
–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

3 citing papers in PubMed.

  1. Article
  2. 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

5 authors.

Yaping ZhangDepartment of Biomedical Engineering, University of Southern California, Los Angeles, CA, 90089, USA.
Kaiqiang HuDepartments of Radiation Oncology and Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA; School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China.
Jan H BeumerCancer Therapeutics Program, University of Pittsburgh Cancer Institute, Pittsburgh, PA, 15213, USA; Department of Pharmaceutical Sciences, University of Pittsburgh School of Pharmacy, Pittsburgh, PA, 15213, USA; Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA.
Christopher J BakkenistDepartments of Radiation Oncology and Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15213, USA.
David Z D'ArgenioDepartment of Biomedical Engineering, University of Southern California, Los Angeles, CA, 90089, USA. Electronic address: dargenio@usc.edu.

Funding

TrainingP41EB001978 · NIBIB · UNIVERSITY OF SOUTHERN CALIFORNIA · PI KHOO, MICHAEL C K · 2003 to 2017
$18.1M
NCI ET-CTN with Phase i Emphasis at UPCIUM1CA186690 · NCI · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI JOHN C. BYRD, Farshid Dayyani · 2014 to 2026
$9.1M
DNA damage signaling to immune checkpointsR01CA204173 · NCI · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI BAKKENIST, CHRISTOPHER J. · 2017 to 2021
$1.8M
NCI NIH HHS R01 CA204173NCI NIH HHS UM1 CA186690NIBIB NIH HHS P41 EB001978
6 · The paper itself

Abstract

We present a comprehensive software program, RAD-ADAPT, for the quantitative analysis of clonogenic assays in radiation biology. Two commonly used models for clonogenic assay analysis, the linear-quadratic model and single-hit multi-target model, are included in the software. RAD-ADAPT uses maximum likelihood estimation method to obtain parameter estimates with the assumption that cell colony count data follow a Poisson distribution. The program has an intuitive interface, generates model prediction plots, tabulates model parameter estimates, and allows automatic statistical comparison of parameters between different groups. The RAD-ADAPT interface is written using the statistical software R and the underlying computations are accomplished by the ADAPT software system for pharmacokinetic/pharmacodynamic systems analysis. The use of RAD-ADAPT is demonstrated using an example that examines the impact of pharmacologic ATM and ATR kinase inhibition on human lung cancer cell line A549 after ionizing radiation.

Indexed as

Models, BiologicalSoftwareA549 CellsAtaxia Telangiectasia Mutated ProteinsCell SurvivalColony-Forming Units AssayHumansLikelihood FunctionsNeoplasmsRadiation, IonizingRadiobiologyAtaxia Telangiectasia Mutated ProteinsATM protein, humanClonogenic assaysClonogenic survival curvesLinear quadratic modelRadiation biologySingle-hit multi-target model

Identifiers

PMID28254357
PMCPMC5396547

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Registered trials

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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.