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A method and system for identifying large deletions in dna
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A large fragment and fragment technology, applied in the field of gene detection, can solve the problems of inaccurate detection and achieve high detection accuracy
Active Publication Date: 2018-11-09
CAPITALBIO GENOMICS
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[0004] Next-generation sequencing technology (NGS) is currently the most widely used sequencing technology, which has the advantages of high sequencing depth, high throughput, high accuracy, good sensitivity, and low price. Large fragment deletions with long read lengths are often not accurately detected. For example, the detection of the 4.383kb whole gene deletion of the CYP2D6*5 genotype is a difficult technical problem for next-generation sequencing technology
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Embodiment 1
[0049] Based on a method and system for identifying large DNA fragment deletions provided by the present invention, it is used to detect CYP2D6 whole gene deletions. The size of the deletion fragment is 4.383kb. Generally speaking, there are three types of deletions, namely: normal (not deleted), heterogeneous Synzygous deletion, homozygous deletion.
[0050] In this embodiment, 500 samples of known CYP2D6 deletion types (325 normal, 125 heterozygous mutations, 50 homozygous mutations) and 30 samples to be tested were tested. The specific process is as follows:
[0051] 1. Design of target area
[0052] Set 5 detection regions in the CYP2D6 deletion region, set 3 internal reference regions on the same chromosome outside the CYP2D6 deletion region, and design 8 pairs of specific primers for a total of 8 regions, including primer information and target positions As shown in Table 1, the schematic diagram of the detection area and internal reference area design reference figure...
Embodiment 2
[0075] Based on a method and system for identifying the deletion of large DNA fragments provided by the present invention, which is used to detect the deletion of the entire CYP2D6 gene, the size of the deletion fragment is 4.383kb. In this example, 100 samples of known CYP2D6*5 gene types (65 normal , 25 heterozygous mutations, 10 homozygous mutations), 10 samples to be tested were tested, and the specific process was as follows:
[0076] 1. Design of target area
[0077] Five detection regions were set in the CYP2D6 deletion region, and three internal reference regions were set on the same chromosome outside the CYP2D6 deletion region. Eight pairs of specific primers were designed for a total of eight regions, as shown in Table 1.
[0078] 2. Library construction and sequencing
[0079] Use specific primers to capture each detection region and each internal reference region, build a library according to the Ion proton platform, perform sequencing, and obtain sequencing data...
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Abstract
The invention discloses a method and system for identifying DNA (Deoxyribonucleic Acid) large fragment deletion. Based on next-generation sequencing, the invention provides the method and system for identifying the DNA large fragment deletion; a detection region is set in a target deletion fragment region and an internal reference region is set on the same chromosome in the target deletion fragment region; sequencing depth of each region is obtained and a reference set and weighting analysis are utilized to obtain a deletion type of a sample to be detected. The method disclosed by the invention has high detection accuracy; a detection result is consistent to Gap-PCR (Polymerase Chain Reaction); the method is especially suitable for detecting CYP2D6 whole gene deletion and the problem in the prior art that the large fragment deletion which exceeds a sequencing read length cannot be accurately detected can be solved.
Description
technical field [0001] The invention belongs to the field of gene detection, and more specifically relates to a method and system for identifying large DNA segment deletions. Background technique [0002] According to the survey report related to safe drug use, the incidence of adverse drug reactions in newborns, children, and adults is 24.4%, 12.9%, and 6.1% respectively; in every four newborns, one child is caused by adverse drug reactions to varying degrees. Organ damage caused by drugs, such as drug-induced deafness, nervous system damage, liver and kidney function damage, etc.; one-third of the global death patients died from irrational drug use, not from natural diseases themselves; therefore, safe, reasonable, effective, Economical medication is the appeal of patients at this stage. At present, genetic testing for safe drug use can realize individualized drug guidance by detecting individual drug-related genes, assist in determining the optimal drug and dosage, and a...
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