Balanced Translocation Breakpoint Detection via SNP Haplotyping
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Solution Overview
Problem
Current methods for identifying balanced translocations in embryos are limited by low resolution, high cost, and inability to accurately determine the position of breakpoints, leading to inaccurate determination of translocation status and potential recombination interchange.
Innovation Solution
A method involving DNA sequencing from embryos and parents, using high-throughput sequencing and copy number analysis to accurately determine the position of balanced translocation breakpoints and haplotyping to identify non-translocation carrying embryos with a small number of SNP loci.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If Comparative Genomic Hybridization is used, then cost is reduced and throughput is increased, but resolution deteriorates to Mb level
Solution Approach 1:
The patent changes the detection parameter from probe-based hybridization signals to SNP allele frequency ratios in sequencing reads. By analyzing the ratio of reads with different alleles at SNP loci across multiple windows, the method achieves high-resolution breakpoint detection without requiring physical probes, thus resolving the contradiction between throughput and resolution.
2Measurement precision
If Fluorescence in situ Hybridization is used, then specific position detection is achieved, but resolution is low and probe design becomes time-consuming and costly
Solution Approach 1:
The patent creates a universal detection system using whole-genome sequencing data that can detect any balanced translocation breakpoint without requiring custom probe design. The method uses SNP allele frequency analysis across the entire genome, making it applicable to all translocation types without time-consuming individual probe design, thus resolving the contradiction between position detection accuracy and time consumption.
3Area of stationary object
If SNP array is used, then whole genome coverage is achieved, but effective loci for linkage analysis become uncertain leading to inability to resolve translocation status
Solution Approach 1:
The patent applies local quality analysis by examining SNP allele frequencies in specific windows around potential breakpoint regions. Instead of relying on uniform SNP distribution across the whole genome, the method focuses on local SNP patterns near copy number variations, calculating allele frequency ratios in adjacent windows to precisely determine breakpoint positions and resolve translocation status.
4Measurement precision
If MicroSeq-PGD is used, then breakpoint position is accurately determined, but operation becomes complicated and detection cycle becomes long
Solution Approach 1:
The patent replaces the mechanical and labor-intensive MicroSeq-PGD process with a computational analysis of whole-genome sequencing data. Instead of physical micro-cutting and manual analysis, the method uses algorithmic processing of sequencing reads to calculate SNP allele frequencies and identify breakpoints, thereby maintaining high accuracy while dramatically reducing operational complexity and detection cycle time.
Data Source
AI summary
Provided is a method for identifying balanced translocation breakpoints and a carrying state for balanced translocations in embryos, comprising the following steps: amplifying and sequencing a sample; comparing the sequence which is obtained by means of sequencing with a reference genome and analyzing copy numbers; accurately determining the position of a translocation breakpoint; detecting single nucleotide polymorphisms (SNPs) around the breakpoint and genotyping the SNPs; analyzing an embryonic haplotype, and comprehensively determining a normal chromosome and a translocation chromosome haplotype; determining the embryonic carrying state and, according to the haplotype, selecting an embryo which does not carry a balanced translocation.