Accurate detection of SNPs using base-specific cleavage and mass spectrometry
Accurate detection of single-nucleotide polymorphisms (SNPs) is crucial for the success of many downstream analyses such as clinical diagnosis, virus identification, genetic mapping and association studies. Among many others, one valuable approach for SNP detection is based on the base-specific clea...
| Main Authors: | , , , , , , |
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| Format: | Conference Paper |
| Language: | English |
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2013
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| Online Access: | https://hdl.handle.net/10356/102864 http://hdl.handle.net/10220/16876 |
| _version_ | 1811689693731880960 |
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| author | Sun, Ruimin Gao, Xiang Han, Nanyu Wu, Qiong Mu, Yuguang Tang, Kai Chen, Xin |
| author2 | School of Biological Sciences |
| author_facet | School of Biological Sciences Sun, Ruimin Gao, Xiang Han, Nanyu Wu, Qiong Mu, Yuguang Tang, Kai Chen, Xin |
| author_sort | Sun, Ruimin |
| collection | NTU |
| description | Accurate detection of single-nucleotide polymorphisms (SNPs) is crucial for the success of many downstream analyses such as clinical diagnosis, virus identification, genetic mapping and association studies. Among many others, one valuable approach for SNP detection is based on the base-specific cleavage of single-stranded nucleic acids followed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis. In this paper, we present a new SNP detection algorithm, which in particular permits an efficient and effective integration of the information in four complementary base-specific mass spectra. The new algorithm was implemented in a program called SnpMs. Comparative evaluation has been carried out on both simulated and real biological datasets, where experimental results clearly demonstrated the high ability of SnpMs as a tool to accurately detect SNPs. |
| first_indexed | 2024-10-01T05:52:10Z |
| format | Conference Paper |
| id | ntu-10356/102864 |
| institution | Nanyang Technological University |
| language | English |
| last_indexed | 2024-10-01T05:52:10Z |
| publishDate | 2013 |
| record_format | dspace |
| spelling | ntu-10356/1028642020-03-07T12:31:20Z Accurate detection of SNPs using base-specific cleavage and mass spectrometry Sun, Ruimin Gao, Xiang Han, Nanyu Wu, Qiong Mu, Yuguang Tang, Kai Chen, Xin School of Biological Sciences School of Physical and Mathematical Sciences IEEE International Conference on Bioinformatics and Biomedicine (2012 : Philadelphia, US) DRNTU::Science::Biological sciences DRNTU::Science::Chemistry Accurate detection of single-nucleotide polymorphisms (SNPs) is crucial for the success of many downstream analyses such as clinical diagnosis, virus identification, genetic mapping and association studies. Among many others, one valuable approach for SNP detection is based on the base-specific cleavage of single-stranded nucleic acids followed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis. In this paper, we present a new SNP detection algorithm, which in particular permits an efficient and effective integration of the information in four complementary base-specific mass spectra. The new algorithm was implemented in a program called SnpMs. Comparative evaluation has been carried out on both simulated and real biological datasets, where experimental results clearly demonstrated the high ability of SnpMs as a tool to accurately detect SNPs. 2013-10-25T02:07:35Z 2019-12-06T21:01:17Z 2013-10-25T02:07:35Z 2019-12-06T21:01:17Z 2012 2012 Conference Paper Sun, R., Gao, X., Han, N., Wu, Q., Mu, Y., Tang, K., et al. (2012). Accurate detection of SNPs using base-specific cleavage and mass spectrometry. 2012 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp.1-4. https://hdl.handle.net/10356/102864 http://hdl.handle.net/10220/16876 10.1109/BIBM.2012.6392727 167807 en |
| spellingShingle | DRNTU::Science::Biological sciences DRNTU::Science::Chemistry Sun, Ruimin Gao, Xiang Han, Nanyu Wu, Qiong Mu, Yuguang Tang, Kai Chen, Xin Accurate detection of SNPs using base-specific cleavage and mass spectrometry |
| title | Accurate detection of SNPs using base-specific cleavage and mass spectrometry |
| title_full | Accurate detection of SNPs using base-specific cleavage and mass spectrometry |
| title_fullStr | Accurate detection of SNPs using base-specific cleavage and mass spectrometry |
| title_full_unstemmed | Accurate detection of SNPs using base-specific cleavage and mass spectrometry |
| title_short | Accurate detection of SNPs using base-specific cleavage and mass spectrometry |
| title_sort | accurate detection of snps using base specific cleavage and mass spectrometry |
| topic | DRNTU::Science::Biological sciences DRNTU::Science::Chemistry |
| url | https://hdl.handle.net/10356/102864 http://hdl.handle.net/10220/16876 |
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