Multi-Indel: A Microhaplotype Marker Can Be Typed Using Capillary Electrophoresis Platforms

Area of Science:

• Forensic genetics
• Molecular biology
• Genotyping technologies

Background:

• Microhaplotypes, defined as variants in short DNA segments, have emerged as valuable forensic markers.
• Current multi-variant genotyping often relies on single-strand analysis via massively parallel sequencing (MPS).
• A need exists for alternative, direct haplotype analysis methods.

Purpose of the Study:

• To develop a capillary electrophoresis (CE) based method for direct haplotype genotyping of multi-variants.
• To screen and validate microhaplotypes composed of multiple insertion/deletion polymorphisms (Indels).
• To establish a multiplex system for comprehensive individual haplotype identification.

Main Methods:

• Developed a capillary electrophoresis (CE) platform for direct haplotype analysis.
• Screened microhaplotypes comprising three or more Indels (<200 bp) with distinct length polymorphisms.
• Established a multiplex amplification system with 18 multi-Indel markers.

Main Results:

• Successfully obtained direct haplotypes from individuals based on Indel length polymorphisms.
• Identified microhaplotypes with at least three distinct haplotypes.
• Achieved high forensic efficiency with a combined power of discrimination (CPD) of 0.999999999997234 and cumulative probability of exclusion (CPE) of 0.9984.

Conclusions:

• The developed CE method enables direct haplotype genotyping of multi-Indel markers.
• This approach offers a powerful tool for forensic applications, including individual identification and mixture analysis.
• The 18-marker multiplex system provides high discriminatory power for human identification.