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VarDetect: a nucleotide sequence variation exploratory tool

VarDetect. Chumpol Ngamphiw 1 , Supasak Kulawonganunchai 2 , Anunchai Assawamakin 3 , Ekachai Jenwitheesuk 1 and Sissades Tongsima 1. VarDetect: a nucleotide sequence variation exploratory tool. 1 Genome Institute, National Center for Genetic Engineering and Biotechnology, Thailand

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VarDetect: a nucleotide sequence variation exploratory tool

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  1. VarDetect Chumpol Ngamphiw1, Supasak Kulawonganunchai2, Anunchai Assawamakin3, Ekachai Jenwitheesuk1 and Sissades Tongsima1 VarDetect: a nucleotide sequence variation exploratory tool 1 Genome Institute, National Center for Genetic Engineering and Biotechnology, Thailand 2 Department of Computer Science, School of Engineering and Technology, Asian Institute of Technology, Thailand 3 Division of Medical Genetics, Siriraj Hospital, Mahidol University, Thailand

  2. Outline • Nucleotide sequence variation • Common sequencing artifacts • VarDetect: algorithms overview • Experimental results • Conclusions 2

  3. Nucleotide sequence variation http://urgi.versailles.inra.fr/projects/GnpSNP/general_documentation.php 3

  4. Common sequencing artifacts http://seqcore.brcf.med.umich.edu/doc/dnaseq/trouble/badseq.html 4

  5. VarDetect: algorithms Reading nucleotide traces Base-Calling Re-sampling Alignment of input sequences to the reference sequence Pre-alignment, Alignment Enhancement SNPs identification CodeMap 5

  6. Chromatogram trace: base-calling Base-calling with BioJava Reading nucleotide traces: base-calling 6

  7. Calculate peak intensity ratio Qv– Qo (δ) for increasing the confidence of SNP detection Reading nucleotide traces: intensity ratio 7

  8. Partitioning and Re-sampling (PnR) technique Reading nucleotide traces: partition and re-sampling 8

  9. Pooled DNA: possible biallelic pattern Base-call parameters setting in VarDetect 9

  10. Pre-alignment & alignment enhancement Alignment 10

  11. CodeMap analysis SNPs identification: CodeMap 11

  12. VarDetect: main graphical user interface http://www.biotec.or.th/GI/tools/vardetect 12

  13. Experimental results - Tocharoentanaphol C, et al. : Evaluation of resequencing on number of tag SNPs of 13 atherosclerosis-related genes in Thai population. J Hum Genet 2008, 53:74–86. - Thailand SNP discovery project : http://www.biotec.or.th/thaisnp 13

  14. Conclusions • We presented novel algorithm to interpret fluorescent-based chromatograms in an automatic fashion and platform independent (Java). • Three main heuristic procedures are employed: • Turning point (bell shape) detection (PnR algorithm). • Increasing the SNP detection confidence by checking the difference between vicinity and observed quality values (Qv - Qo). • Introduction of CodeMap to detect pattern of SNP and Indel. • VarDetect offers the most features including the ability to detect SNPs from pooled DNA samples. • VarDetect use of XML annotated reference sequence to cross check the SNP discovery results within the tool without using external applications. • VarDetect’s heuristics minimize both false positive and negative errors reducing the effort needed to detect and validate SNPs, making it the tool of choice for automatic SNP detection. 14

  15. Acknowledgements • Dr. Mazazumi Takahashi, Centre National • de Genotypage (CNG), France • Dr. Philip Shaw • Dr. Prasit Palittapolgarnpim • Dr. Chintana Tocharoentanaphol, • Chulabhorn Research Institute • Dr. Chanin Limwongse, Siriraj Hospital, • Mahidol University • Thailand SNP discovery project • National Center for Genetic Engineering and • Biotechnology(BIOTEC) 15

  16. VarDetect Chumpol Ngamphiw1, Supasak Kulawonganunchai2, Anunchai Assawamakin3, Ekachai Jenwitheesuk1 and Sissades Tongsima1 Thank You For Your Attention 1 Genome Institute, National Center for Genetic Engineering and Biotechnology, Thailand 2 Department of Computer Science, School of Engineering and Technology, Asian Institute of Technology, Thailand 3 Division of Medical Genetics, Siriraj Hospital, Mahidol University, Thailand

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