Accurate automated clustering of two-dimensional data for single-nucleotide polymorphism genotyping by a combination of clustering methods: evaluation by large-scale real data.
BACKGROUND
The Invader assay is a fluorescence-based high-throughput genotyping technology. If the output data from the Invader assay were classified automatically, then genotypes for individuals would be determined efficiently. However, existing classification methods do not necessarily yield results with the same accuracy as can be achieved by technicians. Our clustering algorithm, Genocluster, is intended to increase the proportion of data points that need not be manually corrected by technicians.


RESULTS
Genocluster worked well even when the number of clusters was unknown in advance and when there were only a few points in a cluster. The use of Genocluster enabled us to achieve an acceptance rate (proportion of assay results that did not need to be corrected by expert technicians) of 84.4% and a proportion of uncorrected points of 95.8%, as determined using the data from over 31 million points.


BACKGROUND
Information for obtaining the executable code, example data and example analysis are available at http://www.genstat.net/genocluster.
Takitoh
Shuichi
S
Laboratory for Statistical Analysis, Waseda University, Shinjuku, Tokyo, Japan.
Fujii
Shogo
S
Mase
Yoichi
Y
Takasaki
Junichi
J
Yamazaki
Toshimasa
T
Ohnishi
Yozo
Y
Yanagisawa
Masao
M
Nakamura
Yusuke
Y
Kamatani
Naoyuki
N
D000465:Algorithms; D001185:Artificial Intelligence; D002874:Chromosome Mapping / Q000379:methods*; D016000:Cluster Analysis; D004252:DNA Mutational Analysis / Q000379:methods*; D030541:Databases, Genetic; D017404:In Situ Hybridization, Fluorescence / Q000379:methods*; D010363:Pattern Recognition, Automated / Q000379:methods*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D013050:Spectrometry, Fluorescence / Q000379:methods*