Xenome--a tool for classifying reads from xenograft samples

Conway, Thomas, Wazny, Jeremy, Bromage, Andrew, Tymms, Martin, Sooraj, Dhanya, Williams, Elizabeth D., & Beresford-Smith, Bryan (2012) Xenome--a tool for classifying reads from xenograft samples. Bioinformatics, 28(12), i172-i178.

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Abstract

Motivation

Shotgun sequence read data derived from xenograft material contains a mixture of reads arising from the host and reads arising from the graft. Classifying the read mixture to separate the two allows for more precise analysis to be performed.

Results

We present a technique, with an associated tool Xenome, which performs fast, accurate and specific classification of xenograft-derived sequence read data. We have evaluated it on RNA-Seq data from human, mouse and human-in-mouse xenograft datasets.

Impact and interest:

30 citations in Scopus
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22 citations in Web of Science®

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Full-text downloads:

38 since deposited on 17 Oct 2014
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ID Code: 77759
Item Type: Journal Article
Refereed: Yes
Keywords: shotgun sequence read data, xenograft, xenome, RNA-seq data, bioinformatics
DOI: 10.1093/bioinformatics/bts236
ISSN: 1460-2059
Subjects: Australian and New Zealand Standard Research Classification > INFORMATION AND COMPUTING SCIENCES (080000) > COMPUTER SOFTWARE (080300) > Bioinformatics Software (080301)
Australian and New Zealand Standard Research Classification > MEDICAL AND HEALTH SCIENCES (110000) > ONCOLOGY AND CARCINOGENESIS (111200) > Cancer Cell Biology (111201)
Australian and New Zealand Standard Research Classification > MEDICAL AND HEALTH SCIENCES (110000) > ONCOLOGY AND CARCINOGENESIS (111200) > Cancer Genetics (111203)
Divisions: Current > Schools > School of Biomedical Sciences
Current > QUT Faculties and Divisions > Faculty of Health
Current > Institutes > Institute of Health and Biomedical Innovation
Copyright Owner: Copyright 2012 The Author(s)
Copyright Statement: This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/
by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Deposited On: 17 Oct 2014 01:09
Last Modified: 20 Oct 2014 03:42

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