Multiplex Y-STR Primer Sets for Short-Amplicon Haplotype Resolution
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Solution Overview
Problem
Current Y-STR analysis kits face limitations such as varying haplotype resolution across populations, inability to exclude male relatives separated by multiple generations, and increased adventitious matches in frequency databases, necessitating improved multiplex analysis systems.
Innovation Solution
Development of amplification primers and kits that amplify at least 11 Y-STR markers with amplicon sizes under 220 base pairs, including rapidly mutating loci, and utilize mobility modifiers and spectrally distinct fluorescent dyes for enhanced discrimination and sensitivity, with methods involving capillary electrophoresis, ion semiconductor detection, or mass spectrometry for allele identification.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If current Y-STR analysis kits are used, then the analysis can be performed with existing technology, but the haplotype resolution varies across populations and cannot exclude male relatives separated by multiple generations
Solution Approach 1:
The Y-STR analysis is divided into multiple loci (at least 11 markers) that are analyzed independently through separate primer sets. Each locus contributes to the overall haplotype resolution, and the combination of results from all loci enables reliable differentiation between male relatives separated by multiple generations, resolving the contradiction between using existing technology and achieving high resolution.
Solution Approach 2:
The patent changes the parameters of the analysis by using primers that produce amplicons of specific base pair sizes (less than 220 bp for at least 11 markers, and less than 410 bp for additional markers). This parameter optimization enables better resolution across diverse populations while maintaining the ability to exclude male relatives, addressing both aspects of the technical contradiction.
2Adaptability or versatility
If more male profiles are added to Y-STR frequency databases, then the database becomes more comprehensive, but adventitious matches increase
Solution Approach 1:
The analysis segments the Y-chromosome into multiple independent loci, each contributing unique information. By analyzing at least 11 markers simultaneously, the system achieves sufficient discrimination power to differentiate between male profiles even when added to comprehensive databases, preventing adventitious matches while maintaining database versatility.
Solution Approach 2:
The patent creates a composite analysis system that combines multiple primer sets targeting different Y-STR loci. This composite approach produces a combined haplotype profile that has higher discriminatory power than individual markers, enabling accurate matching even in comprehensive databases with many male profiles.
3Measurement precision
If the number of Y-STR markers analyzed is increased, then discrimination power improves, but the complexity of the multiplex analysis increases
Solution Approach 1:
The multiplex analysis is segmented into multiple primer sets, each targeting specific Y-STR loci. The primers are designed to produce amplicons of manageable sizes (less than 220 bp for core markers), which simplifies the overall analysis complexity while maintaining high discrimination power through the combined results of all loci.
Solution Approach 2:
The patent optimizes the amplicon size parameters to less than 220 base pairs for at least 11 markers and less than 410 base pairs for additional markers. This parameter control keeps the amplicons within manageable lengths for standard capillary electrophoresis, reducing analysis complexity while maintaining the ability to analyze multiple markers simultaneously for high discrimination power.
Applied Scientific Principles
This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.
Function Achieved in This Case
The solution provides improved haplotype resolution, reduces adventitious matches, and enables differentiation of male individuals with similar paternal lineages, enhancing forensic and paternity testing accuracy.
Implementation Method 1
a set of amplification primers including primers for the amplification of at least 11 Y-STR markers
Implementation Method 2
The mobility-dependent analytical technique may be capillary electrophoresis
Implementation Method 3
The set of amplification primers may be labeled with one of at least 5 fluorescent dyes
Data Source
AI summary
Novel Y-STR multiplex analysis designs, primer design, allelic ladders, methods of use and kits are disclosed, including the use of primer sets designed to provide amplicons for at least 11 Y-STR loci having a base pair size of less than about 220 bp, as well as the use of primer sets designed to provide amplicons for at least 22 Y-STR loci including at least 5 rapidly mutating loci.