METHODS AND SYSTEMS FOR DIAGNOSTICS ACCORDING TO WHOLE GENOME SEQUENCING DATA Russian patent published in 2023 - IPC G16B20/10 G16B20/20 

FIELD: biologic information technology.

SUBSTANCE: method for determining the copy number of the survival motor neuron 1 (SMN1) gene is described. Under the control of a hardware processor, sequencing data containing multiple sequence reads obtained from a sample from a subject aligned to the survival motor neuron gene 1 (SMN1) or survival motor neuron gene 2 (SMN2) is obtained. A first number of sequence reads is determined from a plurality of sequence reads aligned to the first region SMN1 or SMN2 containing at least 1 of the first 6 exons of the SMN1 gene or the SMN2 gene, respectively, and a second number of sequence reads from a plurality of sequence reads aligned to the second region SMN1 or SMN2 containing at least exon 7 or exon 8 of the SMN1 gene or the SMN2 gene. The first normalized number of sequence reads and the second normalized number of sequence reads are determined. The copy number of full-length survival motor neuron (SMN) genes and the copy number of any intact SMN genes are determined. For one set of SMN1 gene-specific bases associated with an intact SMN1 gene, the most likely combination is determined from a plurality of possible combinations, each containing a possible number of copies of the SMN1 gene and a possible number of copies of the SMN2 gene, which add up to the number of copies of any identified intact SMN genes. The number of copies of the SMN1 gene is determined using the most probable combination of the possible number of copies of the SMN1 gene and the possible number of copies of the SMN2 gene, determined for a specific base for the SMN1 gene.

EFFECT: invention makes it possible to determine the number of copies of the SMN1 gene.

45 cl, 32 dwg, 25 tbl, 2 ex