Method and device for detecting exon level deletion of target gene based on reads depth

Abstract

The invention discloses a method and a device for detecting the exon-level deletion of a target gene based on the depth of reads. The method comprises: S1, dividing the reference genome into a plurality of bins, comparing the reads to the reference genome, and calculating the average reads depth and the log2 value of the depth in each bin of the target region and the off-target region respectively; S2 , merge the reads depth statistics of the target region and the off-target region, and standardize them; S3, divide the exon-level missing results according to the first threshold range for the standardized results in S2, and use the second threshold for the log2 obtained after normalization Proceed to define the deletion status of the gene of interest. By applying the technical scheme of the present invention, it is possible to detect the deletion at the exon level of the target gene, and it is also possible to accurately detect whether the target gene is a heterozygous deletion or a homozygous deletion.

Description

technical field [0001] The present invention relates to the field of biotechnology, in particular to a method and device for detecting exon-level deletion of a target gene based on the depth of reads. Background technique [0002] The most common type of mutation of IKZF1 is large fragment deletion, which in most cases will lead to abnormal function of IKZF1 protein, and the deletion of different exons leads to the formation of different isoforms. IKZF1 gene deletion is common in B-ALL patients, especially in Ph-positive ALL patients and Ph-like (Ph-like) ALL patients, with an incidence of about 15% in children and about 40% in adults. Most studies suggest that B-ALL patients with IKZF1 gene deletion have a poor prognosis, and this adverse prognostic effect also exists in Ph-positive ALL patients treated with imatinib. According to a large number of studies on IKZF1 at home and abroad, IKZF1 is currently considered to be an important adverse prognostic factor for children w...

AI Technical Summary

Problems solved by technology

Comparative genomic hybridization (comparative genomic hybridization, CGH) is a molecular cytogenetic method to detect DNA copy number, and it is an effective method to detect the rearrangement of the entire gene, but it cannot detect the type of chromosomal mutation with normal copy number

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