Method for detecting SMN gene copy number of single sample in WES data
A gene copy number and copy number technology, applied in genomics, instrumentation, proteomics, etc., can solve the problems of inability to accurately detect the copy number of SMN genes in a single sample, and the inability to detect the special SMN12+0 carrier status at the same time
Pending Publication Date: 2021-03-02
赛福解码(北京)基因科技有限公司
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[0006] This application provides a method for detecting single-sample SMN gene copy number in WES data, which is used to solve the inability to accurately detect single-sample SMN gene copy number and simultaneously detect the special SMN1 2+0 carrier status in the prior art The problem
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[0095] Aspects of the invention are described in this disclosure with reference to the accompanying drawings, which show a number of illustrated embodiments. Embodiments of the present disclosure are not necessarily defined to include all aspects of the present invention. It should be appreciated that the various concepts and embodiments described above, as well as those described in more detail below, can be implemented in any of numerous ways, since the concepts and embodiments disclosed herein are not limited to any implementation. In addition, some aspects of the present disclosure may be used alone or in any suitable combination with other aspects of the present disclosure.
[0096] In order to solve the problem that the SMN gene copy number of a single sample cannot be accurately detected in the prior art and the special SMN1 2+0 carrier status cannot be detected at the same time, the present invention uses the negative samples of the known SMN gene actual copy number a...
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The invention discloses a method for detecting the SMN gene copy number of a single sample in WES data, and the method comprises the steps: building an SMN1 gene and SMN2 gene copy number score data set through employing a negative sample with the known SMN gene actual copy number and a positive sample with the known SMN gene actual copy number in advance, so as to detect the gene copy number of the single sample; and searching a control interval with high correlation with the SMN gene copy number in a full exon Bed interval. The batch effect among different samples is corrected by utilizing the reads coverage of the area, the accuracy of the detection method is effectively improved, and an SMN1 2+0 silent carrier with mutation of g.27134T larger than G point can be detected. The purposesof accurately detecting the SMN gene copy number of a single sample and detecting an SMN1 2+0 silent carrier with mutation of g.27134T larger than G point are achieved.
Description
technical field [0001] The present invention relates to the field of genome-wide variation detection in biology and precision medicine, and in particular to a method for detecting the copy number of a single-sample SMN gene in WES (Whole Exome Sequence, abbreviated as WES) data. Background technique [0002] Spinal muscular atrophy (English: Spinal muscular atrophy, abbreviated as SMA) is a genetic neurological disease. It causes motor neuron degeneration, muscle wasting, muscle weakness and eventually death. SMA is caused by a deletion or abnormality (mutation) in a gene called Survival Motor Neuron 1 (SMN1) in humans. SMA is mainly closely related to two highly homologous (meaning that the sequences of these two genes are very similar) genes, namely SMN1 and SMN2 ("Motor Neuron Survival 2" gene), these two genes are mainly through exon 7 Two gene loci on exon and exon 8 are distinguished. Generally speaking, most normal individuals have 2 copies of the SMN1 gene and 2 c...
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IPC IPC(8): G16B20/10
CPCG16B20/10
Inventor 余伟师梁萌萌鲍远亮栗海波贺洪鑫
Owner 赛福解码(北京)基因科技有限公司