CRAVAT 4: Cancer-Related Analysis of Variants Toolkit

Cancer Research
David L MasicaRachel Karchin

Abstract

Cancer sequencing studies are increasingly comprehensive and well powered, returning long lists of somatic mutations that can be difficult to sort and interpret. Diligent analysis and quality control can require multiple computational tools of distinct utility and producing disparate output, creating additional challenges for the investigator. The Cancer-Related Analysis of Variants Toolkit (CRAVAT) is an evolving suite of informatics tools for mutation interpretation that includes mutation mapping and quality control, impact prediction and extensive annotation, gene- and mutation-level interpretation, including joint prioritization of all nonsilent mutation consequence types, and structural and mechanistic visualization. Results from CRAVAT submissions are explored in an interactive, user-friendly web environment with dynamic filtering and sorting designed to highlight the most informative mutations, even in the context of very large studies. CRAVAT can be run on a public web portal, in the cloud, or downloaded for local use, and is easily integrated with other methods for cancer omics analysis. Cancer Res; 77(21); e35-38. ©2017 AACR.

References

Nov 7, 2008·Nature·Timothy J LeyRichard K Wilson
Apr 8, 2009·Genome Medicine·Peter D StensonDavid N Cooper
Nov 7, 2012·Nature·UNKNOWN 1000 Genomes Project ConsortiumGil A McVean
Jan 18, 2013·Bioinformatics·Christopher DouvilleRachel Karchin
Mar 30, 2013·Science·Bert VogelsteinKenneth W Kinzler
Oct 31, 2014·Nucleic Acids Research·Simon A ForbesPeter J Campbell
Nov 26, 2015·Cell Systems·Dexter PrattTrey Ideker
Aug 19, 2016·Nature·Monkol LekUNKNOWN Exome Aggregation Consortium

❮ Previous
Next ❯

Citations

Jan 25, 2018·FEBS Letters·Juan Carlos González-SánchezRobert B Russell
Dec 13, 2019·Journal of Human Genetics·Calvin P SjaardaMuhammad Ayub
Aug 29, 2019·Nature Reviews. Cancer·Johannes G ReiterBert Vogelstein
Sep 8, 2018·Science·Johannes G ReiterMartin A Nowak
Nov 9, 2019·NPJ Precision Oncology·Jean-Sébastien MilaneseEdwin Wang
Feb 14, 2021·Genomics, Proteomics & Bioinformatics·Jean-Sébastien MilaneseEdwin Wang
Jan 7, 2021·Signal Transduction and Targeted Therapy·Ruth NussinovFeixiong Cheng
Jul 10, 2021·Investigative Ophthalmology & Visual Science·Claire L SimpsonDwight Stambolian
Jul 20, 2021·Journal of Biomolecular Structure & Dynamics·Samadrita ChatterjeeYasha Hasija
Sep 28, 2021·Current Protocols·Rudolf T PillichDexter Pratt

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.