DDIG-in: Discriminating between diseaseassociated and neutral non-frameshifting micro-indels

Huiying Zhao, Yuedong Yang, Hai Lin, Xinjun Zhang, Matthew Mort, David N. Cooper, Yunlong Liu, Yaoqi Zhou

Research output: Contribution to journalArticle

36 Citations (Scopus)

Abstract

Micro-indels -insertions or deletions shorter than 21 bps- constitute the second most frequent class of human genemutation after single nucleotide variants. Despite the relative abundance of non-frameshifting indels, their damagingeffect on protein structure and function has gone largely unstudied. We have developed a support vector machine-basedmethod named DDIG-in (Detecting disease-causing genetic variations due to indels) to prioritize non-frameshifting indelsby comparing disease-associated mutations with putatively neutral mutations from the 1000 Genomes Project. The finalmodel gives good discrimination for indels and is robust against annotation errors. A webserver implementing DDIG-in isavailable at http://sparks.informatics.iupui.edu/ddig.

Original languageEnglish (US)
Article numberR23
JournalGenome biology
Volume14
Issue number3
DOIs
StatePublished - Mar 13 2013

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mutation
informatics
Mutation
Informatics
protein structure
genetic variation
relative abundance
Nucleotides
genome
nucleotides
Genome
protein
Proteins
1,5-dideoxy-1,5-iminogalactitol
project
support vector machine
Support Vector Machine
support vector machines

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology

Cite this

Zhao, H., Yang, Y., Lin, H., Zhang, X., Mort, M., Cooper, D. N., ... Zhou, Y. (2013). DDIG-in: Discriminating between diseaseassociated and neutral non-frameshifting micro-indels. Genome biology, 14(3), [R23]. https://doi.org/10.1186/gb-2013-14-3-r23

DDIG-in : Discriminating between diseaseassociated and neutral non-frameshifting micro-indels. / Zhao, Huiying; Yang, Yuedong; Lin, Hai; Zhang, Xinjun; Mort, Matthew; Cooper, David N.; Liu, Yunlong; Zhou, Yaoqi.

In: Genome biology, Vol. 14, No. 3, R23, 13.03.2013.

Research output: Contribution to journalArticle

Zhao, Huiying ; Yang, Yuedong ; Lin, Hai ; Zhang, Xinjun ; Mort, Matthew ; Cooper, David N. ; Liu, Yunlong ; Zhou, Yaoqi. / DDIG-in : Discriminating between diseaseassociated and neutral non-frameshifting micro-indels. In: Genome biology. 2013 ; Vol. 14, No. 3.
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