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Preparation method of long fragment capture sequencing probe group

A technology of probe sets and long fragments, applied in biochemical equipment and methods, DNA/RNA fragments, recombinant DNA technology, etc., can solve problems such as high cost, and achieve cost-effective and intensive solutions

Pending Publication Date: 2020-08-07
BEIJING GRANDOMICS BIOTECH
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Problems solved by technology

[0004] Target enrichment based on liquid-phase hybridization probe capture uses thousands to millions of oligonucleotide capture probes designed to be complementary to the target region to capture the target region and then sequence it. The characteristic of the probe design is Flexible, high throughput, capture area can be large or small, and can detect fusion genes; the disadvantage is that the cost of probe synthesis is relatively high, especially for large panels

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  • Preparation method of long fragment capture sequencing probe group
  • Preparation method of long fragment capture sequencing probe group
  • Preparation method of long fragment capture sequencing probe group

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[0024] The invention relates to a method for preparing a long fragment capture sequencing probe set, comprising:

[0025] a) Use the following formula to calculate and obtain the average interval range of probes:

[0026] N=(L+2)×P±3×P;

[0027] in:

[0028] N: the average interval of probes, in bp;

[0029] P: the average length of each probe, in bp;

[0030] L: the average length of genome fragmentation in Kb, an integer;

[0031] b) preparing a probe set for detecting the target region according to the average interval range of the probes.

[0032] A "target region" of a genome (and any grammatical equivalents thereof) refers to the entire genome or any region or regions of the genome identified as targeted and / or selected by one or more of the methods described herein. Target regions of the genome sequenced by the methods and systems described herein include, but are not limited to, introns, exons, intergenic regions, or any combination thereof. In certain instances,...

Embodiment 1

[0079] Dystrophin gene (DMD gene for short) is one of the largest human genes, located at Xp21, with a length of about 2.3Mb. The coding region of the gene includes 79 exons and 7 tissue-specific promoters, and its mRNA sequence is 14Kb long. The most common mutation of Dystrophin gene is the deletion of one or more exons within the gene, accounting for 65% of the total mutation types. The incidence of repetitive mutations varies from 5% to 15% due to the different sensitivity of detection methods. The remaining mutations are point mutations or microdeletions, often resulting in nonsense and frameshift mutations. About 30% of the mutations in the Dystrophin gene are de novo rather than inherited. Among them, mutations that lead to defects in the dystrophin protein encoded by the gene cause the common neuromuscular disease dystrophinopathy (Dystrophinopathy). The disease is divided into Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD) according to age of...

Embodiment 2

[0241] Both TSCl and TSC2 are tumor suppressor genes that negatively regulate cell proliferation and differentiation, and their typical characteristics are benign tumors involving all systems and organs outside the peripheral nerve, skeletal muscle and pineal body. Mutations or deletions of TSC1 and TSC2 genes can lead to tuberous sclerosis complex (TSC), also known as Bourneville disease, which is a clinically common autosomal dominant neurocutaneous syndrome. The incidence rate is relatively high, 1 / 10000-1 / 6000, 60%-70% are sporadic cases, no family history can be found, showing a high spontaneous mutation rate. The male to female incidence ratio is 2:1, and there is no significant racial difference. Current studies have found that the abnormality of the TSC1 and TSC2 genes leads to the abnormal function of the transcription products hamartoma protein and potato protein, which affects the normal cell generation, differentiation and migration process, and the pathology is ma...

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Abstract

The invention belongs to the technical field of biology, and particularly relates to a preparation method of a long fragment capture sequencing probe group. The method comprises the following steps: a) calculating to obtain the average interval range of the probe by using the following formula: N = (L + 2) * P + / -3 * P; wherein N is the average interval of the probes, and the unit is bp; the P isthe average length of each probe, and the unit is bp; l: fragmenting the average length unit Kb of the genome, and taking an integer; and b) preparing a probe group for detecting a target area according to the average interval range of the probes. By using the method to design the probes, the method has the advantages of comprehensiveness, quickness, accuracy and high cost performance, and the problems of dense capture sequencing probes and high synthesis cost are solved.

Description

technical field [0001] The invention belongs to the field of biotechnology, and in particular relates to a method for preparing a long-fragment capture sequencing probe set. Background technique [0002] The human genome is close to 3G in size and contains about 20,000 protein-coding genes. Whole genome sequencing requires a lot of cost and time, and target sequence capture sequencing has become a hot technology in current genomics research. When only the target sequence is sequenced, researchers can measure more samples and deeper depths at the same cost. Especially for some rare mutations or some somatic gene mutations, the sequencing depth determines that target sequence capture sequencing is an effective tool. [0003] Target sequence capture sequencing is to customize the target genomic region of interest into specific probes for hybridization with genomic DNA, enrich the DNA fragments of the target genomic region before sequencing. [0004] Target enrichment based o...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/6806C12Q1/6874C12Q1/6883C12N15/11
CPCC12Q1/6806C12Q1/6874C12Q1/6883C12Q2600/156C12Q2525/204C12Q2537/165C12Q2531/113C12Q2565/50
Inventor 潘世让王洋梁羽吴昕汪德鹏
Owner BEIJING GRANDOMICS BIOTECH
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