A self-tuning method for one-chip SNP identification.
Identifieur interne : 005487 ( Main/Exploration ); précédent : 005486; suivant : 005488A self-tuning method for one-chip SNP identification.
Auteurs : Michael Molla [États-Unis] ; Jude Shavlik ; Todd Richmond ; Steven SmithSource :
- Proceedings. IEEE Computational Systems Bioinformatics Conference [ 1551-7497 ] ; 2004.
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Abstract
Current methods for interpreting oligonucleotide-based SNP-detection microarrays, SNP chips, are based on statistics and require extensive parameter tuning as well as extremely high-resolution images of the chip being processed. We present a method, based on a simple data-classification technique called nearest-neighbors that, on haploid organisms, produces results comparable to the published results of the leading statistical methods and requires very little in the way of parameter tuning. Furthermore, it can interpret SNP chips using lower-resolution scanners of the type more typically used in current microarray experiments. Along with our algorithm, we present the results of a SNP-detection experiment where, when independently applying this algorithm to six identical SARS SNP chips, we correctly identify all 24 SNPs in a particular strain of the SARS virus, with between 6 and 13 false positives across the six experiments.
DOI: 10.1109/csb.2004.1332419
PubMed: 16448001
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We present a method, based on a simple data-classification technique called nearest-neighbors that, on haploid organisms, produces results comparable to the published results of the leading statistical methods and requires very little in the way of parameter tuning. Furthermore, it can interpret SNP chips using lower-resolution scanners of the type more typically used in current microarray experiments. Along with our algorithm, we present the results of a SNP-detection experiment where, when independently applying this algorithm to six identical SARS SNP chips, we correctly identify all 24 SNPs in a particular strain of the SARS virus, with between 6 and 13 false positives across the six experiments.</div></front></TEI><affiliations><list><country><li>États-Unis</li></country></list><tree><noCountry><name sortKey="Richmond, Todd" sort="Richmond, Todd" uniqKey="Richmond T" first="Todd" last="Richmond">Todd Richmond</name><name sortKey="Shavlik, Jude" sort="Shavlik, Jude" uniqKey="Shavlik J" first="Jude" last="Shavlik">Jude Shavlik</name><name sortKey="Smith, Steven" sort="Smith, Steven" uniqKey="Smith S" first="Steven" last="Smith">Steven Smith</name></noCountry><country name="États-Unis"><noRegion><name sortKey="Molla, Michael" sort="Molla, Michael" uniqKey="Molla M" first="Michael" last="Molla">Michael Molla</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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