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Variant alleles on the penta E locus in the PowerPlex 16 kit
Natsuko Mizuno1, Kazumasa Sekiguchi, Hajime Sato
1Biology Section, Department of First Forensic Science, National Research Institute of Police Science, 6-3-1 Kashiwanoha Kashiwa, Chiba, 277-0082, Japan. mizuno@nrips.go.jp
Journal of Forensic Sciences
|April 1, 2003
Summary
The Penta E marker on Chromosome 15 has variant alleles in the Japanese population. Careful interpretation of capillary electrophoresis data is needed for accurate genetic analysis, especially with closely sized alleles.
Area of Science:
- Forensic Genetics
- Human Population Genetics
- Molecular Biology
Background:
- The Penta E marker, a pentanucleotide tandem repeat on Chromosome 15, is utilized in genetic analysis.
- This marker contains an AAAGA repeat motif, crucial for understanding its allelic variations.
Purpose of the Study:
- To investigate variant alleles of the Penta E marker in the Japanese population.
- To analyze the sequence characteristics of these variant alleles and their impact on genetic analysis.
- To assess the reliability of capillary electrophoresis for Penta E allele assignment and identify potential interpretation challenges.
Main Methods:
- Sequence analysis was performed on Penta E marker alleles.
- Capillary electrophoresis was employed for allele size determination.
- Genotyper software was used for allele assignment.
- Peak area to peak height ratios were analyzed to identify complex allele peaks.
Main Results:
- Two variant alleles, 18.4 and 19.4, were identified in the Japanese population.
- Sequence analysis revealed a partial AAAA repeat motif in variant alleles, causing them to be one base shorter than expected.
- Alleles differing by only one base, such as 18.4 and 19, were not resolved by capillary electrophoresis, appearing as single broad peaks.
- Genotyper software sometimes assigned only one allele to these broad peaks.
- The ratio of peak area to peak height proved useful in recognizing peaks containing multiple alleles.
Conclusions:
- Variant alleles of the Penta E marker exist in the Japanese population with distinct sequence features.
- Capillary electrophoresis, while generally accurate for Penta E, can present challenges with closely sized alleles, requiring careful interpretation.
- The peak area to peak height ratio is a valuable tool for identifying complex allele peaks, preventing the oversight of co-amplified alleles.