FACTERA statistics

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Citations per year

Number of citations per year for the bioinformatics software tool FACTERA
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Tool usage distribution map

This map represents all the scientific publications referring to FACTERA per scientific context
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Associated diseases

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Popular tool citations

chevron_left Structural variant detection Inter-chromosomal translocation detection Intra-chromosomal translocation detection chevron_right
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FACTERA specifications

Information


Unique identifier OMICS_05484
Name FACTERA
Alternative name Fusion And Chromosomal Translocation Enumeration and Recovery Algorithm
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format BAM
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainers


  • person_outline Ash Alizadeh
  • person_outline Maximilian Diehn

Publication for Fusion And Chromosomal Translocation Enumeration and Recovery Algorithm

FACTERA citations

 (9)
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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

[…] 00 Genome data sets to remove common 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 manual […]

library_books

Whole genome sequencing of spermatocytic tumors provides insights into the mutational processes operating in the male germline

2017
PLoS One
PMCID: 5439955
PMID: 28542371
DOI: 10.1371/journal.pone.0178169

[…] o of tumor vs. normal read depth for each exon and extracted all exons showing deviation from the expected ratio, that is, corresponding to more than one unit haploid copy number change. The software FACTERA [] with the default settings was used to detect gene fusions and structural variants including deletion, duplication, inversion and translocation. Circos plots that included tracks showing the […]

library_books

Characterization of genetic aberrations in a single case of metastatic thymic adenocarcinoma

2017
BMC Cancer
PMCID: 5432996
PMID: 28506304
DOI: 10.1186/s12885-017-3282-9

[…] Gene fusion analysis using WES data was performed on regions captured by the SureSelectXT Human All Exon V4 + UTR 71 Mb kit (>30X coverage). We used FACTERA [] for inter-gene fusions with options of minimum split reads = 30 and minimum discordant reads = 10. We removed fusion events located in repeated regions from RepeatMasker and GenomicSuperDup […]

call_split

Circulating Tumor DNA Mutation Profiling by Targeted Next Generation Sequencing Provides Guidance for Personalized Treatments in Multiple Cancer Types

2017
Sci Rep
PMCID: 5428730
PMID: 28373672
DOI: 10.1038/s41598-017-00520-1
call_split See protocol

[…] IC database (v76). Annotation was performed using ANNOVAR using the hg19 reference genome and 2014 versions of standard databases and functional prediction programs.Genomic fusions were identified by FACTERA with default parameters. In short, we set minimum number of breakpoint-spanning reads to 5, minimum number of discordant reads to 2 and minimum similarity required for alignment of read to fus […]

call_split

Circulating tumor DNA profiling by next generation sequencing reveals heterogeneity of crizotinib resistance mechanisms in a gastric cancer patient with MET amplification

2017
Oncotarget
PMCID: 5432256
PMID: 28460431
DOI: 10.18632/oncotarget.15457
call_split See protocol

[…] rospectively inspected to detect such mutation with MAF < 1%, but has at least 3 high quality non-paired mutant reads (> Q30) on different strands, and reported (). Genomic fusions were identified by FACTERA with default parameters []. Copy number variations (CNVs) were detected using ADTEx (http://adtex.sourceforge.net) with default parameters. Proposed discrete wavelet transform (DWT) was used t […]

library_books

Lineage specific and single cell chromatin accessibility charts human hematopoiesis and leukemia evolution

2016
Nat Genet
PMCID: 5042844
PMID: 27526324
DOI: 10.1038/ng.3646

[…] ) minimum sequence depth of 25, 2) minimum variant frequency of 5%, 3) less than 90% variant strand bias, 4) not observed in dbSNP. Large-scale genomic events such as translocations were called using FACTERA (v1.3) with no additional filtering. FLT3 internal tandem duplications were called using Pindel (v0.2.4) with no additional filtering. Manual observation was used to clarify borderline mutatio […]


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FACTERA institution(s)
Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA; Division of Oncology, Department of Medicine, Stanford University, Stanford, CA, USA; Department of Radiation Oncology, Stanford University, Stanford, CA, USA; Stanford Cancer Institute, Stanford University, Stanford, CA, USA
FACTERA funding source(s)
Supported by the Stanford Cancer Institute Genomics Initiative; the Doris Duke Charitable Foundation; the US Department of Defense (LCRP Promising Clinician Research Award; W81XWH-12-1-0498); the US National Institutes of Health Director’s New Innovator Award Program (1-DP2-CA186569); the Damon Runyon Cancer Research Foundation; the Lymphoma Research Foundation; the Gabrielle’s Angel Foundation; the Radiological Society of North America (RR1221); and the Thomas & Stacey Siebel Foundation.

FACTERA reviews

 (2)
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Anonymous user #1051's avatar image No country

Anonymous user #1051

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Desktop
very fast, intuitive, and precise tool. optimized for targeted capture data, but performance on RNA-Seq data reasonably good in my hands, though but not tested against other tools. addition of a paired mode (tumor/normal) option would be a nice feature.
Anonymous user #1050's avatar image No country

Anonymous user #1050

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Desktop
Much much better that existing tools, especially for targeted capture data from cancer. Needs for improved a little for BWA-MEM, but still great.