Capture probe composition of three subtypes of thalassemia and its application method and application device

A capture probe and anemia technology, which is applied in the field of capture probe compositions of three subtypes of thalassemia, can solve the problems of low detection scheme and no cost comparison, and achieve the effect of easy detection accuracy

Active Publication Date: 2022-05-03
BEIJING NOVOGENE TECH CO LTD +2
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  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

[0010] Therefore, for batch sample screening, there is no low-cost detection scheme in the prior art

Method used

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  • Capture probe composition of three subtypes of thalassemia and its application method and application device
  • Capture probe composition of three subtypes of thalassemia and its application method and application device
  • Capture probe composition of three subtypes of thalassemia and its application method and application device

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preparation example Construction

[0032] Based on the above research results, in a typical embodiment of the present application, a method for preparing a capture probe composition of the three subtypes of thalassemia is provided, the preparation method comprising: combining the three subtypes of thalassemia The full-length region of the relevant gene is divided into different small fragments according to the preset length (for example, 120bp, 150bp or other suitable length); compare each small fragment to the human reference genome to obtain the first single alignment Region set and multi-comparison region set; the multi-comparison region set is moved forward or backward by kbp on the human reference genome, k≤100, and the new region after the shift is compared with the human reference genome again to obtain the first Two sets of single alignment regions; performing probe design from the first set of single alignment regions and the second set of single alignment regions to obtain a capture probe composition. ...

Embodiment 1

[0059] Embodiment 1 capture probe design

[0060] First, select the full-length regions of the three types of thalassemia genes, SEA deletion, -α4.2 deletion and -α3.7 deletion, and separate them into different small fragments according to the length of 120bp, and compare each small fragment to human by blast On the hg19 reference genome, some unique alignment regions and some multiple alignment regions were obtained.

[0061] Make adjustments for multiple alignment regions. The adjustment method is to move these regions forward or backward on the genome by less than 100 bp, compare the moved new region with hg19, and finally select the region of the unique comparison result generated by the above two steps for probe design. The specific probe design rules are: 1) The probe must have only one alignment result in the deletion region; 2) Evenly cover three different deletion regions. Finally, 71 uniquely aligned probes (as shown in Table 1) were finally determined as the final...

Embodiment 2

[0062] Example 2 Using a negative sample set to establish a reference baseline for coverage depth of negative samples

[0063] DNA extraction was performed on the 25 negative samples collected to build a library, the target region was captured, and then sequenced on the machine.

[0064] The raw data (raw Data, stored in the FASTQ format) obtained by removing adapters and index tags from the sequencing data, filtered out low-quality data through quality control, and obtained effective data (clean data).

[0065] Align the effective data (clean data) to the human reference genome hg19 through general-purpose alignment software (such as BWA), and obtain the bam file of the alignment result.

[0066] Based on the existing negative samples, construct a baseline for subsequent determination of whether there is a copy number deletion: use the above comparison to obtain the bam file of the result, and use the bed file of the capture probe region to calculate the coverage depth of the...

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Abstract

The invention provides a capture probe composition for three subtypes of thalassemia, an application method and an application device. Wherein, the preparation method of the capture probe composition of the three subtypes of thalassemia includes: separating the full-length regions of the genes related to the three subtypes of thalassemia into different small fragments according to preset lengths; The fragments are compared to the human reference genome to obtain the first single alignment region set and multiple alignment region sets; move the multi-alignment region set forward or backward on the human reference genome by a length of kbp, k≤100, and move The final new region is re-aligned with the human reference genome to obtain a second single alignment region set; probe design is performed from the first single alignment region set and the second single alignment region set to obtain a capture probe composition. The capture probe composition obtained by the method can not only mark the whole region but also can distinguish three different thalassemia types, so that the detection is more accurate.

Description

technical field [0001] The invention relates to the field of gene mutation detection, in particular to a capture probe composition for three subtypes of thalassemia and its application method and application device. Background technique [0002] Thalassemia, also known as thalassemia, is a common monogenic hereditary hemolytic blood disease with autosomal recessive inheritance. The biosynthesis of one or more globin peptide chains is reduced or cannot be synthesized at all due to hereditary globin gene defects (mutation, deletion, etc.), resulting in the failure to maintain the normal balance between globin peptide chains, and adult Hb (HbA : A hereditary hemoglobinopathy in which α2β2) synthesis is reduced. [0003] Specifically, it can be divided into two types: α-thalassemia and β-thalassemia, which are caused by defects such as α-globin gene or β-globin gene deletion or mutation, which lead to inhibition of the synthesis of the corresponding globin chain or loss of func...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): C12Q1/6883C12N15/11G16B30/10
CPCC12Q1/6883G16B30/10
Inventor 林志伟李琳呼锦涛王远田怡李瑞强
Owner BEIJING NOVOGENE TECH CO LTD
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