STRC Copy Number Detection Using WGS Differential Sites

Solution Overview

Problem

Current methods for detecting STRC gene copy number variations, such as quantitative PCR or MLPA, are costly and time-consuming due to the high homology between the STRC gene and its pseudogene STRCP1, leading to inaccurate detection and increased experimental time and cost.

Innovation Solution

A method and device for detecting STRC gene copy number variations using whole genome sequencing (WGS) that involves sequence alignment to identify differentiated sites between STRC and STRCP1, calculating copy numbers based on these sites, and determining exon-specific copy numbers, reducing the need for additional amplification steps.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Measurement precision

If quantitative PCR or MLPA is used for STRC copy number detection, then detection accuracy is improved, but detection cost and experimental time increase

Engineering Contradiction:

Improvedetection accuracyVSAvoidexperimental time

Core Design Contradiction:

Measurement precisionVSLoss of time

Solution Approach 1:

The patent combines STRC gene detection with whole genome sequencing, merging two separate processes into one. The STRC copy number detection is performed as part of the WGS workflow by analyzing sequencing data from multiple differentiated sites between STRC and STRCP1, eliminating the need for separate quantitative PCR or MLPA experiments.

Inventive Principle:

Principle #5Merging (Combining)

Solution Approach 2:

The WGS method serves multiple functions simultaneously: it performs whole genome sequencing for various genetic analyses and also specifically detects STRC copy number variations. The same sequencing data and analysis pipeline are used for both purposes, making the detection process universal and eliminating the need for specialized assays.

Inventive Principle:

Principle #6Universality (Multi-functionality)

2Measurement precision

If quantitative PCR or MLPA is used for STRC copy number detection, then detection accuracy is improved, but detection cost increases

Engineering Contradiction:

Improvedetection accuracyVSAvoiddetection cost

Core Design Contradiction:

Measurement precisionVSQuantity of substance

Solution Approach 1:

The patent combines STRC gene detection with whole genome sequencing, merging two separate processes into one. The STRC copy number detection is performed as part of the WGS workflow by analyzing sequencing data from multiple differentiated sites between STRC and STRCP1, eliminating the need for separate quantitative PCR or MLPA experiments.

Inventive Principle:

Principle #5Merging (Combining)

Solution Approach 2:

The WGS method serves multiple functions simultaneously: it performs whole genome sequencing for various genetic analyses and also specifically detects STRC copy number variations. The same sequencing data and analysis pipeline are used for both purposes, making the detection process universal and eliminating the need for specialized assays.

Inventive Principle:

Principle #6Universality (Multi-functionality)

3Reliability

If high homology between STRC and STRCP1 is considered, then accurate differentiation becomes difficult, but current methods still achieve detection with additional steps

Engineering Contradiction:

Improvedetection reliabilityVSAvoiddetection process complexity

Core Design Contradiction:

ReliabilityVSDevice complexity

Solution Approach 1:

The patent segments the detection process by identifying and utilizing multiple specific differentiated sites between STRC and STRCP1 genes. Instead of treating the highly homologous regions as a single difficult-to-differentiate unit, the method divides the gene into multiple segments and selects specific sites (SNPs, indels) where the genes differ, enabling accurate differentiation through targeted analysis of these segmented regions.

Inventive Principle:

Principle #1Segmentation

Solution Approach 2:

The patent uses differentiated sites (SNPs and indels) as intermediaries to distinguish between STRC and STRCP1. These specific genetic variants serve as markers that mediate the differentiation process, allowing the highly similar genes to be distinguished without requiring complex experimental procedures. The analysis of these intermediary markers enables accurate copy number detection despite high overall homology.

Inventive Principle:

Principle #24Intermediary (Mediator)

Data Source

PatentEP4697335A1STRC gene copy number variation detection method based on whole genome sequencing

Publication Date: 2026.02.18 BGI GENOMICS CO LTD

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AI summary

An STRC gene copy number variation detection method based on whole genome sequencing, comprising: carrying out sequence comparison on an STRC gene and an STRCP1 gene to find out differential sites of the STRC gene and the STRCP1 gene; for each differential site, reading sequences of corresponding STRC positions and STRCP1 positions in a genome from a variation detection file; calculating the total copy number of true genes and pseudogenes by using a preset reference site in the genome as a benchmark; calculating an STRC gene copy ratio on each differential site; calculating the STRC gene copy number on each differential site according to the total copy number and the STRC gene copy ratio; and determining the STRC gene copy number on each exon according to the STRC gene copy number on each differential site. The method can implement measurement of the STRC copy number, simplifies a detection process, improves the detection throughput, and reduces costs.