Fusion detection method based on homologous genes of differential SNP markers

Abstract

The invention relates to a fusion detection method based on homologous genes of differential SNP markers. The fusion detection method utilizes differential SNP signals of two genes to distinguish, bypasses the difference in sequencing depth, and performs consistency comparison on each sequencing reads sequence and the homologous gene sequence by using abnormal inserted fragment length of double-ended reads and the soft clip signal of single-end reads, so as to look for a continuous consistency SNP mark and infer the breakpoint interval. The fusion detection method based on homologous genes ofdifferential SNP markers can obtain the interval where the breakpoint is located, that is, the last site of the first half and the first site of the second half, and the separation distance of the interval depends on the physical distance of the detected two sites, thus avoiding the problem that the conventional structural variation detection method encounters in the detection of repeated sequences.

Description

technical field [0001] The invention relates to the field of DNA sequencing, in particular to a fusion detection method of homologous genes based on differential SNP markers. Background technique [0002] DNA (deoxyribonucleic acid) sequencing is an important experimental technology widely used in biological research. There have been related reports since the publication of the DNA double helix structure theory, but the operation process is complicated and has not formed a scale. [0003] In 1977, the end-termination sequencing method was born out of Sanger's research efforts. Sanger sequencing first fragments the genomic DNA, then clones it into a plasmid vector, and then transforms E. coli. For each sequencing reaction, single clones were picked and plasmid DNA was purified. Each cycle sequencing reaction is terminated with a dideoxynucleoside triphosphate (ddNTP), which, since ddNTP lacks the 3-OH group required for elongation, enables the elongated oligonucleotide to s...

AI Technical Summary

Problems solved by technology

While the second-generation sequencing technology greatly reduces the cost of sequencing, it also greatly increases the sequencing speed and maintains high accuracy. It used to take 3 years to complete the sequencing of a human genome, but it only takes 1 week using the second-generation sequencing technology , but the sequence read length is much shorter than that of the first generation sequencing technology

The first is a method that relies solely on coverage information. This method is the first method to detect structural variation. It is relatively intuitive to understand, but it cannot detect small tandem duplications, chromosomal inversions, and balanced translocations. Now it is rarely used alone. use

The second method mainly relies on non-consistent sequences in paired-end sequencing data and discovers structural variation information through clustering. This method is difficult to determine specific structural variation site information, and can only roughly find the range of breakpoints. The insertion length of the end sequence

The third method is to use Split Reads to accurately discover structural variation. This method can accurately locate the information of structural variation sites, but repeated sequences have a great influence on it

The similarity of the two genes causes the detection result to be not a soft truncated signal, but some SNP mark markers of sequence differences between CYP11B1 and CYP11B2, so such signals cannot be detected

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