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ADTEx specifications

Information


Unique identifier OMICS_03365
Name ADTEx
Alternative names Aberration Detection in Tumour Exome, CoNVEX
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python, R
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Documentation


Publication for Aberration Detection in Tumour Exome

ADTEx citations

 (21)
call_split

SMAD4 and NF1 mutations as potential biomarkers for poor prognosis to cetuximab based therapy in Chinese metastatic colorectal cancer patients

2018
BMC Cancer
PMCID: 5921972
PMID: 29703253
DOI: 10.1186/s12885-018-4298-5
call_split See protocol

[…] SNPs. Mutations identified within the whole blood controls were subtracted to exclude germline mutations where applicable. Structural variants were detected using FACTERA with default parameters []. ADTEx (https://adtex.sourceforge.net) was used to identify copy number variations (CNVs) with default parameters. All the genetic alterations identified were manually reviewed on Integrative Genomics […]

library_books

Targeted next generation sequencing identified clinically actionable mutations in patients with esophageal sarcomatoid carcinoma

2018
BMC Cancer
PMCID: 5838991
PMID: 29506494
DOI: 10.1186/s12885-018-4159-2

[…] inimum base quality = 15, minimum variant allele frequency (VAF) = 0.01, minimum variant supporting reads = 5, variant supporting reads mapped to both strands, and strand bias no greater than 10% []. ADTEx (http://adtex.sourceforge.net) was used to identify copy number variations (CNVs) using a normal human HapMap DNA sample NA18535, and the cutoff of log2 ratio was set at ±0.6 for copy number cha […]

library_books

Integrated Molecular Characterization of Gastrointestinal Stromal Tumors (GIST) Harboring the Rare D842V Mutation in PDGFRA Gene

2018
Int J Mol Sci
PMCID: 5877593
PMID: 29510530
DOI: 10.3390/ijms19030732

[…] f on protein function and stability.Moreover, on paired tumor/normal WES data, the analysis of amplifications and large deletions was performed applying two different tools, Control FREEC v7.2 [] and ADTEX v2.0 []. A consensus method was implemented with the aim of selecting the overlapping regions given by the two algorithms (overlap of gain or loss ≥ 80%) followed by a downstream filtering proce […]

library_books

NSAID use and somatic exomic mutations in Barrett’s esophagus

2018
Genome Med
PMCID: 5830331
PMID: 29486792
DOI: 10.1186/s13073-018-0520-y

[…] t NSAID use slowed or reduced the accumulation of somatic chromosomal alterations (SCA) []. In our study, SCA was quantified from exome data using an expanded algorithm based on a modified version of ADTEx (Additional file : Table S15) and binned into SCA classes including homozygous deletions (HD), copy loss, cnLOH, balanced gain (> 2 N copies with balanced allele-specific copy number), allele-sp […]

library_books

Exome sequencing of primary breast cancers with paired metastatic lesions reveals metastasis enriched mutations in the A kinase anchoring protein family (AKAPs)

2018
BMC Cancer
PMCID: 5810006
PMID: 29433456
DOI: 10.1186/s12885-018-4021-6

[…] around known indels and base-quality recalibrated by GATK. Somatic single nucleotide variants (SNVs) were detected by Mutect [] with the high-confidence mode. Copy number alterations were detected by ADTEx []. All pipelines and analyses were run using Anduril [], a workflow framework for scientific data analysis. Mean coverage per sample is given in (Additional file : Figure S2b). […]

call_split

Single cell profiling of human gliomas reveals macrophage ontogeny as a basis for regional differences in macrophage activation in the tumor microenvironment

2017
Genome Biol
PMCID: 5738907
PMID: 29262845
DOI: 10.1186/s13059-017-1362-4
call_split See protocol

[…] /) and the GATK toolkit [] carried out quality score re-calibration, duplicate-removal, and re-alignment around indels. Large-scale (>100 Exons) somatic copy number variants (CNVs) were inferred with ADTex []. To increase CNV size, proximal (< 1 Mbp) CNVs were merged. Somatic SNVs were inferred with MuTect (https://www.broadinstitute.org/cancer/cga/mutect) for each tumor/control pair and annotated […]

Citations

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ADTEx institution(s)
Department of Mechanical Engineering, University of Melbourne, Parkville, VIC, Australia

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