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Method and system for determining whether No.7 exon deletion exists in SMN1 gene of samples to be tested or not

A technology of exon deletion and exon, applied in the field of bioinformatics

Active Publication Date: 2020-01-17
TIANJIN MEDICAL LAB BGI +4
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

Although there are individual reports on the method of using target region capture + high-throughput sequencing to detect exon 7 deletion of SMN1 gene, due to the defects of the literature method, there is no mature product on the market using this method

Method used

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  • Method and system for determining whether No.7 exon deletion exists in SMN1 gene of samples to be tested or not
  • Method and system for determining whether No.7 exon deletion exists in SMN1 gene of samples to be tested or not
  • Method and system for determining whether No.7 exon deletion exists in SMN1 gene of samples to be tested or not

Examples

Experimental program
Comparison scheme
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Embodiment 1

[0096] Embodiment 1 Original off-board data processing

[0097] Step A, apply filtering software (SOAPnuke software, version: 1.5.2) to the off-machine data to filter out low-quality sequencing reads (reads).

[0098] Step B, align the reads to the human reference genome (HG19) using alignment software (BWA software, version: 0.7.12), use Picard (a basic sequence processing software, version: 1.87) to mark repetitive sequences, and apply GATK ( A software for next-generation resequencing data analysis, version: 3.2) for re-alignment and base quality value correction.

[0099] Step C, apply the DepthofCoverage tool of GATK to obtain the reads coverage information of the capture area. It is necessary to output the locus reads number information file and the regional average coverage file (the suffix is ​​.sample_interval_summary file).

Embodiment 2

[0100] Example 2 Estimate the copy number of exon 7 of SMN1 / 2 gene

[0101] Step A, calculate the number of reads aligned to SMN1 gene and SMN2 gene. There is only one site difference between the SMN1 gene and the SMN2 gene in the sequence of exon 7 (chr5: 70247773 on SMN1; chr5: 69372353 on SMN2, denoted as site b). Each intron has 1 site difference (chr5: 70247724 on the SMN1 gene and chr5: 69372304 on the SMN2 gene are recorded as site a, chr5: 70247921 on the SMN1 gene and chr5: 69372501 on the SMN2 gene are recorded as site c). Assuming that there are a total of N samples in the batch, calculate the ratio y of the number of SMN1 gene reads at site b to the total number of SMN reads i =B i / b i , where B i is the number of reads aligned to the b site of the SMN1 gene in the i-th sample, b i is the total number of reads compared to SMN. Also for sites a and c, calculate x i =A i / a i ,z i =C i / c i . Remember R i is the number of reads aligned to exon 7 of SM...

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Abstract

The invention provides a method and system for determining whether No.7 exon deletion exists in an SMN1 gene of samples to be tested or not. Compared with the prior art, the method and system providedby the invention have the advantages that in an aspect of No.7 exon deletion detection of the SMN1 gene, the sensitivity and the specificity are obviously improved; heterozygous deletion samples andhomozygous deletion samples can be effectively distinguished; and when the proportion of normal samples in the batch (No.7 exons of the SMN1 gene and the MSN2gene are respectively 2 copies) is small,the detection precision is greatly improved by selecting a control sample set.

Description

technical field [0001] The present invention relates to the field of biological information, in particular, the present invention relates to a method and a system for determining whether exon 7 deletion exists in the SMN1 gene of a sample to be tested. Background technique [0002] Spinal muscular atrophy (SMA) is an autosomal recessive genetic disease, a group of diseases that can start in infancy, childhood or adolescence, and is characterized by anterior horn cells of the spinal cord and motor nuclei in the brainstem Skeletal muscle atrophy caused by progressive degeneration does not affect the patient's intelligence. The main clinical manifestations are progressive symmetric muscle weakness and muscle atrophy of the lower motor neurons, the proximal end is heavier than the distal end, and the lower extremity is heavier than the upper extremity. The incidence of the disease is 1 / 6000~1 / 10000, ranking second among fatal autosomal recessive genetic diseases, and there is n...

Claims

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Application Information

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IPC IPC(8): C12Q1/6858
CPCC12Q1/6858C12Q2537/16C12Q2535/122C12Q2545/113
Inventor 郭凤禹宋立洁孙隽王亚玲范林林彭智宇
Owner TIANJIN MEDICAL LAB BGI
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