Novel algorithm for automated genotyping of microsatellites.
Microsatellites or short tandem repeats (STRs) are abundant in the human genome with easily assayed polymorphisms, providing powerful genetic tools for mapping both Mendelian and complex traits. Microsatellite genotyping requires detection of the products of polymerase chain reaction (PCR) amplification by electrophoresis, and analysis of the peak data for discrimination of the true allele. A high-throughput genotyping approach requires computer-based automation at both the detection and analysis phases. In order to achieve this, complicated peak patterns from individual alleles must be interpreted in order to assign alleles. Previous methods consider limited types of noise peaks and cannot provide enough accuracy. By pattern recognition of various types of noise peaks, such as stutter peaks and additional peaks, we have achieved an overall average accuracy of 94% for allele calling in our actual data. Our algorithm is crucial for a high-throughput genotyping system for microsatellite markers by reducing manual editing and human errors.
Matsumoto
Toshiko
T
Japan Biological Information Research Center, Japan Biological Informatics Consortium, Tokyo, Japan. tmatsumoto@hitachisoft.jp
Yukawa
Wataru
W
Nozaki
Yasuyuki
Y
Nakashige
Ryo
R
Shinya
Minori
M
Makino
Satoshi
S
Yagura
Masaru
M
Ikuta
Tomoki
T
Imanishi
Tadashi
T
Inoko
Hidetoshi
H
Tamiya
Gen
G
Gojobori
Takashi
T
D000465:Algorithms; D000483:Alleles; D005819:Genetic Markers; D005838:Genotype; D018895:Microsatellite Repeats; D016133:Polymerase Chain Reaction; D017422:Sequence Analysis, DNA / Q000379:methods*
D005819:Genetic Markers