CHASM statistics

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Associated diseases

Associated diseases

CHASM specifications


Unique identifier OMICS_00127
Alternative names Cancer-specific High-throughput Annotation of Somatic Mutations, CHASM/SNV-Box, CHASMplus
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C++, Python, R, Shell (Bash)
Database management system MySQL
Computer skills Advanced
Version 3.0
Stability Stable
Maintained Yes


  • Primates
    • Homo sapiens


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  • person_outline Rachel Karchin <>
  • person_outline Rachel Karchin <>

Publications for Cancer-specific High-throughput Annotation of Somatic Mutations

CHASM in publications

PMCID: 5945519
PMID: 29755676
DOI: 10.18632/oncotarget.25041

[…] respective primary tumors. mutations associated with loh of the wild-type allele in the metastasis but not in the corresponding primary tumor were defined as ‘loh in metastasis’., mutationtaster, chasm (breast) and fathmm [–] were used to define the potential functional effect of missense single nucleotide variants as previously described [–, , ] (). frameshift, splice-site and nonsense […]

PMCID: 5902451
PMID: 29662108
DOI: 10.1038/s41598-018-24286-2

[…] protein structural information is also helpful. polyphen-2 is a prominent tool that uses both sequence- and structure-based features in a naïve bayes classification,. as a cancer-specific tool, chasm (cancer-specific high-throughput annotation of somatic mutations) is a major machine-learning approach employing a random forest algorithm and was trained using 49 predictive features, […]

PMCID: 5865730
PMID: 29570743
DOI: 10.1371/journal.pone.0194790

[…] variants were manually re-validated individually against hg-19 and then evaluated for a potential resulting cancer driver phenotype. missense mutations were scored with two algorithms, chasm and fathmm, which are considered reliable predictors [, ]. cancer-specific high-throughput annotation of somatic mutations (chasm) is a computational method based on a random forest classifier […]

PMCID: 5748693
PMID: 29292755
DOI: 10.3390/genes8120375

[…] included in the list of cancer gene census in cosmic database ( here we have analyzed all somatic mutations of bard1 deposited in cosmic database by using the cancer-specific high-throughput annotation of somatic mutations (chasm) [] tool to distinguish passenger variation events from driver ones across a cohort of tumors and the variant effect scoring […]

PMCID: 5610688
PMID: 28975082
DOI: 10.3389/fonc.2017.00214

[…] web application. the ensembl database provides a variation of position-specific condel predictions that combine sift and polyphen-2 for every possible amino acid substitution in all human proteins., cancer-specific high-throughput annotation of somatic mutations, or chasm, is a computational method that identifies and prioritizes the missense mutations likely to enhance tumor cell proliferation […]

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CHASM institution(s)
Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA; Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, USA; Department of Oncology, Johns Hopkins University, Baltimore, MD, USA
CHASM funding source(s)
Supported by the National Cancer Institute (NCI) Grant F31CA200266 and NCI Grant U24CA204817.

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