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Functional analysis of novel SNPs and mutations in human and
Chuan-Kun Liu1, Yan-Hau Chen1, Cheng-Yang Tang1, Shu-Chuan Chang1, Yi-
Jung Lin1, Ming-Fang Tsai1, Yuan-Tsong Chen1,2 and Adam Yao*1,2
Address: 1National Genotyping Center (NGC), Academia Sinica, Taipei, Taiwan 11529, R.O.C and 2Institute of Biomedical Sciences (IBMS),
Academia Sinica, Taipei, Taiwan 11529, R.O.C
Email: Chuan-Kun Liu - email@example.com; Yan-Hau Chen - firstname.lastname@example.org; Cheng-
Yang Tang - email@example.com; Shu-Chuan Chang - firstname.lastname@example.org; Yi-Jung Lin - email@example.com; Ming-
Fang Tsai - firstname.lastname@example.org; Yuan-Tsong Chen - email@example.com; Adam Yao* - firstname.lastname@example.org
* Corresponding author
Background: With the flood of information generated by the new generation of sequencing
technologies, more efficient bioinformatics tools are needed for in-depth impact analysis of novel
genomic variations. FANS (Functional Analysis of Novel SNPs) was developed to streamline
comprehensive but tedious functional analysis steps into a few clicks and to offer a carefully
designed presentation of results so researchers can focus more on thinking instead of typing and
Results: FANS http://fans.ngc.sinica.edu.tw/ harnesses the power of public information databases
and powerful tools from six well established websites to enhance the efficiency of analysis of novel
variations. FANS can process any point change in any coding region or GT-AG splice site to provide
a clear picture of the disease risk of a prioritized variation by classifying splicing and functional
alterations into one of nine risk subtypes with five risk levels.
Conclusion: FANS significantly simplifies the analysis operations to a four-step procedure while
still covering all major areas of interest to researchers. FANS offers a convenient way to prioritize
the variations and select the ones with most functional impact for validation. Additionally, the
program offers a distinct improvement in efficiency over manual operations in our benchmark test.
As sequencing technologies continue to advance rapidly
and the cost of large-scale genotyping and sequencing falls
markedly as a result, there is an increasing need for more
efficient bioinformatics tools with which to analyze the
flood of information regarding novel variations in human
and mouse genomes. For instance, when novel mutations
are found in a cancer genome re-sequencing project or
from Asia Pacific Bioinformatics Network (APBioNet) Seventh International Conference on Bioinformatics (InCoB2008)
Taipei, Taiwan. 20–23 October 2008
Published: 12 December 2008
BMC Bioinformatics 2008, 9(Suppl 12):S10 doi:10.1186/1471-2105-9-S12-S10
<supplement> <title> <p>Seventh International Conference on Bioinformatics (InCoB2008)</p> </title> <editor>Shoba Ranganathan, Wen-Lian Hsu, Ueng-Cheng Yang and Tin Wee Tan</editor> <note>Proceedings</note> </supplement>
This article is available from: http://www.biomedcentral.com/1471-2105/9/S12/S10
© 2008 Liu et al; licensee BioMed Central Ltd.
This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0),
which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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versity of California, Santa Cruz; CSV: Comma Separated
The authors declare that they have no competing interests.
CKL designed the analysis flow and wrote the manuscript.
CKL, YHC, CYT, and SCC implemented the program.
CKL, YHC, YJL, MFT, and AY had substantial contribution
to the user interface design. AY and YTC supervised the
The authors thank Dr. Chih-Cheng Chen (IBMS) for his contribution
towards the initiation of the project. Special thanks to Dr. Jer-Yuarn Wu
(NGC) who provided skillful programmers and to Dr. Harry Wilson for
manuscript editing. This work was supported by grants from National Sci-
ence Council, Taiwan, under NRPGM program and Academia Sinica.
This article has been published as part of BMC Bioinformatics Volume 9 Sup-
plement 12, 2008: Asia Pacific Bioinformatics Network (APBioNet) Seventh
International Conference on Bioinformatics (InCoB2008). The full contents
of the supplement are available online at http://www.biomedcentral.com/
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